From 673364cd3a7848067dc3ecb69c7f8a4f3a28f6d5 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sun, 21 Oct 2018 19:49:10 +0200 Subject: [PATCH 01/58] gnu: Add emacs-slime-repl-ansi-color. * gnu/packages/emacs.scm (emacs-slime-repl-ansi-color): New variable. --- gnu/packages/emacs.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 1069b9e3c3..47e984e101 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -12386,3 +12386,23 @@ have special meaning. It is also handy for aligning text across long vertical distances. Multi-column characters, such as @kbd{TAB} are treated correctly.") (license license:gpl2+))) + +(define-public emacs-slime-repl-ansi-color + (let ((commit "ad03263f5d4de473bc173b64a6fc3dc1106393d7")) + (package + (name "emacs-slime-repl-ansi-color") + (version (git-version "0.0.0" "1" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/deadtrickster/slime-repl-ansi-color") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0bpg7gxz310x7bnlg324c507sxc5gxwwz6h64h6kdq141r73vbi4")))) + (build-system emacs-build-system) + (home-page "https://github.com/deadtrickster/slime-repl-ansi-color") + (synopsis "Color ANSI codes in the REPL of SLIME") + (description "Color ANSI codes in the REPL of SLIME") + (license license:gpl2+)))) From 9ab6c680ba7e42d3a7cf13c74a7bbcb53c5c390e Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Sun, 21 Oct 2018 14:56:44 -0400 Subject: [PATCH 02/58] gnu: linux-libre@4.4: Update to 4.4.162. * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.162. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 2aeddc2a34..5cbf87b68c 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -452,8 +452,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.4 - (make-linux-libre "4.4.161" - "1q6bsndpjgw72mybhl5l8vrxs4mimg6821bjgi1pjkxbc7nd921b" + (make-linux-libre "4.4.162" + "1anb2k9i03369lvbwlw24vimxvk8zpcql4ryz0ydvf3pxv8lirm2" %intel-compatible-systems #:configuration-file kernel-config)) From c4a7a512922467313f5cc18fc61029c44ac5360e Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Sun, 21 Oct 2018 14:57:24 -0400 Subject: [PATCH 03/58] gnu: linux-libre@4.9: Update to 4.9.135. * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.135. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 5cbf87b68c..09f64d5e04 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -446,8 +446,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.9 - (make-linux-libre "4.9.134" - "0f5qif27k0mhc57d98arbfkq7zlvg0ra2gz6g5fasblyjz3j7w7h" + (make-linux-libre "4.9.135" + "07v5s6hl08ls2z9xdkbqq1s210mqayfchqbckhp8hlaw089ap71f" %intel-compatible-systems #:configuration-file kernel-config)) From 668834cae0f6b761d88533c91475d9184a8ab4ad Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Sun, 21 Oct 2018 14:58:03 -0400 Subject: [PATCH 04/58] gnu: linux-libre@4.14: Update to 4.14.78. * gnu/packages/linux.scm (%linux-libre-4.14-version): Update to 4.14.78. (%linux-libre-4.14-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 09f64d5e04..61560b7a1b 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -436,8 +436,8 @@ It has been modified to remove all non-free binary blobs.") #:patches %linux-libre-4.18-patches #:configuration-file kernel-config)) -(define %linux-libre-4.14-version "4.14.77") -(define %linux-libre-4.14-hash "18y81rga2lhsk7bjckglxz52pvnzf103ar0z2zj611g37wyf83r5") +(define %linux-libre-4.14-version "4.14.78") +(define %linux-libre-4.14-hash "07dhhw6zdnqn2dznpmkniz58hfkdx89yx7csm9vbx45blnyhjw5z") (define-public linux-libre-4.14 (make-linux-libre %linux-libre-4.14-version From f7618bf18e00f6ece8e886f2fc6328314d1ed544 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Sun, 21 Oct 2018 14:59:30 -0400 Subject: [PATCH 05/58] gnu: linux-libre: Update to 4.18.16. * gnu/packages/linux.scm (%linux-libre-version): Update to 4.18.16. (%linux-libre-hash): Update hash. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 61560b7a1b..bc53a88bfc 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -405,8 +405,8 @@ It has been modified to remove all non-free binary blobs.") ;; supports qemu "virt" machine and possibly a large number of ARM boards. ;; See : https://wiki.debian.org/DebianKernel/ARMMP. -(define %linux-libre-version "4.18.15") -(define %linux-libre-hash "0v6xs85qn1iy2dj3m6s3cfnhbwb1mjy21d9lagjni8dg3jic26hf") +(define %linux-libre-version "4.18.16") +(define %linux-libre-hash "15apfgswp2lrwjpi3vwnanlkdw3q6rkvwrbgrb71rjsy9gazlz62") (define %linux-libre-4.18-patches (list %boot-logo-patch From 9a6808e0c00d6acb00b7be4aa573f252fa7d9635 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 11:54:44 +0200 Subject: [PATCH 06/58] gnu: tophat: Update to 2.1.1. * gnu/packages/bioinformatics.scm (tophat): Update to 2.1.1. * gnu/packages/patches/tophat-build-with-later-seqan.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch. --- gnu/local.mk | 1 - gnu/packages/bioinformatics.scm | 7 +++--- .../tophat-build-with-later-seqan.patch | 24 ------------------- 3 files changed, 3 insertions(+), 29 deletions(-) delete mode 100644 gnu/packages/patches/tophat-build-with-later-seqan.patch diff --git a/gnu/local.mk b/gnu/local.mk index 1c48fd3d6e..c167e6753c 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1177,7 +1177,6 @@ dist_patch_DATA = \ %D%/packages/patches/tk-find-library.patch \ %D%/packages/patches/ttf2eot-cstddef.patch \ %D%/packages/patches/ttfautohint-source-date-epoch.patch \ - %D%/packages/patches/tophat-build-with-later-seqan.patch \ %D%/packages/patches/totem-meson-easy-codec.patch \ %D%/packages/patches/tuxpaint-stamps-path.patch \ %D%/packages/patches/twinkle-include-qregexpvalidator.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1e04081ceb..0dc81c8f61 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1332,7 +1332,7 @@ gapped, local, and paired-end alignment modes.") (define-public tophat (package (name "tophat") - (version "2.1.0") + (version "2.1.1") (source (origin (method url-fetch) (uri (string-append @@ -1340,13 +1340,12 @@ gapped, local, and paired-end alignment modes.") version ".tar.gz")) (sha256 (base32 - "168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7")) - (patches (search-patches "tophat-build-with-later-seqan.patch")) + "19add02kv2xhd6ihd779dr7x35ggym3jqr0m5c4315i1yfb0p11p")) (modules '((guix build utils))) (snippet '(begin ;; Remove bundled SeqAn and samtools - (delete-file-recursively "src/SeqAn-1.3") + (delete-file-recursively "src/SeqAn-1.4.2") (delete-file-recursively "src/samtools-0.1.18") #t)))) (build-system gnu-build-system) diff --git a/gnu/packages/patches/tophat-build-with-later-seqan.patch b/gnu/packages/patches/tophat-build-with-later-seqan.patch deleted file mode 100644 index fc742e2a7d..0000000000 --- a/gnu/packages/patches/tophat-build-with-later-seqan.patch +++ /dev/null @@ -1,24 +0,0 @@ -This patch resolves a build failure when building TopHat 2.1.0 with SeqAn 1.4. -This is the relevant part of a patch originally posted here: -https://lists.fu-berlin.de/pipermail/seqan-dev/2014-July/msg00001.html - ---- a/src/segment_juncs.cpp -+++ b/src/segment_juncs.cpp -@@ -2050,10 +2050,13 @@ void juncs_from_ref_segs(RefSequenceTabl - typedef map MotifMap; - - MotifMap ims; -- -- seqan::DnaStringReverseComplement rev_donor_dinuc(donor_dinuc); -- seqan::DnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc); -- -+ -+ typedef seqan::ModifiedString< -+ seqan::ModifiedString > >, -+ seqan::ModReverse> ConstDnaStringReverseComplement; -+ ConstDnaStringReverseComplement rev_donor_dinuc(donor_dinuc); -+ ConstDnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc); -+ - if (talkative) - fprintf(stderr, "Collecting potential splice sites in islands\n"); - From 1d18ee6dfd99d9945a0e8eae7557250a1bdc6306 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 12:00:41 +0200 Subject: [PATCH 07/58] gnu: bwa-pssm: Fetch from git. * gnu/packages/bioinformatics.scm (bwa-pssm)[source]: Fetch from git. --- gnu/packages/bioinformatics.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0dc81c8f61..593b5b6202 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1449,13 +1449,14 @@ and more accurate. BWA-MEM also has better performance than BWA-backtrack for (name "bwa-pssm") (version "0.5.11") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/pkerpedjiev/bwa-pssm/" - "archive/" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/pkerpedjiev/bwa-pssm.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "02p7mpbs4mlxmn84g2x4ghak638vbj4lqix2ipx5g84pz9bhdavg")))) + "076c4q0cdqz8jgylb067y9zmvxglppnzi3qiscn0xiypgc6lgb5r")))) (build-system gnu-build-system) (inputs `(("gdsl" ,gdsl) From 2ba2d62c69409255e0c00c480c424c668cba845f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 12:33:01 +0200 Subject: [PATCH 08/58] gnu: python2-bx-python: Update to 0.8.2. * gnu/packages/bioinformatics.scm (python2-bx-python): Update to 0.8.2. [source]: Remove obsolete snippet. [inputs]: Move python2-numpy from here... [propagated-inputs]: ...to here; add python2-six. [native-inputs]: Add python2-lzo and python2-cython. [home-page]: Update to new home at Github. --- gnu/packages/bioinformatics.scm | 24 ++++++++++-------------- 1 file changed, 10 insertions(+), 14 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 593b5b6202..dee8a975b9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1477,31 +1477,27 @@ well as many of the command line options.") (define-public python2-bx-python (package (name "python2-bx-python") - (version "0.7.3") + (version "0.8.2") (source (origin (method url-fetch) (uri (pypi-uri "bx-python" version)) (sha256 (base32 - "15z2w3bvnc0n4qmb9bd6d8ylc2h2nj883x2w9iixf4x3vki9b22i")) - (modules '((guix build utils))) - (snippet - '(begin - (substitute* "setup.py" - ;; remove dependency on outdated "distribute" module - (("^from distribute_setup import use_setuptools") "") - (("^use_setuptools\\(\\)") "")) - #t)))) + "11kksg2rbzihpmcid823xvg42xi88m7sz58rzk29abybkxy0rszs")))) (build-system python-build-system) (arguments `(#:tests? #f ;tests fail because test data are not included #:python ,python-2)) - (inputs + (propagated-inputs `(("python-numpy" ,python2-numpy) - ("zlib" ,zlib))) + ("python-six" ,python2-six))) + (inputs + `(("zlib" ,zlib))) (native-inputs - `(("python-nose" ,python2-nose))) - (home-page "http://bitbucket.org/james_taylor/bx-python/") + `(("python-lzo" ,python2-lzo) + ("python-nose" ,python2-nose) + ("python-cython" ,python2-cython))) + (home-page "https://github.com/bxlab/bx-python") (synopsis "Tools for manipulating biological data") (description "bx-python provides tools for manipulating biological data, particularly From f5cec0068a7e6f9ca1b7542d1839b832ee057648 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 12:36:53 +0200 Subject: [PATCH 09/58] gnu: Add python-bx-python. * gnu/packages/bioinformatics.scm (python-bx-python): New variable. (python2-bx-python): Define in terms of python-bx-python. --- gnu/packages/bioinformatics.scm | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dee8a975b9..7cd9172446 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1474,9 +1474,9 @@ the original BWA alignment program and shares the genome index structure as well as many of the command line options.") (license license:gpl3+))) -(define-public python2-bx-python +(define-public python-bx-python (package - (name "python2-bx-python") + (name "python-bx-python") (version "0.8.2") (source (origin (method url-fetch) @@ -1485,18 +1485,17 @@ well as many of the command line options.") (base32 "11kksg2rbzihpmcid823xvg42xi88m7sz58rzk29abybkxy0rszs")))) (build-system python-build-system) - (arguments - `(#:tests? #f ;tests fail because test data are not included - #:python ,python-2)) + ;; Tests fail because test data are not included + (arguments '(#:tests? #f)) (propagated-inputs - `(("python-numpy" ,python2-numpy) - ("python-six" ,python2-six))) + `(("python-numpy" ,python-numpy) + ("python-six" ,python-six))) (inputs `(("zlib" ,zlib))) (native-inputs - `(("python-lzo" ,python2-lzo) - ("python-nose" ,python2-nose) - ("python-cython" ,python2-cython))) + `(("python-lzo" ,python-lzo) + ("python-nose" ,python-nose) + ("python-cython" ,python-cython))) (home-page "https://github.com/bxlab/bx-python") (synopsis "Tools for manipulating biological data") (description @@ -1504,6 +1503,9 @@ well as many of the command line options.") multiple sequence alignments.") (license license:expat))) +(define-public python2-bx-python + (package-with-python2 python-bx-python)) + (define-public python-pysam (package (name "python-pysam") From 8640f9ec91f7a9e81457a3651a06465fd8dd03a3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 12:42:14 +0200 Subject: [PATCH 10/58] gnu: python-twobitreader: Update to 3.1.6. * gnu/packages/bioinformatics.scm (python-twobitreader): Update to 3.1.6. [source]: Fetch from git. --- gnu/packages/bioinformatics.scm | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7cd9172446..795b0f208e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1595,19 +1595,19 @@ also includes an interface for tabix.") (define-public python-twobitreader (package (name "python-twobitreader") - (version "3.1.4") + (version "3.1.6") (source (origin - (method url-fetch) - (uri (pypi-uri "twobitreader" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/benjschiller/twobitreader") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1q8wnj2kga9nz1lwc4w7qv52smfm536hp6mc8w6s53lhyj0mpi22")))) + "1qbxvv1h58cismbk1anpjrkpghsaiy64a11ir3lhy6qch6xf8n62")))) (build-system python-build-system) - (arguments - '(;; Tests are not distributed in the PyPi release. - ;; TODO Try building from the Git repo or asking the upstream maintainer - ;; to distribute the tests on PyPi. - #:tests? #f)) + ;; Tests are not included + (arguments '(#:tests? #f)) (native-inputs `(("python-sphinx" ,python-sphinx))) (home-page "https://github.com/benjschiller/twobitreader") From 7321920cd3c9c1d7532024dfcdb958cce54b6368 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 12:51:31 +0200 Subject: [PATCH 11/58] gnu: crossmap: Update to 0.2.9. * gnu/packages/bioinformatics.scm (crossmap): Update to 0.2.9. * gnu/packages/patches/crossmap-allow-system-pysam.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch. --- gnu/local.mk | 1 - gnu/packages/bioinformatics.scm | 25 +--- .../patches/crossmap-allow-system-pysam.patch | 121 ------------------ 3 files changed, 6 insertions(+), 141 deletions(-) delete mode 100644 gnu/packages/patches/crossmap-allow-system-pysam.patch diff --git a/gnu/local.mk b/gnu/local.mk index c167e6753c..c76908f92f 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -634,7 +634,6 @@ dist_patch_DATA = \ %D%/packages/patches/cracklib-fix-buffer-overflow.patch \ %D%/packages/patches/crawl-upgrade-saves.patch \ %D%/packages/patches/crda-optional-gcrypt.patch \ - %D%/packages/patches/crossmap-allow-system-pysam.patch \ %D%/packages/patches/clucene-contribs-lib.patch \ %D%/packages/patches/cube-nocheck.patch \ %D%/packages/patches/cursynth-wave-rand.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 795b0f208e..6469e9e1a1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1894,31 +1894,18 @@ time.") (define-public crossmap (package (name "crossmap") - (version "0.2.1") + (version "0.2.9") (source (origin (method url-fetch) - (uri (string-append "mirror://sourceforge/crossmap/CrossMap-" - version ".tar.gz")) + (uri (pypi-uri "CrossMap" version)) (sha256 (base32 - "07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f")) - ;; This patch has been sent upstream already and is available - ;; for download from Sourceforge, but it has not been merged. - (patches (search-patches "crossmap-allow-system-pysam.patch")) - (modules '((guix build utils))) - (snippet '(begin - ;; remove bundled copy of pysam - (delete-file-recursively "lib/pysam") - #t)))) + "1byhclrqnqpvc1rqkfh4jwj6yhn0x9y7jk47i0qcjlhk0pjkw92p")))) (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'set-env - (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1") #t))))) + (arguments `(#:python ,python-2)) (inputs - `(("python-numpy" ,python2-numpy) + `(("python-bx-python" ,python2-bx-python) + ("python-numpy" ,python2-numpy) ("python-pysam" ,python2-pysam) ("zlib" ,zlib))) (native-inputs diff --git a/gnu/packages/patches/crossmap-allow-system-pysam.patch b/gnu/packages/patches/crossmap-allow-system-pysam.patch deleted file mode 100644 index 611c4ff74d..0000000000 --- a/gnu/packages/patches/crossmap-allow-system-pysam.patch +++ /dev/null @@ -1,121 +0,0 @@ -This patch modifies the build process such that the bundled copy of pysam does -not need to be built if CROSSMAP_USE_SYSTEM_PYSAM is set and the pysam module -can be imported. - -Upstream has agreed to apply the patch in the next maintenance release of -crossmap. The patch has already been uploaded to -http://sourceforge.net/projects/crossmap/files/patch/. - -diff --git a/setup.py b/setup.py ---- a/setup.py 2015-02-26 15:28:49.771189185 +0100 -+++ b/setup.py 2015-02-26 15:55:03.440327752 +0100 -@@ -19,6 +19,15 @@ - except: - have_numpy = False - -+try: -+ import pysam -+ if os.environ['CROSSMAP_USE_SYSTEM_PYSAM']: -+ have_pysam = True -+ else: -+ have_pysam = False -+except ImportError: -+ have_pysam = False -+ - if platform.system()=='Windows': - print >> sys.stderr, "Sorry, Windows platform is not supported!" - sys.exit() -@@ -165,49 +174,50 @@ - - - #================= pysam samtools ==================== -- extensions.append(Extension( -- "pysam.csamtools", -- csamtools_sources + [ "lib/pysam/%s" % x for x in ("pysam_util.c", )] +\ -- glob.glob( os.path.join( "lib/samtools", "*.pysam.c" )) +\ -- os_c_files + \ -- glob.glob( os.path.join( "lib/samtools", "*", "*.pysam.c" ) ), -- library_dirs=[], -- include_dirs=[ "lib/samtools", "lib/pysam" ] + include_os, -- libraries=[ "z", ], -- language="c", -- define_macros = [('_FILE_OFFSET_BITS','64'),('_USE_KNETFILE','')], -- )) -- -- extensions.append(Extension( -- "pysam.ctabix", -- tabix_sources + [ "lib/pysam/%s" % x for x in ( "tabix_util.c", )] +\ -- os_c_files + \ -- glob.glob( os.path.join( "lib/tabix", "*.pysam.c" ) ), -- library_dirs=[], -- include_dirs=[ "lib/tabix", "lib/pysam" ] + include_os, -- libraries=[ "z", ], -- language="c", -- define_macros = [('_FILE_OFFSET_BITS','64'), -- ('_USE_KNETFILE','')], -- )) -- -- extensions.append(Extension( -- "pysam.TabProxies", -- tabproxies_sources + os_c_files, -- library_dirs=[], -- include_dirs= include_os, -- libraries=[ "z", ], -- language="c", -- )) -- -- extensions.append(Extension( -- "pysam.cvcf", -- cvcf_sources + os_c_files, -- library_dirs=[], -- include_dirs= ["lib/tabix",] + include_os, -- libraries=[ "z", ], -- language="c", -- )) -+ if not have_pysam: -+ extensions.append(Extension( -+ "pysam.csamtools", -+ csamtools_sources + [ "lib/pysam/%s" % x for x in ("pysam_util.c", )] +\ -+ glob.glob( os.path.join( "lib/samtools", "*.pysam.c" )) +\ -+ os_c_files + \ -+ glob.glob( os.path.join( "lib/samtools", "*", "*.pysam.c" ) ), -+ library_dirs=[], -+ include_dirs=[ "lib/samtools", "lib/pysam" ] + include_os, -+ libraries=[ "z", ], -+ language="c", -+ define_macros = [('_FILE_OFFSET_BITS','64'),('_USE_KNETFILE','')], -+ )) -+ -+ extensions.append(Extension( -+ "pysam.ctabix", -+ tabix_sources + [ "lib/pysam/%s" % x for x in ( "tabix_util.c", )] +\ -+ os_c_files + \ -+ glob.glob( os.path.join( "lib/tabix", "*.pysam.c" ) ), -+ library_dirs=[], -+ include_dirs=[ "lib/tabix", "lib/pysam" ] + include_os, -+ libraries=[ "z", ], -+ language="c", -+ define_macros = [('_FILE_OFFSET_BITS','64'), -+ ('_USE_KNETFILE','')], -+ )) -+ -+ extensions.append(Extension( -+ "pysam.TabProxies", -+ tabproxies_sources + os_c_files, -+ library_dirs=[], -+ include_dirs= include_os, -+ libraries=[ "z", ], -+ language="c", -+ )) -+ -+ extensions.append(Extension( -+ "pysam.cvcf", -+ cvcf_sources + os_c_files, -+ library_dirs=[], -+ include_dirs= ["lib/tabix",] + include_os, -+ libraries=[ "z", ], -+ language="c", -+ )) - - - return extensions From a5b0038cbdfd8ad81472279089aaebc4270c683a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 12:57:43 +0200 Subject: [PATCH 12/58] gnu: Add python-dnaio. * gnu/packages/bioinformatics.scm (python-dnaio): New variable. --- gnu/packages/bioinformatics.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6469e9e1a1..58b29e2a30 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1919,6 +1919,29 @@ files between different genome assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") (license license:gpl2+))) +(define-public python-dnaio + (package + (name "python-dnaio") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "dnaio" version)) + (sha256 + (base32 + "0f16m7hdlm0fz1n7y5asy0v9ghyrq17ni1p9iybq22ddzyd49r27")))) + (build-system python-build-system) + (native-inputs + `(("python-cython" ,python-cython) + ("python-pytest" ,python-pytest) + ("python-xopen" ,python-xopen))) + (home-page "https://github.com/marcelm/dnaio/") + (synopsis "Read FASTA and FASTQ files efficiently") + (description + "dnaio is a Python library for fast parsing of FASTQ and also FASTA +files. The code was previously part of the cutadapt tool.") + (license license:expat))) + (define-public cutadapt (package (name "cutadapt") From 6b7260bad124d3d63ce5ae305d7b74da28e9a947 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 12:57:53 +0200 Subject: [PATCH 13/58] gnu: cutadapt: Update to 1.18. * gnu/packages/bioinformatics.scm (cutadapt): Update to 1.18. [inputs]: Add python-dnaio. --- gnu/packages/bioinformatics.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 58b29e2a30..995cbc76eb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1945,19 +1945,20 @@ files. The code was previously part of the cutadapt tool.") (define-public cutadapt (package (name "cutadapt") - (version "1.16") + (version "1.18") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/marcelm/cutadapt.git") (commit (string-append "v" version)))) - (file-name (string-append name "-" version "-checkout")) + (file-name (git-file-name name version)) (sha256 (base32 - "09pr02067jiks19nc0aby4xp70hhgvb554i2y1c04rv1m401w7q8")))) + "08bbfwyc0kvcd95jf2s95xiv9s3cbsxm39ydl0qck3fw3cviwxpg")))) (build-system python-build-system) (inputs - `(("python-xopen" ,python-xopen))) + `(("python-dnaio" ,python-dnaio) + ("python-xopen" ,python-xopen))) (native-inputs `(("python-cython" ,python-cython) ("python-pytest" ,python-pytest))) From 6b31040ae6865436c1a21378a8b9a09e25ec4adc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 13:42:22 +0200 Subject: [PATCH 14/58] gnu: python-py2bit: Update to 0.3.0. * gnu/packages/bioinformatics.scm (python-py2bit): Update to 0.3.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 995cbc76eb..feb4928a93 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2091,14 +2091,14 @@ trees (phylogenies) and characters.") (define-public python-py2bit (package (name "python-py2bit") - (version "0.2.1") + (version "0.3.0") (source (origin (method url-fetch) (uri (pypi-uri "py2bit" version)) (sha256 (base32 - "1cdf4qlmgwsh1f4k0wdv2sr8x9qn4366p0k3614vbd0fpqiarxrl")))) + "1vw2nvw1yrl7ikkqsqs1pg239yr5nspvd969r1x9arms1k25a1a5")))) (build-system python-build-system) (home-page "https://github.com/dpryan79/py2bit") (synopsis "Access 2bit files using lib2bit") From 42643fc24dd1f418f5f2e0991181d526c0419c1a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 13:43:07 +0200 Subject: [PATCH 15/58] gnu: python-dendropy: Fetch from git. * gnu/packages/bioinformatics.scm (python-dendropy)[source]: Fetch from git. --- gnu/packages/bioinformatics.scm | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index feb4928a93..60e8f6e55a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2053,15 +2053,15 @@ accessing bigWig files.") (version "4.4.0") (source (origin - (method url-fetch) + (method git-fetch) ;; Source from GitHub so that tests are included. - (uri - (string-append "https://github.com/jeetsukumaran/DendroPy/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (uri (git-reference + (url "https://github.com/jeetsukumaran/DendroPy.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0v2fccny5xjaah546bsch1mw4kh61qq5frz2ibllxs9mp6ih9bsn")))) + "097hfyv2kaf4x92i4rjx0paw2cncxap48qivv8zxng4z7nhid0x9")))) (build-system python-build-system) (home-page "http://packages.python.org/DendroPy/") (synopsis "Library for phylogenetics and phylogenetic computing") From e6b65bd219a909514b32a46536a94e288da006fd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 13:43:33 +0200 Subject: [PATCH 16/58] gnu: eolie: Update to 0.9.45. * gnu/packages/gnome.scm (eolie): Update to 0.9.45. --- gnu/packages/gnome.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 7d2742f08d..4b94b2f271 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -4092,15 +4092,15 @@ work and the interface is well tested.") (define-public eolie (package (name "eolie") - (version "0.9.38") + (version "0.9.45") (source (origin (method url-fetch) (uri (string-append "https://gitlab.gnome.org/World/eolie/" - "uploads/9814c06a1bc83ea09c3da8719a9ed11b/" + "uploads/020f3f686e2b938731752a1d9f5bfa7e/" "eolie-" version ".tar.xz")) (sha256 (base32 - "10vrh91rapgfmqwc6jkcybpmlvn4q0y8bnklw3rddzigf9kvqsff")))) + "0371p7g13r0b7zjc48fdcil43ddwpmyvkd2a4vv6ifsqmny6kl42")))) (build-system meson-build-system) (arguments `(#:glib-or-gtk? #t From 4d494a4fa3ebb2d1deacede405d0b0d8e5dbc32b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 13:52:27 +0200 Subject: [PATCH 17/58] gnu: deeptools: Update to 3.1.3. * gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 60e8f6e55a..bc21848367 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2110,7 +2110,7 @@ with Python.") (define-public deeptools (package (name "deeptools") - (version "3.1.2") + (version "3.1.3") (source (origin (method git-fetch) (uri (git-reference @@ -2119,7 +2119,7 @@ with Python.") (file-name (git-file-name name version)) (sha256 (base32 - "06fdpp6cg3xiwryxjhixvfysl4z0ps1crjgia587qa9ikqpsa7fd")))) + "1vggnf52g6q2vifdl4cyi7s2fnfqq0ky2zrkj5zv2qfzsc3p3siw")))) (build-system python-build-system) (arguments `(#:phases From 7a1e62ca67849f9ca19ded4d26c542021db71e38 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 14:00:07 +0200 Subject: [PATCH 18/58] gnu: delly: Update to 0.7.9. * gnu/packages/bioinformatics.scm (delly): Update to 0.7.9. [source]: Fetch from git. [arguments]: Add phase install-templates; use default install phase. [native-inputs]: Remove python-2. [home-page]: Use new home page. * gnu/packages/patches/delly-use-system-libraries.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch. --- gnu/local.mk | 1 - gnu/packages/bioinformatics.scm | 40 ++++++------- .../patches/delly-use-system-libraries.patch | 56 ------------------- 3 files changed, 20 insertions(+), 77 deletions(-) delete mode 100644 gnu/packages/patches/delly-use-system-libraries.patch diff --git a/gnu/local.mk b/gnu/local.mk index c76908f92f..d155b4c613 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -642,7 +642,6 @@ dist_patch_DATA = \ %D%/packages/patches/datamash-arm-tests.patch \ %D%/packages/patches/dbus-helper-search-path.patch \ %D%/packages/patches/deja-dup-use-ref-keyword-for-iter.patch \ - %D%/packages/patches/delly-use-system-libraries.patch \ %D%/packages/patches/dfu-programmer-fix-libusb.patch \ %D%/packages/patches/diffutils-gets-undeclared.patch \ %D%/packages/patches/diffutils-getopt.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bc21848367..78debbc873 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2155,42 +2155,42 @@ identify enrichments with functional annotations of the genome.") (define-public delly (package (name "delly") - (version "0.7.7") + (version "0.7.9") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/tobiasrausch/delly/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/dellytools/delly.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "0dkwy3pyxmi6dhh1lpsr3698ri5sslw9qz67hfys0bz8dgrqwabj")) - (patches (search-patches "delly-use-system-libraries.patch")))) + (base32 "034jqsxswy9gqdh2zkgc1js99qkv75ks4xvzgmh0284sraagv61z")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "src/htslib") + #t)))) (build-system gnu-build-system) (arguments `(#:tests? #f ; There are no tests to run. - #:make-flags '("PARALLEL=1") ; Allow parallel execution at run-time. + #:make-flags + (list "PARALLEL=1" ; Allow parallel execution at run-time. + (string-append "prefix=" (assoc-ref %outputs "out"))) #:phases (modify-phases %standard-phases (delete 'configure) ; There is no configure phase. - (replace 'install - (lambda _ - (let ((bin (string-append (assoc-ref %outputs "out") "/bin")) - (templates (string-append (assoc-ref %outputs "out") + (add-after 'install 'install-templates + (lambda* (#:key outputs #:allow-other-keys) + (let ((templates (string-append (assoc-ref outputs "out") "/share/delly/templates"))) - (mkdir-p bin) (mkdir-p templates) (copy-recursively "excludeTemplates" templates) - (install-file "src/cov" bin) - (install-file "src/delly" bin) - (install-file "src/dpe" bin))))))) - (native-inputs - `(("python" ,python-2))) + #t)))))) (inputs `(("boost" ,boost) ("htslib" ,htslib) ("zlib" ,zlib) ("bzip2" ,bzip2))) - (home-page "https://github.com/tobiasrausch/delly") + (home-page "https://github.com/dellytools/delly") (synopsis "Integrated structural variant prediction method") (description "Delly is an integrated structural variant prediction method that can discover and genotype deletions, tandem duplications, inversions and diff --git a/gnu/packages/patches/delly-use-system-libraries.patch b/gnu/packages/patches/delly-use-system-libraries.patch deleted file mode 100644 index 3315c2a176..0000000000 --- a/gnu/packages/patches/delly-use-system-libraries.patch +++ /dev/null @@ -1,56 +0,0 @@ ---- a/Makefile 2017-04-09 12:48:15.000000000 +0200 -+++ b/Makefile 2017-06-21 14:26:02.749282787 +0200 -@@ -9,8 +9,8 @@ - - # Flags - CXX=g++ --CXXFLAGS += -isystem ${SEQTK_ROOT} -isystem ${BOOST_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing --LDFLAGS += -L${SEQTK_ROOT} -L${BOOST_ROOT}/stage/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -+CXXFLAGS += -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing -+LDFLAGS += -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time - - # Additional flags for release/debug - ifeq (${PARALLEL}, 1) -@@ -23,7 +23,7 @@ - ifeq (${STATIC}, 1) - LDFLAGS += -static -static-libgcc -pthread -lhts -lz - else -- LDFLAGS += -lhts -lz -Wl,-rpath,${SEQTK_ROOT},-rpath,${BOOST_ROOT}/stage/lib -+ LDFLAGS += -lhts -lz - endif - ifeq (${DEBUG}, 1) - CXXFLAGS += -g -O0 -fno-inline -DDEBUG -@@ -41,29 +41,17 @@ - DELLYSOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp) - - # Targets --TARGETS = .htslib .bcftools .boost src/delly src/cov src/dpe -+TARGETS = src/delly src/cov src/dpe - - all: $(TARGETS) - --.htslib: $(HTSLIBSOURCES) -- cd src/htslib && make && make lib-static && cd ../../ && touch .htslib -- --.bcftools: $(HTSLIBSOURCES) -- cd src/bcftools && make && cd ../../ && touch .bcftools -- --.boost: $(BOOSTSOURCES) -- cd src/modular-boost && ./bootstrap.sh --prefix=${PWD}/src/modular-boost --without-icu --with-libraries=iostreams,filesystem,system,program_options,date_time && ./b2 && ./b2 headers && cd ../../ && touch .boost -- --src/delly: .htslib .bcftools .boost $(DELLYSOURCES) -- $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) -- --src/cov: .htslib .bcftools .boost $(DELLYSOURCES) -+src/cov: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - --src/dpe: .htslib .bcftools .boost $(DELLYSOURCES) -+src/dpe: $(DELLYSOURCES) - $(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS) - - clean: - cd src/htslib && make clean - cd src/modular-boost && ./b2 --clean-all -- rm -f $(TARGETS) $(TARGETS:=.o) .htslib .boost .bcftools -+ rm -f $(TARGETS) $(TARGETS:=.o) From 1c0639935809cc64150192517c58d95411748407 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 14:04:37 +0200 Subject: [PATCH 19/58] gnu: diamond: Fetch from git. * gnu/packages/bioinformatics.scm (diamond)[source]: Fetch from git. --- gnu/packages/bioinformatics.scm | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 78debbc873..35611f7b1c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2204,14 +2204,14 @@ accurately delineate genomic rearrangements throughout the genome.") (name "diamond") (version "0.9.22") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/bbuchfink/diamond/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/bbuchfink/diamond.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0adp87r9ak63frdrdmrdfhsn6g0jnnyq1lr2wibvqbxcl37iir9m")))) + "0bky78v79g3wmdpsd706cscckgw1v09fg8vdd0z8z0d5b97aj9zl")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target From 49b2e86adf2b0788c627120ae4c3cf55d3eb9afa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 20:51:02 +0200 Subject: [PATCH 20/58] gnu: Add texlive-latex-doi. * gnu/packages/tex.scm (texlive-latex-doi): New variable. --- gnu/packages/tex.scm | 40 +++++++++++++++++++++++++++++++++++++++- 1 file changed, 39 insertions(+), 1 deletion(-) diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 6a76cbf866..e4c307e54f 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2016, 2018 Efraim Flashner ;;; Copyright © 2016 Federico Beffa ;;; Copyright © 2016 Thomas Danckaert -;;; Copyright © 2016, 2017 Ricardo Wurmus +;;; Copyright © 2016, 2017, 2018 Ricardo Wurmus ;;; Copyright © 2017 Leo Famulari ;;; Copyright © 2017 Marius Bakke ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice @@ -2274,6 +2274,44 @@ space-stripped macros.") to something that's not a float.") (license license:lppl))) +(define-public texlive-latex-doi + (package + (name "texlive-latex-doi") + (version (number->string %texlive-revision)) + (source (origin + (method svn-fetch) + (uri (svn-reference + (url (string-append "svn://www.tug.org/texlive/tags/" + %texlive-tag "/Master/texmf-dist/" + "/tex/latex/doi")) + (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0378rdmrgr2lzbfi4qqy4dfpj5im20diyd8z8b9m4mlg05r7wgnb")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let ((target (string-append (assoc-ref %outputs "out") + "/share/texmf-dist/tex/latex/doi"))) + (mkdir-p target) + (copy-recursively (assoc-ref %build-inputs "source") target) + #t)))) + (home-page "https://www.ctan.org/pkg/doi") + (synopsis "Create correct hyperlinks for DOI numbers") + (description + "You can hyperlink DOI numbers to doi.org. However, some publishers have +elected to use nasty characters in their DOI numbering scheme (@code{<}, +@code{>}, @code{_} and @code{;} have all been spotted). This will either +upset LaTeX, or your PDF reader. This package contains a single user-level +command @code{\\doi{}}, which takes a DOI number, and creates a correct +hyperlink to the target of the DOI.") + ;; Any version of the LPPL. + (license license:lppl1.3+))) + (define-public texlive-latex-etoolbox (package (name "texlive-latex-etoolbox") From 893fbf1285fe2298366a5f1631a191e5daccf3d0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 20:51:27 +0200 Subject: [PATCH 21/58] gnu: Add texlive-generic-listofitems. * gnu/packages/tex.scm (texlive-generic-listofitems): New variable. --- gnu/packages/tex.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index e4c307e54f..8994349e3d 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -4775,3 +4775,37 @@ Since every package has its own version number, the version number quoted only refers to the version of scrbook, scrreprt, scrartcl, scrlttr2 and typearea (which are the main parts of the bundle).") (license license:lppl1.3+))) + +(define-public texlive-generic-listofitems + (package + (name "texlive-generic-listofitems") + (version (number->string %texlive-revision)) + (source (origin + (method svn-fetch) + (uri (svn-reference + (url (string-append "svn://www.tug.org/texlive/tags/" + %texlive-tag "/Master/texmf-dist/" + "/tex/generic/listofitems")) + (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1k50z6ixgwwzy84mi0dr5vcjah5p7wvgq66y45bilm91a4m8sgla")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let ((target (string-append (assoc-ref %outputs "out") + "/share/texmf-dist/tex/generic/listofitems"))) + (mkdir-p target) + (copy-recursively (assoc-ref %build-inputs "source") target) + #t)))) + (home-page "https://www.ctan.org/pkg/listofitems") + (synopsis "Grab items in lists using user-specified seperation character") + (description + "This package allows one to capture all the items of a list, for which +the parsing character has been selected by the user, and to access any of +these items with a simple syntax.") + (license license:lppl1.3c+))) From 1d0669f4b4658d2d9bef7cf38366099dee40d272 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 20:51:54 +0200 Subject: [PATCH 22/58] gnu: Add texlive-latex-readarray. * gnu/packages/tex.scm (texlive-latex-readarray): New variable. --- gnu/packages/tex.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 8994349e3d..e796fe4c88 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -4809,3 +4809,40 @@ typearea (which are the main parts of the bundle).") the parsing character has been selected by the user, and to access any of these items with a simple syntax.") (license license:lppl1.3c+))) + +(define-public texlive-latex-readarray + (package + (name "texlive-latex-readarray") + (version (number->string %texlive-revision)) + (source (origin + (method svn-fetch) + (uri (svn-reference + (url (string-append "svn://www.tug.org/texlive/tags/" + %texlive-tag "/Master/texmf-dist/" + "/tex/latex/readarray")) + (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0c53k180ivn1n7fz3ngvd2w1i5dw3kxml0n64vhki88xsylz7lxp")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let ((target (string-append (assoc-ref %outputs "out") + "/share/texmf-dist/tex/latex/readarray"))) + (mkdir-p target) + (copy-recursively (assoc-ref %build-inputs "source") target) + #t)))) + (propagated-inputs + `(("texlive-generic-listofitems" ,texlive-generic-listofitems))) + (home-page "https://www.ctan.org/pkg/readarray") + (synopsis "Read, store and recall array-formatted data") + (description + "This package allows the user to input formatted data into elements of a +2-D or 3-D array and to recall that data at will by individual cell number. +The data can be but need not be numerical in nature. It can be, for example, +formatted text.") + (license license:lppl1.3))) From f50f343e0d138adb328132fb6e17f170261b8798 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 20:52:07 +0200 Subject: [PATCH 23/58] gnu: Add texlive-latex-verbatimbox. * gnu/packages/tex.scm (texlive-latex-verbatimbox): New variable. --- gnu/packages/tex.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index e796fe4c88..46f013b7db 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -4846,3 +4846,42 @@ these items with a simple syntax.") The data can be but need not be numerical in nature. It can be, for example, formatted text.") (license license:lppl1.3))) + +(define-public texlive-latex-verbatimbox + (package + (name "texlive-latex-verbatimbox") + (version (number->string %texlive-revision)) + (source (origin + (method svn-fetch) + (uri (svn-reference + (url (string-append "svn://www.tug.org/texlive/tags/" + %texlive-tag "/Master/texmf-dist/" + "/tex/latex/verbatimbox")) + (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0qh1cgvfs463zsi2pjg490gj0mkjfdpfc381j10cbb5la304psna")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let ((target (string-append (assoc-ref %outputs "out") + "/share/texmf-dist/tex/latex/verbatimbox"))) + (mkdir-p target) + (copy-recursively (assoc-ref %build-inputs "source") target) + #t)))) + (propagated-inputs + `(("texlive-latex-readarray" ,texlive-latex-readarray))) + (home-page "https://www.ctan.org/pkg/verbatimbox") + (synopsis "Deposit verbatim text in a box") + (description + "The package provides a @code{verbbox} environment to place its contents +into a globally available box, or into a box specified by the user. The +global box may then be used in a variety of situations (for example, providing +a replica of the @code{boxedverbatim} environment itself). A valuable use is +in places where the standard @code{verbatim} environment (which is based on a +@code{trivlist}) may not appear.") + (license license:lppl1.3+))) From 4348a059e527969b55875ad33525d6023cd82201 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 20:53:20 +0200 Subject: [PATCH 24/58] gnu: Add texlive-latex-examplep. * gnu/packages/tex.scm (texlive-latex-examplep): New variable. --- gnu/packages/tex.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/tex.scm b/gnu/packages/tex.scm index 46f013b7db..f8b11f7e1a 100644 --- a/gnu/packages/tex.scm +++ b/gnu/packages/tex.scm @@ -4885,3 +4885,44 @@ a replica of the @code{boxedverbatim} environment itself). A valuable use is in places where the standard @code{verbatim} environment (which is based on a @code{trivlist}) may not appear.") (license license:lppl1.3+))) + +(define-public texlive-latex-examplep + (package + (name "texlive-latex-examplep") + (version (number->string %texlive-revision)) + (source (origin + (method svn-fetch) + (uri (svn-reference + (url (string-append "svn://www.tug.org/texlive/tags/" + %texlive-tag "/Master/texmf-dist/" + "/tex/latex/examplep")) + (revision %texlive-revision))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0fsvvmz68ij0zwfzrny6x13d92grxr4ap59lxgah4smbkccd6s27")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let ((target (string-append (assoc-ref %outputs "out") + "/share/texmf-dist/tex/latex/examplep"))) + (mkdir-p target) + (copy-recursively (assoc-ref %build-inputs "source") target) + #t)))) + (home-page "https://www.ctan.org/pkg/examplep") + (synopsis "Verbatim phrases and listings in LaTeX") + (description + "Examplep provides sophisticated features for typesetting verbatim source +code listings, including the display of the source code and its compiled LaTeX +or METAPOST output side-by-side, with automatic width detection and enabled +page breaks (in the source), without the need for specifying the source twice. +Special care is taken that section, page and footnote numbers do not interfere +with the main document. For typesetting short verbatim phrases, a replacement +for the @code{\\verb} command is also provided in the package, which can be +used inside tables and moving arguments such as footnotes and section +titles.") + ;; No version of the GPL is specified. + (license license:gpl3+))) From 5748fe5fccef9653ed1e16f83d0fe3e889de6a26 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 20:53:40 +0200 Subject: [PATCH 25/58] gnu: discrover: Fetch from git. * gnu/packages/bioinformatics.scm (discrover)[source]: Fetch from git. --- gnu/packages/bioinformatics.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 35611f7b1c..b6bd2c619a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2239,13 +2239,14 @@ data and settings.") (version "1.6.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/maaskola/discrover/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/maaskola/discrover.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0rah9ja4m0rl5mldd6vag9rwrivw1zrqxssfq8qx64m7961fp68k")))) + "173fwi2vb6a5kp406hm3jj6j7v4whww796f2qcygp4rpvamh307y")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; there are no tests From 949fa34b84ce8c8027e568878db648c20ff37a5c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 20:58:45 +0200 Subject: [PATCH 26/58] gnu: eigensoft: Update to 7.2.1. * gnu/packages/bioinformatics.scm (eigensoft): Update to 7.2.1. [arguments]: Remove Makefile modification. --- gnu/packages/bioinformatics.scm | 113 +++++++++++++++----------------- 1 file changed, 52 insertions(+), 61 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b6bd2c619a..d0f4429a4c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2274,72 +2274,63 @@ of nucleic acid binding proteins.") (license license:gpl3+))) (define-public eigensoft - (let ((revision "1") - (commit "b14d1e202e21e532536ff8004f0419cd5e259dc7")) - (package - (name "eigensoft") - (version (string-append "6.1.2-" - revision "." - (string-take commit 9))) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/DReichLab/EIG.git") - (commit commit))) - (file-name (string-append "eigensoft-" commit "-checkout")) - (sha256 - (base32 - "0f5m6k2j5c16xc3xbywcs989xyc26ncy1zfzp9j9n55n9r4xcaiq")) - (modules '((guix build utils))) - ;; Remove pre-built binaries. - (snippet '(begin - (delete-file-recursively "bin") - (mkdir "bin") - #t)))) - (build-system gnu-build-system) - (arguments - `(#:tests? #f ; There are no tests. - #:make-flags '("CC=gcc") - #:phases - (modify-phases %standard-phases - ;; There is no configure phase, but the Makefile is in a - ;; sub-directory. - (replace 'configure - (lambda _ - (chdir "src") - ;; The link flags are incomplete. - (substitute* "Makefile" - (("-lgsl") "-lgsl -lm -llapack -llapacke -lpthread")) - #t)) - ;; The provided install target only copies executables to - ;; the "bin" directory in the build root. - (add-after 'install 'actually-install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin"))) - (for-each (lambda (file) - (install-file file bin)) - (find-files "../bin" ".*")) - #t)))))) - (inputs - `(("gsl" ,gsl) - ("lapack" ,lapack) - ("openblas" ,openblas) - ("perl" ,perl) - ("gfortran" ,gfortran "lib"))) - (home-page "https://github.com/DReichLab/EIG") - (synopsis "Tools for population genetics") - (description "The EIGENSOFT package provides tools for population + (package + (name "eigensoft") + (version "7.2.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/DReichLab/EIG.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1c141fqvhnzibmnf22sv23vbmzm20kjjyrib44cfh75wyndp2d9k")) + (modules '((guix build utils))) + ;; Remove pre-built binaries. + (snippet '(begin + (delete-file-recursively "bin") + (mkdir "bin") + #t)))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests. + #:make-flags '("CC=gcc") + #:phases + (modify-phases %standard-phases + ;; There is no configure phase, but the Makefile is in a + ;; sub-directory. + (replace 'configure + (lambda _ (chdir "src") #t)) + ;; The provided install target only copies executables to + ;; the "bin" directory in the build root. + (add-after 'install 'actually-install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (for-each (lambda (file) + (install-file file bin)) + (find-files "../bin" ".*")) + #t)))))) + (inputs + `(("gsl" ,gsl) + ("lapack" ,lapack) + ("openblas" ,openblas) + ("perl" ,perl) + ("gfortran" ,gfortran "lib"))) + (home-page "https://github.com/DReichLab/EIG") + (synopsis "Tools for population genetics") + (description "The EIGENSOFT package provides tools for population genetics and stratification correction. EIGENSOFT implements methods commonly used in population genetics analyses such as PCA, computation of Tracy-Widom statistics, and finding related individuals in structured populations. It comes with a built-in plotting script and supports multiple file formats and quantitative phenotypes.") - ;; The license of the eigensoft tools is Expat, but since it's - ;; linking with the GNU Scientific Library (GSL) the effective - ;; license is the GPL. - (license license:gpl3+)))) + ;; The license of the eigensoft tools is Expat, but since it's + ;; linking with the GNU Scientific Library (GSL) the effective + ;; license is the GPL. + (license license:gpl3+))) (define-public edirect (package From c96ca68f31619ed678720fc1dc6bbf0906ce5638 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 21:11:37 +0200 Subject: [PATCH 27/58] gnu: edirect: Update to 10.2.20181018. * gnu/packages/bioinformatics.scm (edirect): Update to 10.2.20181018. [arguments]: Add simple check phase; simplify other phases. [inputs]: Add perl-xml-simple. --- gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++-------------- 1 file changed, 26 insertions(+), 20 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d0f4429a4c..a806fd5f22 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2335,36 +2335,41 @@ quantitative phenotypes.") (define-public edirect (package (name "edirect") - (version "4.10") + (version "10.2.20181018") (source (origin (method url-fetch) - (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/" - "versions/2016-05-03/edirect.tar.gz")) + (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect" + "/versions/" version + "/edirect-" version ".tar.gz")) (sha256 (base32 - "15zsprak5yh8c1yrz4r1knmb5s8qcmdid4xdhkh3lqcv64l60hli")))) + "091f4aigzpbqih6h82nq566gkp3y07i72yqndmqskfgar1vwgci7")))) (build-system perl-build-system) (arguments - `(#:tests? #f ;no "check" target - #:phases + `(#:phases (modify-phases %standard-phases (delete 'configure) (delete 'build) + (delete 'check) ; simple check after install (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((target (string-append (assoc-ref outputs "out") - "/bin"))) - (mkdir-p target) - (install-file "edirect.pl" target) - #t))) - (add-after - 'install 'wrap-program - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Make sure 'edirect.pl' finds all perl inputs at runtime. - (let* ((out (assoc-ref outputs "out")) - (path (getenv "PERL5LIB"))) - (wrap-program (string-append out "/bin/edirect.pl") - `("PERL5LIB" ":" prefix (,path))))))))) + (lambda* (#:key outputs #:allow-other-keys) + (install-file "edirect.pl" + (string-append (assoc-ref outputs "out") "/bin")) + #t)) + (add-after 'install 'wrap-program + (lambda* (#:key outputs #:allow-other-keys) + ;; Make sure 'edirect.pl' finds all perl inputs at runtime. + (let* ((out (assoc-ref outputs "out")) + (path (getenv "PERL5LIB"))) + (wrap-program (string-append out "/bin/edirect.pl") + `("PERL5LIB" ":" prefix (,path)))) + #t)) + (add-after 'wrap-program 'check + (lambda* (#:key outputs #:allow-other-keys) + (invoke (string-append (assoc-ref outputs "out") + "/bin/edirect.pl") + "-filter" "-help") + #t))))) (inputs `(("perl-html-parser" ,perl-html-parser) ("perl-encode-locale" ,perl-encode-locale) @@ -2380,6 +2385,7 @@ quantitative phenotypes.") ("perl-net-http" ,perl-net-http) ("perl-uri" ,perl-uri) ("perl-www-robotrules" ,perl-www-robotrules) + ("perl-xml-simple" ,perl-xml-simple) ("perl" ,perl))) (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/") (synopsis "Tools for accessing the NCBI's set of databases") From 38622ccd14c5d2df152ff8d72f1f5269afb36565 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 21:26:35 +0200 Subject: [PATCH 28/58] gnu: express-beta-diversity: Update to 1.0.8. * gnu/packages/bioinformatics.scm (express-beta-diversity): Update to 1.0.8. [source]: Fetch from git. [arguments]: Use INVOKE; remove "exit-source" build phase; simplify. --- gnu/packages/bioinformatics.scm | 31 +++++++++++++------------------ 1 file changed, 13 insertions(+), 18 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a806fd5f22..9a04118588 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2481,17 +2481,16 @@ ChIP-Seq, and analysis of metagenomic data.") (define-public express-beta-diversity (package (name "express-beta-diversity") - (version "1.0.7") + (version "1.0.8") (source (origin - (method url-fetch) - (uri - (string-append - "https://github.com/dparks1134/ExpressBetaDiversity/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/dparks1134/ExpressBetaDiversity.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr")))) + "0s0yzg5c21349rh7x4w9266jsvnp7j1hp9cf8sk32hz8nvrj745x")))) (build-system gnu-build-system) (arguments `(#:phases @@ -2499,17 +2498,13 @@ ChIP-Seq, and analysis of metagenomic data.") (delete 'configure) (add-before 'build 'enter-source (lambda _ (chdir "source") #t)) (replace 'check - (lambda _ (zero? (system* "../bin/ExpressBetaDiversity" - "-u")))) - (add-after 'check 'exit-source (lambda _ (chdir "..") #t)) + (lambda _ (invoke "../bin/ExpressBetaDiversity" "-u") #t)) (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") - "/bin"))) - (mkdir-p bin) - (install-file "scripts/convertToEBD.py" bin) - (install-file "bin/ExpressBetaDiversity" bin) - #t)))))) + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "../scripts/convertToEBD.py" bin) + (install-file "../bin/ExpressBetaDiversity" bin) + #t)))))) (inputs `(("python" ,python-2))) (home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity") From 0db75f7a79126a368e0c8fb2d71abf76da065a3f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 21:30:53 +0200 Subject: [PATCH 29/58] gnu: fasttree: Use INVOKE. * gnu/packages/bioinformatics.scm (fasttree)[arguments]: Use INVOKE; simplify install phase. --- gnu/packages/bioinformatics.scm | 45 ++++++++++++++++----------------- 1 file changed, 22 insertions(+), 23 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9a04118588..a99deeb0a6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2537,31 +2537,30 @@ similarity of community members.") (delete 'configure) (replace 'build (lambda* (#:key source #:allow-other-keys) - (and (zero? (system* "gcc" - "-O3" - "-finline-functions" - "-funroll-loops" - "-Wall" - "-o" - "FastTree" - source - "-lm")) - (zero? (system* "gcc" - "-DOPENMP" - "-fopenmp" - "-O3" - "-finline-functions" - "-funroll-loops" - "-Wall" - "-o" - "FastTreeMP" - source - "-lm"))))) + (invoke "gcc" + "-O3" + "-finline-functions" + "-funroll-loops" + "-Wall" + "-o" + "FastTree" + source + "-lm") + (invoke "gcc" + "-DOPENMP" + "-fopenmp" + "-O3" + "-finline-functions" + "-funroll-loops" + "-Wall" + "-o" + "FastTreeMP" + source + "-lm") + #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") - "/bin"))) - (mkdir-p bin) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (install-file "FastTree" bin) (install-file "FastTreeMP" bin) #t)))))) From 50e33c3a8c591af8a6112ea42d53ed6f0ec80208 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 22:58:30 +0200 Subject: [PATCH 30/58] gnu: python-screed: Update to 1.0. * gnu/packages/bioinformatics.scm (python-screed): Update to 1.0. [arguments]: Run tests after installation. [native-inputs]: Add python-pytest, python-pytest-cov, and python-pytest-runner; remove python-nose. --- gnu/packages/bioinformatics.scm | 31 ++++++++++++++++++++++--------- 1 file changed, 22 insertions(+), 9 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a99deeb0a6..9afb2c1197 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5602,25 +5602,38 @@ complexity samples.") (define-public python-screed (package (name "python-screed") - (version "0.9") + (version "1.0") (source (origin (method url-fetch) (uri (pypi-uri "screed" version)) (sha256 (base32 - "18czszp9fkx3j6jr7y5kp6dfialscgddk05mw1zkhh2zhn0jd8i0")))) + "148vcb7w2wr6a4w6vs2bsxanbqibxfk490zbcbg4m61s8669zdjx")))) (build-system python-build-system) (arguments - `(#:phases + '(#:phases (modify-phases %standard-phases - (replace 'check - (lambda _ - (setenv "PYTHONPATH" - (string-append (getenv "PYTHONPATH") ":.")) - (zero? (system* "nosetests" "--attr" "!known_failing"))))))) + ;; Tests must be run after installation, as the "screed" command does + ;; not exist right after building. + (delete 'check) + (add-after 'install 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (setenv "PYTHONPATH" + (string-append out "/lib/python" + (string-take (string-take-right + (assoc-ref inputs "python") + 5) 3) + "/site-packages:" + (getenv "PYTHONPATH"))) + (setenv "PATH" (string-append out "/bin:" (getenv "PATH")))) + (invoke "python" "setup.py" "test") + #t))))) (native-inputs - `(("python-nose" ,python-nose))) + `(("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-runner" ,python-pytest-runner))) (inputs `(("python-bz2file" ,python-bz2file))) (home-page "https://github.com/dib-lab/screed/") From 4b8f4536ce6107bf3417252b2206d14912399344 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 22:59:37 +0200 Subject: [PATCH 31/58] gnu: khmer: Update to 2.1.2. * gnu/packages/bioinformatics.scm (khmer): Update to 2.1.2. [source]: Fetch from git; remove bundled libraries in snippet. [arguments]: Remove "set-paths" phase; remove "post-install-check" phase; remove "reset-gzip-timestamps" phase. [native-inputs]: Remove seqan and python-nose; add python-cython, python-pytest, and python-pytest-runner. [inputs]: Remove gcc-4.9. --- gnu/packages/bioinformatics.scm | 83 +++++++++++---------------------- 1 file changed, 28 insertions(+), 55 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9afb2c1197..9163b5dc8a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3742,75 +3742,48 @@ command, or queried for specific k-mers with @code{jellyfish query}.") (define-public khmer (package (name "khmer") - (version "2.0") + (version "2.1.2") (source (origin - (method url-fetch) - (uri (pypi-uri "khmer" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/dib-lab/khmer.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0wb05shqh77v00256qlm68vbbx3kl76fyzihszbz5nhanl4ni33a")) - (patches (search-patches "khmer-use-libraries.patch")))) + "02x38d9jw2r58y8dmnj4hffy9wxv1yc1jwbvdbhby9dxndv94r9m")) + (patches (search-patches "khmer-use-libraries.patch")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Delete bundled libraries. We do not replace the bundled seqan + ;; as it is a modified subset of the old version 1.4.1. + ;; + ;; We do not replace the bundled MurmurHash as the canonical + ;; repository for this code 'SMHasher' is unsuitable for providing + ;; a library. See + ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html + (delete-file-recursively "third-party/zlib") + (delete-file-recursively "third-party/bzip2") + #t)))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'set-paths - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; Delete bundled libraries. - (delete-file-recursively "third-party/zlib") - (delete-file-recursively "third-party/bzip2") - ;; Replace bundled seqan. - (let* ((seqan-all "third-party/seqan") - (seqan-include (string-append - seqan-all "/core/include"))) - (delete-file-recursively seqan-all) - (copy-recursively (string-append (assoc-ref inputs "seqan") - "/include/seqan") - (string-append seqan-include "/seqan"))) - ;; We do not replace the bundled MurmurHash as the canonical - ;; repository for this code 'SMHasher' is unsuitable for - ;; providing a library. See - ;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html - #t)) (add-after 'unpack 'set-cc - (lambda _ - (setenv "CC" "gcc") - #t)) - ;; It is simpler to test after installation. - (delete 'check) - (add-after 'install 'post-install-check - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (setenv "PATH" - (string-append - (getenv "PATH") - ":" - (assoc-ref outputs "out") - "/bin")) - (setenv "PYTHONPATH" - (string-append - (getenv "PYTHONPATH") - ":" - out - "/lib/python" - (string-take (string-take-right - (assoc-ref inputs "python") 5) 3) - "/site-packages")) - (with-directory-excursion "build" - (zero? (system* "nosetests" "khmer" "--attr" - "!known_failing"))))))))) + (lambda _ (setenv "CC" "gcc") #t)) + ;; FIXME: This fails with "permission denied". + (delete 'reset-gzip-timestamps)))) (native-inputs - `(("seqan" ,seqan) - ("python-nose" ,python-nose))) + `(("python-cython" ,python-cython) + ("python-pytest" ,python-pytest) + ("python-pytest-runner" ,python-pytest-runner))) (inputs `(("zlib" ,zlib) ("bzip2" ,bzip2) ("python-screed" ,python-screed) - ("python-bz2file" ,python-bz2file) - ;; Tests fail when gcc-5 is used for compilation. Use gcc-4.9 at least - ;; until the next version of khmer (likely 2.1) is released. - ("gcc" ,gcc-4.9))) + ("python-bz2file" ,python-bz2file))) (home-page "https://khmer.readthedocs.org/") (synopsis "K-mer counting, filtering and graph traversal library") (description "The khmer software is a set of command-line tools for From 4d93a9a36c3ddc431789fa38201b0fd657412dbe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 23:03:57 +0200 Subject: [PATCH 32/58] gnu: seqan: Update to 2.4.0. * gnu/packages/bioinformatics.scm (seqan): Update to 2.4.0. [native-inputs]: Replace bzip2 with xz. (seqan-1): New variable. (tophat)[inputs]: Use seqan-1. --- gnu/packages/bioinformatics.scm | 58 ++++++++++++++++++++++++++------- 1 file changed, 47 insertions(+), 11 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9163b5dc8a..cdb82aee8b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1382,7 +1382,7 @@ gapped, local, and paired-end alignment modes.") ("python" ,python-2) ("perl" ,perl) ("zlib" ,zlib) - ("seqan" ,seqan))) + ("seqan" ,seqan-1))) (home-page "http://ccb.jhu.edu/software/tophat/index.shtml") (synopsis "Spliced read mapper for RNA-Seq data") (description @@ -5732,6 +5732,51 @@ writing files into the .sra format.") (define-public seqan (package + (name "seqan") + (version "2.4.0") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/seqan/seqan/releases/" + "download/seqan-v" version + "/seqan-library-" version ".tar.xz")) + (sha256 + (base32 + "19a1rlxx03qy1i1iriicly68w64yjxbv24g9gdywnfmq998v35yx")))) + ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it + ;; makes sense to split the outputs. + (outputs '("out" "doc")) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let ((tar (assoc-ref %build-inputs "tar")) + (xz (assoc-ref %build-inputs "xz")) + (out (assoc-ref %outputs "out")) + (doc (assoc-ref %outputs "doc"))) + (setenv "PATH" (string-append tar "/bin:" xz "/bin")) + (invoke "tar" "xvf" (assoc-ref %build-inputs "source")) + (chdir (string-append "seqan-library-" ,version)) + (copy-recursively "include" (string-append out "/include")) + (copy-recursively "share" (string-append doc "/share")) + #t)))) + (native-inputs + `(("source" ,source) + ("tar" ,tar) + ("xz" ,xz))) + (home-page "http://www.seqan.de") + (synopsis "Library for nucleotide sequence analysis") + (description + "SeqAn is a C++ library of efficient algorithms and data structures for +the analysis of sequences with the focus on biological data. It contains +algorithms and data structures for string representation and their +manipulation, online and indexed string search, efficient I/O of +bioinformatics file formats, sequence alignment, and more.") + (license license:bsd-3))) + +(define-public seqan-1 + (package (inherit seqan) (name "seqan") (version "1.4.2") (source (origin @@ -5763,16 +5808,7 @@ writing files into the .sra format.") (native-inputs `(("source" ,source) ("tar" ,tar) - ("bzip2" ,bzip2))) - (home-page "http://www.seqan.de") - (synopsis "Library for nucleotide sequence analysis") - (description - "SeqAn is a C++ library of efficient algorithms and data structures for -the analysis of sequences with the focus on biological data. It contains -algorithms and data structures for string representation and their -manipulation, online and indexed string search, efficient I/O of -bioinformatics file formats, sequence alignment, and more.") - (license license:bsd-3))) + ("bzip2" ,bzip2))))) (define-public seqmagick (package From f8ee22fc8b486612a9f041bb351d99ba0ce16dc0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 21 Oct 2018 23:05:11 +0200 Subject: [PATCH 33/58] gnu: flexbar: Update to 3.4.0. * gnu/packages/bioinformatics.scm (flexbar): Update to 3.4.0. [source]: Fetch from git. [arguments]: Adjust check and install phases. [home-page]: Update to new home at Github. [license]: Change to bsd-3. --- gnu/packages/bioinformatics.scm | 39 +++++++++++++++++---------------- 1 file changed, 20 insertions(+), 19 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cdb82aee8b..96ea07bdc4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2607,38 +2607,39 @@ results. The FASTX-Toolkit tools perform some of these preprocessing tasks.") (define-public flexbar (package (name "flexbar") - (version "2.5") + (version "3.4.0") (source (origin - (method url-fetch) - (uri - (string-append "mirror://sourceforge/flexbar/" - version "/flexbar_v" version "_src.tgz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/seqan/flexbar.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf")))) + "1pq9sxvdnldl14libk234m72dqhwgzs3acgl943wchwdqlcsi5r2")))) (build-system cmake-build-system) (arguments - `(#:configure-flags (list - (string-append "-DFLEXBAR_BINARY_DIR=" - (assoc-ref %outputs "out") - "/bin/")) - #:phases + `(#:phases (modify-phases %standard-phases (replace 'check (lambda* (#:key outputs #:allow-other-keys) - (setenv "PATH" (string-append - (assoc-ref outputs "out") "/bin:" - (getenv "PATH"))) - (chdir "../flexbar_v2.5_src/test") - (zero? (system* "bash" "flexbar_validate.sh")))) - (delete 'install)))) + (setenv "PATH" (string-append (getcwd) ":" (getenv "PATH"))) + (with-directory-excursion "../source/test" + (invoke "bash" "flexbar_test.sh")) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (string-append (assoc-ref outputs "out"))) + (bin (string-append out "/bin/"))) + (install-file "flexbar" bin)) + #t))))) (inputs `(("tbb" ,tbb) ("zlib" ,zlib))) (native-inputs `(("pkg-config" ,pkg-config) ("seqan" ,seqan))) - (home-page "http://flexbar.sourceforge.net") + (home-page "https://github.com/seqan/flexbar") (synopsis "Barcode and adapter removal tool for sequencing platforms") (description "Flexbar preprocesses high-throughput nucleotide sequencing data @@ -2647,7 +2648,7 @@ Moreover, trimming and filtering features are provided. Flexbar increases read mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform.") - (license license:gpl3))) + (license license:bsd-3))) (define-public fraggenescan (package From aff38cb199fc847f97059600a6c9c99ee754fc07 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 20 Oct 2018 17:39:53 +0200 Subject: [PATCH 34/58] =?UTF-8?q?install:=20Make=20/var/guix/=E2=80=A6/gui?= =?UTF-8?q?x-profile=20a=20relative=20symlink.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/build/install.scm (populate-single-profile-directory): Make /var/guix/profiles/per-user/root/guix-profile a relative symlink. --- gnu/build/install.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/build/install.scm b/gnu/build/install.scm index 5a5e703872..c602d69489 100644 --- a/gnu/build/install.scm +++ b/gnu/build/install.scm @@ -199,7 +199,7 @@ This is used to create the self-contained tarballs with 'guix pack'." (mkdir-p* %root-profile) (symlink* profile (string-append %root-profile "/guix-profile-1-link")) - (symlink* (string-append %root-profile "/guix-profile-1-link") + (symlink* "guix-profile-1-link" (string-append %root-profile "/guix-profile")) (mkdir-p* "/root") From 16d212510aa597639ffe5a847503a07170e239cd Mon Sep 17 00:00:00 2001 From: Luther Thompson Date: Sun, 21 Oct 2018 23:45:52 +0200 Subject: [PATCH 35/58] gnu: Add python-ilinkedlist. * gnu/packages/python.scm (python-ilinkedlist): New variable. --- gnu/packages/python.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 29ce213afb..9c749227de 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -55,6 +55,7 @@ ;;; Copyright © 2018 Oleg Pykhalov ;;; Copyright © 2018 Clément Lassieur ;;; Copyright © 2018 Maxim Cournoyer +;;; Copyright © 2018 Luther Thompson ;;; ;;; This file is part of GNU Guix. ;;; @@ -14504,3 +14505,28 @@ extend common interfaces like NumPy, Pandas, or Python iterators to larger-than-memory or distributed environments. These parallel collections run on top of the dynamic task schedulers. ") (license license:bsd-3))) + +(define-public python-ilinkedlist + (package + (name "python-ilinkedlist") + (version "0.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "ilinkedlist" version)) + (sha256 + (base32 + "063c2gm4jkgkv0nsg7mrc8y0w82ms98l4xchmbrvr68cscglhk69")))) + (build-system python-build-system) + (native-inputs `(("python-pytest" ,python-pytest))) + (inputs `(("python" ,python))) + (home-page "https://github.com/luther9/ilinkedlist-py") + (synopsis "Immutable linked list library") + (description + "This is a implementation of immutable linked lists for Python. It +contains @code{nil} (the empty linked list) and a @code{Pair} class for nodes. +Since a linked list is treated as immutable, it is hashable, and its length +can be retrieved in constant time. Some of the terminology is inspired by +LISP. It is possible to create an improper list by creating a @code{Pair} +with a non-list @code{cdr}.") + (license license:gpl3+))) From ff598353c01b1953243ba0ecb87efbd73c66720e Mon Sep 17 00:00:00 2001 From: Pierre Langlois Date: Sat, 20 Oct 2018 11:17:24 +0100 Subject: [PATCH 36/58] gnu: light: Update to 1.2. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/linux.scm (light): Update to 1.2. [source]: Switch to url-fetch. [arguments]: Remove. [native-inputs]: Remove help2man. Add autoconf and automake. Signed-off-by: Ludovic Courtès --- gnu/packages/linux.scm | 30 +++++++++++------------------- 1 file changed, 11 insertions(+), 19 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index bc53a88bfc..2c6bd79231 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -30,6 +30,7 @@ ;;; Copyright © 2018 Pierre-Antoine Rouby ;;; Copyright © 2018 Brendan Tildesley ;;; Copyright © 2018 Manuel Graf +;;; Copyright © 2018 Pierre Langlois ;;; ;;; This file is part of GNU Guix. ;;; @@ -4167,30 +4168,21 @@ monitoring tools for Linux. These include @code{mpstat}, @code{iostat}, (define-public light (package (name "light") - (version "1.1.2") + (version "1.2") (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/haikarainen/light") - (commit version))) + (method url-fetch) + (uri (string-append + "https://github.com/haikarainen/light/archive/v" + version ".tar.gz")) (sha256 (base32 - "0c934gxav9cgdf94li6dp0rfqmpday9d33vdn9xb2mfp4war9n4w")))) + "1gfvsw7gh5pis733l7j54vzp272pvjyzbg8a0pvapfmg0s7mip97")) + (file-name (string-append name "-" version ".tar.gz")))) (build-system gnu-build-system) - (arguments - '(#:tests? #f ; no tests - #:make-flags (list "CC=gcc" - (string-append "PREFIX=" %output)) - #:phases - (modify-phases %standard-phases - (delete 'configure) ; no configure script - (add-after 'unpack 'patch-makefile - (lambda _ - (substitute* "Makefile" (("chown") "#")) - #t))))) (native-inputs - `(("help2man" ,help2man))) - (home-page "https://haikarainen.github.io/light") + `(("autoconf" ,autoconf) + ("automake" ,automake))) + (home-page "https://haikarainen.github.io/light/") (synopsis "GNU/Linux application to control backlights") (description "Light is a program to send commands to screen backlight controllers From df71447e992e82d029ac57d0d721af02fc6a5061 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 20 Oct 2018 12:26:51 -0400 Subject: [PATCH 37/58] gnu: OpenSSH: Update to 7.9p1. * gnu/packages/ssh.scm (openssh): Update to 7.9p1. --- gnu/packages/ssh.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ssh.scm b/gnu/packages/ssh.scm index 829977f5c5..e806fc80f2 100644 --- a/gnu/packages/ssh.scm +++ b/gnu/packages/ssh.scm @@ -147,14 +147,14 @@ a server that supports the SSH-2 protocol.") (define-public openssh (package (name "openssh") - (version "7.8p1") + (version "7.9p1") (source (origin (method url-fetch) (uri (string-append "mirror://openbsd/OpenSSH/portable/" name "-" version ".tar.gz")) (sha256 (base32 - "1jj4f586r9lhakp2w0zv7j616d6x62m15q8l4nxq7haja6qlnj0s")))) + "1b8sy6v0b8v4ggmknwcqx3y1rjcpsll0f1f8f4vyv11x4ni3njvb")))) (build-system gnu-build-system) (native-inputs `(("groff" ,groff))) (inputs `(("openssl" ,openssl) From dc3dfa131f97105baefeb34e5155e89946dc1eba Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 22 Oct 2018 00:38:26 +0200 Subject: [PATCH 38/58] gnu: knot: Update to 2.7.3. * gnu/packages/dns.scm (knot): Update to 2.7.3. --- gnu/packages/dns.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index ad1a8638bc..1dcf73771b 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -569,14 +569,14 @@ Extensions} (DNSSEC).") (define-public knot (package (name "knot") - (version "2.7.2") + (version "2.7.3") (source (origin (method url-fetch) (uri (string-append "https://secure.nic.cz/files/knot-dns/" name "-" version ".tar.xz")) (sha256 (base32 - "0cc4wgb02ch09x99a1fnr7vsdik8k920q7jafzcamjvy3kpb4w6b")) + "1pwjcv7hzhqawisibybma160k77a6f1v94xw6ay9c7j49vrw05w7")) (modules '((guix build utils))) (snippet '(begin From 69c69c2d8e4922ee997f213772acabb95d33a467 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sun, 21 Oct 2018 23:16:50 -0400 Subject: [PATCH 39/58] gnu: libmpdclient: Update to 2.16. * gnu/packages/mpd.scm (libmpdclient): Update to 2.16. --- gnu/packages/mpd.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm index 3e69ddba69..b69be2965f 100644 --- a/gnu/packages/mpd.scm +++ b/gnu/packages/mpd.scm @@ -58,7 +58,7 @@ (define-public libmpdclient (package (name "libmpdclient") - (version "2.15") + (version "2.16") (source (origin (method url-fetch) (uri @@ -67,7 +67,7 @@ "/libmpdclient-" version ".tar.xz")) (sha256 (base32 - "1la60ar6i4ghpscrlgm45kci9b74bvkpsfybhg0ygs4rzpwzdnxl")))) + "0r24cl3i9nvs6a47mvwaxk1kb5wmnhkhrw1q5cq9010fgjvdlszs")))) (build-system meson-build-system) (native-inputs `(("pkg-config" ,pkg-config) From 318ec0a896dff7f311d67c6ac9f1bea31efb5e3e Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 22 Oct 2018 03:31:51 -0400 Subject: [PATCH 40/58] gnu: livemedia-utils: Update to 2018.10.17 [fixes CVE-2018-4013]. * gnu/packages/video.scm (livemedia-utils): Update to 2018.10.17. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index a6930abfda..4fcd15e4aa 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -2645,7 +2645,7 @@ many codecs and formats supported by libmediainfo.") (define-public livemedia-utils (package (name "livemedia-utils") - (version "2017.10.28") + (version "2018.10.17") (source (origin (method url-fetch) (uri (string-append @@ -2653,7 +2653,7 @@ many codecs and formats supported by libmediainfo.") version ".tar.gz")) (sha256 (base32 - "0f5kxpayqn3yhabqrd2cqlc74i6x2xr01jfkank1lcilxnfyrsnq")) + "1s69ipvdc6ldscp0cr1zpsll8xc3qcagr95nl84x7b1rbg4xjs3w")) (modules '((guix build utils))) (snippet '(begin ;; As of glibc 2.26, no longer is. From 09aa3d063a0eacf3fca8d4803fbb62bd7b1ee663 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 22 Oct 2018 13:00:06 +0200 Subject: [PATCH 41/58] gnu: Add r-ruvseq. * gnu/packages/bioconductor.scm (r-ruvseq): New variable. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1b779855b2..92b67453f6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -913,3 +913,29 @@ can be analyzed regarding their minimal, maximal and average distances between barcodes. Finally, reads that start with a (possibly mutated) barcode can be demultiplexed, i.e. assigned to their original reference barcode.") (license license:gpl2))) + +(define-public r-ruvseq + (package + (name "r-ruvseq") + (version "1.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RUVSeq" version)) + (sha256 + (base32 + "16i5sm5af761k4zvspfi8jknsgln48bn538hxqqmlaq7wvlfxqxj")))) + (properties `((upstream-name . "RUVSeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-edaseq" ,r-edaseq) + ("r-edger" ,r-edger) + ("r-mass" ,r-mass))) + (home-page "https://github.com/drisso/RUVSeq") + (synopsis "Remove unwanted variation from RNA-Seq data") + (description + "This package implements methods to @dfn{remove unwanted variation} (RUV) +of Risso et al. (2014) for the normalization of RNA-Seq read counts between +samples.") + (license license:artistic2.0))) From 3a352a44056f4680bbb1de038bd0292803c35b1e Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 22 Oct 2018 15:56:38 +0200 Subject: [PATCH 42/58] gnu: snap: Update to 4.2.2.2. * gnu/packages/education.scm (snap): Update to 4.2.2.2. Update source URL. --- gnu/packages/education.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/education.scm b/gnu/packages/education.scm index 8b02adc182..b333bb9d35 100644 --- a/gnu/packages/education.scm +++ b/gnu/packages/education.scm @@ -243,17 +243,17 @@ easy.") (define-public snap (package (name "snap") - (version "4.2.1.4") + (version "4.2.2.2") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/jmoenig/Snap--Build-Your-Own-Blocks.git") + (url "https://github.com/jmoenig/Snap.git") (commit version))) (file-name (git-file-name name version)) (sha256 (base32 - "0yc0w0cdhvi0nwqqrann2v3y0n7shxh7irgixqvlavp4k49d7aqj")))) + "0bay08yr58qj8wzpjg33gdj78rfhyskfzidknpdl3cr1jrj6i4p9")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -265,7 +265,7 @@ easy.") (share (string-append out "/share/snap"))) (copy-recursively source share) ;; Replace the sole minified file in the package. - (with-directory-excursion share + (with-directory-excursion (string-append share "/src") (delete-file "FileSaver.min.js") (symlink (string-append (assoc-ref %build-inputs "js-filesaver") "/share/javascript/FileSaver.min.js") From 51f4e36cb9cc45493397bc799f7a87e5de92560d Mon Sep 17 00:00:00 2001 From: Christopher Lemmer Webber Date: Mon, 22 Oct 2018 09:59:42 -0400 Subject: [PATCH 43/58] gnu: Add emacs-scribble-mode. * gnu/packages/emacs.scm (emacs-scribble-mode): New variable. --- gnu/packages/emacs.scm | 29 ++++++++++++++++++++++++++++- 1 file changed, 28 insertions(+), 1 deletion(-) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 47e984e101..ce98dbaeb8 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2015 Federico Beffa ;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018 Chris Marusich -;;; Copyright © 2015, 2016 Christopher Allan Webber +;;; Copyright © 2015, 2016, 2018 Christopher Lemmer Webber ;;; Copyright © 2016 Adriano Peluso ;;; Copyright © 2016, 2017, 2018 Efraim Flashner ;;; Copyright © 2016 David Thompson @@ -654,6 +654,33 @@ Gitlab APIs from Emacs packages. It abstracts access to API resources using only a handful of functions that are not resource-specific.") (license license:gpl3+))) +(define-public emacs-scribble-mode + (let ((commit "34e9e5edb921813b6483e0fefa848efb6ee4b314") + (version "0.0") + (revision 0)) + (package + (name "emacs-scribble-mode") + (version (if (zero? revision) + version + (string-append version "-" + (number->string revision) + "." (string-take commit 7)))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emacs-pe/scribble-mode.git") + (commit commit))) + (sha256 + (base32 + "0598byqpz2q6yi2q4dwd77jj9z3n99z34d3an51s9m2za0nh1qvp")))) + (build-system emacs-build-system) + (home-page "https://github.com/emacs-pe/scribble-mode") + (synopsis "Emacs mode for editing the Scribble documentation syntax.") + (description + "This package provides basic syntax highlighting and editing support +for editing Racket's Scribble documentation syntax in Emacs.") + (license license:gpl3+)))) + (define-public emacs-haskell-mode (package (name "emacs-haskell-mode") From 50401c2a6853a65d89ab9be3f24a4f5386e3b684 Mon Sep 17 00:00:00 2001 From: Meiyo Peng Date: Thu, 18 Oct 2018 09:22:36 +0800 Subject: [PATCH 44/58] gnu: libqtxdg: Update to 3.2.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (libqtxdg): Update to 3.2.0. Signed-off-by: 宋文武 --- gnu/packages/lxqt.scm | 33 +++++++++++++++++++++------------ 1 file changed, 21 insertions(+), 12 deletions(-) diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index c84d26d4cb..57dd5b9c2f 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2016 Efraim Flashner ;;; Copyright © 2017 Nils Gillmann ;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; Copyright © 2018 Meiyo Peng ;;; ;;; This file is part of GNU Guix. ;;; @@ -36,25 +37,33 @@ (define-public libqtxdg (package (name "libqtxdg") - (version "1.2.0") + (version "3.2.0") (source (origin (method url-fetch) - (uri - (string-append "https://github.com/lxde/libqtxdg/releases/" - "download/" version "/" name "-" version ".tar.xz")) + (uri (string-append + "https://github.com/lxqt/" name "/releases/download/" + version "/" name "-" version ".tar.xz")) (sha256 - (base32 - "1ncqs0lcll5nx69hxfg33m3jfkryjqrjhr2kdci0b8pyaqdv1jc8")))) + (base32 "0lq548pa69hfvnbj2ypba5ygm8n6v6g7bqqm8p5g538l1l3394cl")))) (build-system cmake-build-system) (arguments - `(#:tests? #f ; test fails with message "Exception" - #:configure-flags '("-DBUILD_TESTS=ON"))) - (native-inputs - `(("pkg-config" ,pkg-config))) + `(#:configure-flags + `("-DBUILD_TESTS=ON" + ,(string-append "-DQTXDGX_ICONENGINEPLUGIN_INSTALL_PATH=" + %output "/lib/qt5/plugins/iconengines")) + #:phases + (modify-phases %standard-phases + (add-before 'check 'pre-check + (lambda _ + ;; Run the tests offscreen. + (setenv "QT_QPA_PLATFORM" "offscreen") + #t))))) (propagated-inputs - `(("qtbase" ,qtbase))) ; according to Qt5Xdg.pc - (home-page "https://github.com/lxde/libqtxdg") + ;; required by Qt5XdgIconLoader.pc + `(("qtbase" ,qtbase) + ("qtsvg" ,qtsvg))) + (home-page "https://github.com/lxqt/libqtxdg") (synopsis "Qt implementation of freedesktop.org xdg specifications") (description "Libqtxdg implements the freedesktop.org xdg specifications in Qt.") From 9861bcd182b1ba89a93630a2178b170a088f0a6b Mon Sep 17 00:00:00 2001 From: Meiyo Peng Date: Thu, 18 Oct 2018 10:30:35 +0800 Subject: [PATCH 45/58] gnu: liblxqt: Update to 0.13.0. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/lxqt.scm (liblxqt): Update to 0.13.0. [source]: Remove patches. [home-page]: Use HTTPS. * gnu/packages/patches/liblxqt-include.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. Signed-off-by: 宋文武 --- gnu/local.mk | 1 - gnu/packages/lxqt.scm | 39 ++++++++++++++-------- gnu/packages/patches/liblxqt-include.patch | 14 -------- 3 files changed, 26 insertions(+), 28 deletions(-) delete mode 100644 gnu/packages/patches/liblxqt-include.patch diff --git a/gnu/local.mk b/gnu/local.mk index d155b4c613..47883f829e 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -885,7 +885,6 @@ dist_patch_DATA = \ %D%/packages/patches/libjxr-fix-function-signature.patch \ %D%/packages/patches/libjxr-fix-typos.patch \ %D%/packages/patches/libotr-test-auth-fix.patch \ - %D%/packages/patches/liblxqt-include.patch \ %D%/packages/patches/libmad-armv7-thumb-pt1.patch \ %D%/packages/patches/libmad-armv7-thumb-pt2.patch \ %D%/packages/patches/libmad-frame-length.patch \ diff --git a/gnu/packages/lxqt.scm b/gnu/packages/lxqt.scm index 57dd5b9c2f..c4d0662e99 100644 --- a/gnu/packages/lxqt.scm +++ b/gnu/packages/lxqt.scm @@ -32,7 +32,9 @@ #:use-module (gnu packages glib) #:use-module (gnu packages kde-frameworks) #:use-module (gnu packages pkg-config) - #:use-module (gnu packages qt)) + #:use-module (gnu packages polkit) + #:use-module (gnu packages qt) + #:use-module (gnu packages xorg)) (define-public libqtxdg (package @@ -72,29 +74,40 @@ in Qt.") (define-public liblxqt (package (name "liblxqt") - (version "0.9.0") + (version "0.13.0") (source (origin (method url-fetch) - (uri - (string-append "https://github.com/lxde/" name - "/archive/" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (uri (string-append + "https://github.com/lxqt/" name "/releases/download/" + version "/" name "-" version ".tar.xz")) (sha256 - (base32 - "0mbl3qc0yfgfsndqrw8vg8k5irsy0pg2wrad8nwv0aphphd4n7rg")) - (patches (search-patches "liblxqt-include.patch")))) + (base32 "0fba0nq5b9fvvmklcikcd4nwhzlp5d6k1q1f80r34kncdzfvj7dl")))) (build-system cmake-build-system) (arguments - `(#:tests? #f)) - (native-inputs `(("pkg-config" ,pkg-config))) + `(#:tests? #f ; no tests + #:configure-flags + ;; TODO: prefetch translations files from 'lxqt-l10n'. + '("-DPULL_TRANSLATIONS=NO") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-source + (lambda _ + (substitute* "CMakeLists.txt" + (("DESTINATION \"\\$\\{POLKITQT-1_POLICY_FILES_INSTALL_DIR\\}") + "DESTINATION \"${CMAKE_INSTALL_PREFIX}/share/polkit-1/actions")) + #t))))) (inputs `(("kwindowsystem" ,kwindowsystem) ("libqtxdg" ,libqtxdg) - ("qtbase" ,qtbase) + ("libxscrnsaver" ,libxscrnsaver) + ("polkit-qt" ,polkit-qt) + ("qtsvg" ,qtsvg) ("qttools" ,qttools) ("qtx11extras" ,qtx11extras))) - (home-page "http://lxqt.org/") + (native-inputs + `(("lxqt-build-tools" ,lxqt-build-tools))) + (home-page "https://lxqt.org/") (synopsis "Core utility library for all LXQt components") (description "liblxqt provides the basic libraries shared by the components of the LXQt desktop environment.") diff --git a/gnu/packages/patches/liblxqt-include.patch b/gnu/packages/patches/liblxqt-include.patch deleted file mode 100644 index 4e8cf04789..0000000000 --- a/gnu/packages/patches/liblxqt-include.patch +++ /dev/null @@ -1,14 +0,0 @@ -Patch to fix build with Qt 5.5, taken from upstream: - https://github.com/lxde/liblxqt/commit/7303ea207de0771d6f450a31ec4a1ce69202869b - -diff -u -r liblxqt-0.9.0.orig/lxqtnotification.h liblxqt-0.9.0/lxqtnotification.h ---- liblxqt-0.9.0.orig/lxqtnotification.h 2015-07-27 22:49:05.365166482 +0200 -+++ liblxqt-0.9.0/lxqtnotification.h 2015-07-27 22:49:36.897606619 +0200 -@@ -25,6 +25,7 @@ - #ifndef LXQTNOTIFICATION_H - #define LXQTNOTIFICATION_H - -+#include - #include - #include "lxqtglobals.h" - From b45688313b525a8c590136adb62624d109ee73c4 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 21 Oct 2018 23:38:29 +0200 Subject: [PATCH 46/58] gnu: python-mistune: Update to 0.8.4. * gnu/packages/python.scm (python-mistune): Update to 0.8.4. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 9c749227de..d189438dec 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6004,14 +6004,14 @@ plugins that intend to support Flake8 2.x and 3.x simultaneously.") (define-public python-mistune (package (name "python-mistune") - (version "0.8.3") + (version "0.8.4") (source (origin (method url-fetch) (uri (pypi-uri "mistune" version)) (sha256 (base32 - "06b662p6kf46wh2jsabaqhaq4bz1srh2zxkrnx4yg96azlxw645w")))) + "0vkmsh0x480rni51lhyvigfdf06b9247z868pk3bal1wnnfl58sr")))) (build-system python-build-system) (native-inputs `(("python-nose" ,python-nose) From f232c875d2d591eac99e0168652ecbcb3d21a8ff Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 21 Oct 2018 23:53:16 +0200 Subject: [PATCH 47/58] gnu: python-lazy-object-proxy: Update to 1.3.1. * gnu/packages/python.scm (python-lazy-object-proxy): Update to 1.3.1. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index d189438dec..c39a53d8d9 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -9578,13 +9578,13 @@ docstring and colored output.") (define-public python-lazy-object-proxy (package (name "python-lazy-object-proxy") - (version "1.2.2") + (version "1.3.1") (source (origin (method url-fetch) (uri (pypi-uri "lazy-object-proxy" version)) (sha256 (base32 - "0s22aqqkdscyh8sjspyyax7qa1aiz8p4midrnyf39717fhfczm6x")))) + "0yha7q9bhw857fwaby785d63mffhngl9npwzlk9i0pwlkwvbx4gb")))) (build-system python-build-system) (home-page "https://github.com/ionelmc/python-lazy-object-proxy") (synopsis "Lazy object proxy for python") From 3ad0a35890ea3142e0ac16a8be6addd1693a10a1 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 12 Sep 2018 13:45:34 +0200 Subject: [PATCH 48/58] gnu: Add GN. * gnu/packages/build-tools.scm (gn): New public variable. --- gnu/packages/build-tools.scm | 58 ++++++++++++++++++++++++++++++++++++ 1 file changed, 58 insertions(+) diff --git a/gnu/packages/build-tools.scm b/gnu/packages/build-tools.scm index 4fc2d5acf7..42de56f8c3 100644 --- a/gnu/packages/build-tools.scm +++ b/gnu/packages/build-tools.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; Copyright © 2018 Fis Trivial ;;; Copyright © 2018 Tomáš Čech +;;; Copyright © 2018 Marius Bakke ;;; ;;; This file is part of GNU Guix. ;;; @@ -98,6 +99,63 @@ it is easy to re-run the compilation with alternate programs. Bear is used to generate such a compilation database.") (license license:gpl3+))) +(define-public gn + (let ((commit "f73698ebb33e26a0bf120e2b55d12528fd1dbe7d") + (revision "1481")) ;as returned by `git describe`, used below + (package + (name "gn") + (version (git-version "0.0" revision commit)) + (home-page "https://gn.googlesource.com/gn") + (source (origin + (method git-fetch) + (uri (git-reference (url home-page) (commit commit))) + (sha256 + (base32 + "078ydwak4424bkqh3hd7q955zxp2c3qlw44lsb29i8jqap140f9d")) + (file-name (git-file-name name version)))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ;FIXME: How to run? + #:phases (modify-phases %standard-phases + (add-before 'configure 'set-build-environment + (lambda _ + (setenv "CC" "gcc") (setenv "CXX" "g++") + (setenv "AR" "ar") + #t)) + (replace 'configure + (lambda _ + (invoke "python" "build/gen.py" "--no-sysroot" + "--no-last-commit-position"))) + (add-after 'configure 'create-last-commit-position + (lambda _ + ;; Create "last_commit_position.h" to avoid a dependency + ;; on 'git' (and the checkout..). + (call-with-output-file "out/last_commit_position.h" + (lambda (port) + (format port + "#define LAST_COMMIT_POSITION \"~a (~a)\"\n" + ,revision ,(string-take commit 8)) + #t)))) + (replace 'build + (lambda _ + (invoke "ninja" "-C" "out" "gn" + "-j" (number->string (parallel-job-count))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (install-file "out/gn" (string-append out "/bin")) + #t)))))) + (native-inputs + `(("ninja" ,ninja) + ("python" ,python-2))) + (synopsis "Generate Ninja build files") + (description + "GN is a tool that collects information about a project from @file{.gn} +files and generates build instructions for the Ninja build system.") + ;; GN is distributed as BSD-3, but bundles some files from ICU using the + ;; X11 license. + (license (list license:bsd-3 license:x11))))) + (define-public meson (package (name "meson") From f38eedd518816707cd407879f2f862095960b9fc Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 22 Oct 2018 18:12:37 +0200 Subject: [PATCH 49/58] gnu: samba: Update to 4.8.6. * gnu/packages/samba.scm (samba): Update to 4.8.6. --- gnu/packages/samba.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/samba.scm b/gnu/packages/samba.scm index a6d6ee30cd..458ff50ae8 100644 --- a/gnu/packages/samba.scm +++ b/gnu/packages/samba.scm @@ -150,14 +150,14 @@ anywhere.") (define-public samba (package (name "samba") - (version "4.8.5") + (version "4.8.6") (source (origin (method url-fetch) (uri (string-append "https://download.samba.org/pub/samba/stable/" "samba-" version ".tar.gz")) (sha256 (base32 - "0mailvhjsma19k6b6zjl02z9n2hbbyfybvicjfw2hh9d4sqyd3p5")))) + "15hawqdm37l6lp9k14c634315p77cllsx89bvbw9h38fg1hj3fbk")))) (build-system gnu-build-system) (arguments `(#:phases From 3743e117a6424f6463d8abfca4dd71ce576a918a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 22 Oct 2018 18:15:02 +0200 Subject: [PATCH 50/58] gnu: libmd: Update to 1.0.1. * gnu/packages/crypto.scm (libmd): Update to 1.0.1. --- gnu/packages/crypto.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index 77b4dba6d4..29d9a3d6ab 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -94,7 +94,7 @@ communication, encryption, decryption, signatures, etc.") (define-public libmd (package (name "libmd") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri @@ -105,7 +105,7 @@ communication, encryption, decryption, signatures, etc.") version ".tar.xz"))) (sha256 (base32 - "1iv45npzv0gncjgcpx5m081861zdqxw667ysghqb8721yrlyl6pj")))) + "0waclg2d5qin3r26gy5jvy4584ik60njc8pqbzwk0lzq3j9ynkp1")))) (build-system gnu-build-system) (synopsis "Message Digest functions from BSD systems") (description From 4350cacdf73f6e589a7d19b147f3707836e30210 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 22 Oct 2018 18:19:16 +0200 Subject: [PATCH 51/58] gnu: xf86-input-libinput: Update to 0.28.1. * gnu/packages/xorg.scm (xf86-input-libinput): Update to 0.28.1. --- gnu/packages/xorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index 4cf8eb2de4..dff50e9919 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -2448,7 +2448,7 @@ including most mice, keyboards, tablets and touchscreens.") (define-public xf86-input-libinput (package (name "xf86-input-libinput") - (version "0.28.0") + (version "0.28.1") (source (origin (method url-fetch) (uri (string-append @@ -2456,7 +2456,7 @@ including most mice, keyboards, tablets and touchscreens.") name "-" version ".tar.bz2")) (sha256 (base32 - "189h8vl0005yizwrs4d0sng6j8lwkd3xi1zwqg8qavn2bw34v691")))) + "12yr0yki94j2416bfhmkz5jpacffm27jkra89fl7h03c0y749nls")))) (build-system gnu-build-system) (arguments '(#:configure-flags From 90fb136ff72533d138ae0153bee1f88a8bf58115 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 22 Oct 2018 18:21:08 +0200 Subject: [PATCH 52/58] gnu: xorg-server: Update to 1.20.2. * gnu/packages/xorg.scm (xorg-server): Update to 1.20.2. --- gnu/packages/xorg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm index dff50e9919..86b4470aa0 100644 --- a/gnu/packages/xorg.scm +++ b/gnu/packages/xorg.scm @@ -5065,7 +5065,7 @@ over Xlib, including: (define-public xorg-server (package (name "xorg-server") - (version "1.20.1") + (version "1.20.2") (source (origin (method url-fetch) @@ -5074,7 +5074,7 @@ over Xlib, including: name "-" version ".tar.bz2")) (sha256 (base32 - "0679942x1ma2p30vlvqylpjc5v1ak1pgqysnqrj82nz7dzl9zjar")) + "1qnf7jdygdgbgjfm5mfr691dl8d56mpssa82mvhm8bzj92yggm8f")) (patches (list ;; See: From e810de3e68db1e892688dc21a8804df066ff218b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 22 Oct 2018 18:23:15 +0200 Subject: [PATCH 53/58] gnu: python-m2crypto: python-typing is only needed for python2. * gnu/packages/python-crypto.scm (python-m2crypto)[propagated-inputs]: Remove. [properties]: New field. (python2-m2crypto)[propagated-inputs]: Add PYTHON2-TYPING. --- gnu/packages/python-crypto.scm | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index bda547417c..8bee14c695 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -859,7 +859,6 @@ in userspace) (base32 "1h16gpilrnlzc0iyj1mnd1iqh8wchzjsxjqw9n344glimg2s5zm0")))) (build-system python-build-system) (inputs `(("openssl" ,openssl))) - (propagated-inputs `(("python-typing" ,python-typing))) (home-page "https://gitlab.com/m2crypto/m2crypto") (synopsis "Python crypto and TLS toolkit") (description "@code{M2Crypto} is a complete Python wrapper for OpenSSL @@ -869,10 +868,15 @@ extensions to Python's httplib, urllib, and xmlrpclib; unforgeable HMAC'ing AuthCookies for web session management; FTP/TLS client and server; S/MIME; M2Crypto can also be used to provide TLS for Twisted. Smartcards supported through the Engine interface.") + (properties `((python2-variant . ,(delay python2-m2crypto)))) (license license:expat))) (define-public python2-m2crypto - (package-with-python2 python-m2crypto)) + (let ((m2crypto (package-with-python2 + (strip-python2-variant python-m2crypto)))) + (package (inherit m2crypto) + (propagated-inputs + `(("python2-typing" ,python2-typing)))))) (define-public python-pylibscrypt (package From cb61baf0e72e0756c3386acb0d7745c507daa3ac Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 22 Oct 2018 18:24:28 +0200 Subject: [PATCH 54/58] gnu: python-m2crypto: Update to 0.30.1. * gnu/packages/python-crypto.scm (python-m2crypto): Update to 0.30.1. --- gnu/packages/python-crypto.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-crypto.scm b/gnu/packages/python-crypto.scm index 8bee14c695..f71b8a3467 100644 --- a/gnu/packages/python-crypto.scm +++ b/gnu/packages/python-crypto.scm @@ -850,13 +850,13 @@ in userspace) (define-public python-m2crypto (package (name "python-m2crypto") - (version "0.29.0") + (version "0.30.1") (source (origin (method url-fetch) (uri (pypi-uri "M2Crypto" version)) (sha256 - (base32 "1h16gpilrnlzc0iyj1mnd1iqh8wchzjsxjqw9n344glimg2s5zm0")))) + (base32 "1iizrpkn4c2n70nvcjqlmnk6fz3vddkrjmwavz1zlsnwv8f7bcm1")))) (build-system python-build-system) (inputs `(("openssl" ,openssl))) (home-page "https://gitlab.com/m2crypto/m2crypto") From 1b50df7d5b13921eb61bfd81787d4d5596064cc6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 22 Oct 2018 18:31:56 +0200 Subject: [PATCH 55/58] gnu: python-markdown: Update home page. * gnu/packages/python.scm (python-markdown)[home-page]: Change to current. --- gnu/packages/python.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index c39a53d8d9..b95774e9f7 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6046,7 +6046,7 @@ Python.") (native-inputs `(("python-nose" ,python-nose) ("python-pyyaml" ,python-pyyaml))) - (home-page "https://pythonhosted.org/Markdown/") + (home-page "https://python-markdown.github.io/") (synopsis "Python implementation of Markdown") (description "This package provides a Python implementation of John Gruber's From 9b9aaa57e3bf8e75305b557e79b79f90e4fb331c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 22 Oct 2018 18:32:41 +0200 Subject: [PATCH 56/58] gnu: python-markdown: Update to 3.0.1. * gnu/packages/python.scm (python-markdown): Update to 3.0.1. [arguments]: Remove. --- gnu/packages/python.scm | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index b95774e9f7..7e2082e5f2 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6028,21 +6028,15 @@ Python.") (define-public python-markdown (package (name "python-markdown") - (version "2.6.11") + (version "3.0.1") (source (origin (method url-fetch) (uri (pypi-uri "Markdown" version)) (sha256 (base32 - "108g80ryzykh8bj0i7jfp71510wrcixdi771lf2asyghgyf8cmm8")))) + "0z6v8649sr434d5r5zmrhydka7v7f9yas4bwcgkcs0650jdhybnh")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda _ - (zero? (system* "python" "run-tests.py"))))))) (native-inputs `(("python-nose" ,python-nose) ("python-pyyaml" ,python-pyyaml))) From 47d7c10387f391b107acd612137f247be506c46a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 22 Oct 2018 18:37:49 +0200 Subject: [PATCH 57/58] gnu: python-sure: Update to 1.4.11. * gnu/packages/python.scm (python-sure): Update to 1.4.11. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 7e2082e5f2..664f7720ff 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -11933,14 +11933,14 @@ Supported metrics are: (define-public python-sure (package (name "python-sure") - (version "1.4.6") + (version "1.4.11") (source (origin (method url-fetch) (uri (pypi-uri "sure" version)) (sha256 (base32 - "1iyqsy2d6radi88g1qf0lziy5b39h5cpb3g5jiqyb4xi46ig3x1z")))) + "1and0drq8w9iplsic22n2h7hkpyq03a1mbqk4sgcdqhqzdqm539w")))) (build-system python-build-system) (propagated-inputs `(("python-mock" ,python-mock) From 63abd1e2a36d48e1f8f7057a4c844b9cf5733be7 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 22 Oct 2018 18:53:38 +0200 Subject: [PATCH 58/58] gnu: python-pymongo: Update to 3.7.2. * gnu/packages/python.scm (python-pymongo): Update to 3.7.2. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 664f7720ff..dee7d9a06a 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10060,13 +10060,13 @@ reasoning, wrappers for natural language processing libraries.") (define-public python-pymongo (package (name "python-pymongo") - (version "3.3.0") + (version "3.7.2") (source (origin (method url-fetch) (uri (pypi-uri "pymongo" version)) (sha256 (base32 - "07mra6w86wjqy4lx5fvimidjhhfzd562gfjn8grsnbv2q8pk0i9x")))) + "0zis4707r9hdg5qgkhp3wss9camr9h56ixyfc8n9dxwlnnly4x4c")))) (build-system python-build-system) (propagated-inputs `(("python-certifi" ,python-certifi)))