gnu: metabat: Update to 2.11.1.
* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.1. [source]: Add patch to fix compilation. [arguments]: Adjust regular expressions modifying 'SConstruct'. * gnu/packages/patches/metabat-fix-compilation.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
This commit is contained in:
Ben Woodcroft
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897ab082b2
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@ -840,6 +840,7 @@ dist_patch_DATA = \
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%D%/packages/patches/mesa-skip-disk-cache-test.patch \
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%D%/packages/patches/mesa-wayland-egl-symbols-check-mips.patch \
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%D%/packages/patches/metabat-remove-compilation-date.patch \
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%D%/packages/patches/metabat-fix-compilation.patch \
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%D%/packages/patches/mhash-keygen-test-segfault.patch \
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%D%/packages/patches/mingw-w64-5.0rc2-gcc-4.9.3.patch \
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%D%/packages/patches/mpc123-initialize-ao.patch \
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@ -3467,23 +3467,20 @@ form of assemblies or reads.")
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license:cpl1.0)))) ; Open Bloom Filter
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(define-public metabat
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;; We package from a git commit because compilation of the released version
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;; fails.
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(let ((commit "cbdca756993e66ae57e50a27970595dda9cbde1b"))
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(package
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(name "metabat")
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(version (string-append "0.32.4-1." (string-take commit 8)))
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://bitbucket.org/berkeleylab/metabat.git")
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(commit commit)))
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(file-name (string-append name "-" version))
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(sha256
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(base32
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"0byia8nsip6zvc4ha0qkxkxxyjf4x7jcvy48q2dvb0pzr989syzr"))
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(patches (search-patches "metabat-remove-compilation-date.patch"))))
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(package
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(name "metabat")
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(version "2.11.1")
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(source
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(origin
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(method url-fetch)
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(uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v"
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version ".tar.gz"))
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(file-name (string-append name "-" version ".tar.gz"))
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(sha256
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(base32
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"0ll00l81aflscgggs5nfhj12cbvdiz3gg7f7n5f537a3xhx60vn9"))
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(patches (search-patches "metabat-remove-compilation-date.patch"
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"metabat-fix-compilation.patch"))))
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(build-system gnu-build-system)
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(arguments
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`(#:phases
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@ -3500,35 +3497,35 @@ form of assemblies or reads.")
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"#include \"htslib/kseq.h\""))
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#t))
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(add-after 'unpack 'fix-scons
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "SConstruct"
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(("^htslib_dir = 'samtools'")
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(string-append "hitslib_dir = '"
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(assoc-ref inputs "htslib")
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"'"))
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(("^samtools_dir = 'samtools'")
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(string-append "samtools_dir = '"
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(assoc-ref inputs "htslib")
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"'"))
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(("^findStaticOrShared\\('bam', hts_lib")
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(string-append "findStaticOrShared('bam', '"
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(assoc-ref inputs "samtools")
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"/lib'"))
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;; Do not distribute README.
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(("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") ""))
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#t))
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "SConstruct"
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(("^htslib_dir += 'samtools'")
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(string-append "htslib_dir = '"
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(assoc-ref inputs "htslib")
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"'"))
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(("^samtools_dir = 'samtools'")
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(string-append "samtools_dir = '"
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(assoc-ref inputs "samtools")
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"'"))
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(("^findStaticOrShared\\('bam', hts_lib")
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(string-append "findStaticOrShared('bam', '"
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(assoc-ref inputs "samtools")
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"/lib'"))
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;; Do not distribute README.
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(("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") ""))
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#t))
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(delete 'configure)
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(replace 'build
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(mkdir (assoc-ref outputs "out"))
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(zero? (system* "scons"
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(string-append
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"PREFIX="
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(assoc-ref outputs "out"))
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(string-append
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"BOOST_ROOT="
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(assoc-ref inputs "boost"))
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"install"))))
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(mkdir (assoc-ref outputs "out"))
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(zero? (system* "scons"
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(string-append
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"PREFIX="
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(assoc-ref outputs "out"))
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(string-append
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"BOOST_ROOT="
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(assoc-ref inputs "boost"))
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"install"))))
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;; Check and install are carried out during build phase.
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(delete 'check)
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(delete 'install))))
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@ -3549,8 +3546,8 @@ sequences to deconvolute complex microbial communities, or metagenome binning,
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enables the study of individual organisms and their interactions. MetaBAT is
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an automated metagenome binning software, which integrates empirical
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probabilistic distances of genome abundance and tetranucleotide frequency.")
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(license (license:non-copyleft "file://license.txt"
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"See license.txt in the distribution.")))))
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(license (license:non-copyleft "file://license.txt"
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"See license.txt in the distribution."))))
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(define-public minced
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(package
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@ -0,0 +1,39 @@
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This patch changes metabat so that (1) it is not build statically, (2) it uses
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shared libraries rather than static libraries where possible.
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diff --git a/SConstruct b/SConstruct
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index 69cdc0a..ac99bcb 100644
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--- a/SConstruct
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+++ b/SConstruct
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@@ -26,8 +26,6 @@ debug = ARGUMENTS.get('DEBUG', None)
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build_flags = ['-Wall', '-g', '-std=c++11', '-fopenmp']
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link_flags = ['-lstdc++', '-lm', '-fopenmp']
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-if platform.platform(True, True).find('Darwin') == -1:
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- link_flags.extend(['-static', '-static-libgcc', '-static-libstdc++'])
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if debug is None:
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build_flags.extend(['-O3', '-DNDEBUG', '-Wno-unknown-pragmas', '-Wno-deprecated-declarations', '-Wno-overflow', '-Wno-unused-variable'])
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@@ -110,17 +108,17 @@ def findStaticOrShared( lib, testPaths, static_source_list, link_flag_list, stat
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for path in testPaths:
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if not os.path.isdir(path):
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continue
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+ for testfile in ('%s/lib%s.so' % (path, lib), '%s/lib%s.dylib' % (path, lib)):
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+ if os.path.isfile(testfile):
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+ print "Found shared library %s as %s" % (lib, testfile)
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+ link_flag_list.extend( ["-L%s" % (path), "-l%s" % (lib) ] )
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+ return
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for suffix in staticSuffixes:
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testfile = '%s/lib%s%s' % (path, lib, suffix)
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if os.path.isfile(testfile):
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static_source_list.append(testfile)
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print "Found static library %s as %s" % (lib, testfile)
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return
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- for testfile in ('%s/lib%s.so' % (path, lib), '%s/lib%s.dylib' % (path, lib)):
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- if os.path.isfile(testfile):
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- print "Found shared library %s as %s" % (lib, testfile)
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- link_flag_list.extend( ["-L%s" % (path), "-l%s" % (lib) ] )
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- return
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print "Could not find library for %s!!! Looked in %s" % (lib, testPaths)
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return
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