gnu: Add Blast+.
* gnu/packages/bioinformatics.scm (blast+): New variable.
This commit is contained in:
Ricardo Wurmus
parent
11906b2c38
commit
82c370dea1
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@ -33,6 +33,7 @@
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#:use-module (gnu packages base)
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#:use-module (gnu packages boost)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages cpio)
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#:use-module (gnu packages file)
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#:use-module (gnu packages java)
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#:use-module (gnu packages linux)
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@ -260,6 +261,153 @@ into separate processes; and more.")
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(inputs
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`(("python2-numpy" ,python2-numpy)))))
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(define-public blast+
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(package
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(name "blast+")
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(version "2.2.31")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/"
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version "/ncbi-blast-" version "+-src.tar.gz"))
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(sha256
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(base32
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"19gq6as4k1jrgsd26158ads6h7v4jca3h4r5dzg1y0m6ya50x5ph"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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;; Remove bundled bzip2 and zlib
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(delete-file-recursively "c++/src/util/compress/bzip2")
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(delete-file-recursively "c++/src/util/compress/zlib")
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(substitute* "c++/src/util/compress/Makefile.in"
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(("bzip2 zlib api") "api"))
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;; Remove useless msbuild directory
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(delete-file-recursively
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"c++/src/build-system/project_tree_builder/msbuild")
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#t))))
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(build-system gnu-build-system)
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(arguments
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`(;; There are three(!) tests for this massive library, and all fail with
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;; "unparsable timing stats".
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;; ERR [127] -- [util/regexp] test_pcre.sh (unparsable timing stats)
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;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats)
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;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats)
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#:tests? #f
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#:out-of-source? #t
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#:parallel-build? #f ; not supported
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#:phases
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(modify-phases %standard-phases
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(add-before
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'configure 'set-HOME
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;; $HOME needs to be set at some point during the configure phase
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(lambda _ (setenv "HOME" "/tmp") #t))
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(add-after
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'unpack 'enter-dir
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(lambda _ (chdir "c++") #t))
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(add-after
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'enter-dir 'fix-build-system
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(lambda _
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(define (which* cmd)
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(cond ((string=? cmd "date")
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;; make call to "date" deterministic
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"date -d @0")
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((which cmd)
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=> identity)
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(else
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(format (current-error-port)
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"WARNING: Unable to find absolute path for ~s~%"
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cmd)
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#f)))
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;; Rewrite hardcoded paths to various tools
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(substitute* (append '("src/build-system/configure.ac"
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"src/build-system/configure"
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"scripts/common/impl/if_diff.sh"
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"scripts/common/impl/run_with_lock.sh"
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"src/build-system/Makefile.configurables.real"
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"src/build-system/Makefile.in.top"
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"src/build-system/Makefile.meta.gmake=no"
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"src/build-system/Makefile.meta.in"
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"src/build-system/Makefile.meta_l"
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"src/build-system/Makefile.meta_p"
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"src/build-system/Makefile.meta_r"
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"src/build-system/Makefile.mk.in"
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"src/build-system/Makefile.requirements"
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"src/build-system/Makefile.rules_with_autodep.in")
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(find-files "scripts/common/check" "\\.sh$"))
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(("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd)
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(or (which* cmd) all)))
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(substitute* (find-files "src/build-system" "^config.*")
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(("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln")))
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(("^PATH=.*") ""))
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;; rewrite "/var/tmp" in check script
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(substitute* "scripts/common/check/check_make_unix.sh"
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(("/var/tmp") "/tmp"))
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;; do not reset PATH
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(substitute* (find-files "scripts/common/impl/" "\\.sh$")
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(("^ *PATH=.*") "")
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(("action=/bin/") "action=")
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(("export PATH") ":"))
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#t))
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(replace
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'configure
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let ((out (assoc-ref outputs "out"))
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(lib (string-append (assoc-ref outputs "lib") "/lib"))
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(include (string-append (assoc-ref outputs "include")
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"/include/ncbi-tools++")))
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;; The 'configure' script doesn't recognize things like
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;; '--enable-fast-install'.
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(zero? (system* "./configure.orig"
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(string-append "--with-build-root=" (getcwd) "/build")
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(string-append "--prefix=" out)
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(string-append "--libdir=" lib)
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(string-append "--includedir=" include)
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(string-append "--with-bz2="
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(assoc-ref inputs "bzip2"))
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(string-append "--with-z="
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(assoc-ref inputs "zlib"))
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;; Each library is built twice by default, once
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;; with "-static" in its name, and again
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;; without.
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"--without-static"
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"--with-dll"))))))))
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(outputs '("out" ; 19 MB
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"lib" ; 203 MB
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"include")) ; 32 MB
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(inputs
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`(("bzip2" ,bzip2)
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("zlib" ,zlib)))
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(native-inputs
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`(("cpio" ,cpio)))
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(home-page "http://blast.ncbi.nlm.nih.gov")
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(synopsis "Basic local alignment search tool")
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(description
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"BLAST is a popular method of performing a DNA or protein sequence
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similarity search, using heuristics to produce results quickly. It also
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calculates an “expect value” that estimates how many matches would have
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occurred at a given score by chance, which can aid a user in judging how much
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confidence to have in an alignment.")
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;; Most of the sources are in the public domain, with the following
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;; exceptions:
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;; * Expat:
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;; * ./c++/include/util/bitset/
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;; * ./c++/src/html/ncbi_menu*.js
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;; * Boost license:
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;; * ./c++/include/util/impl/floating_point_comparison.hpp
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;; * LGPL 2+:
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;; * ./c++/include/dbapi/driver/odbc/unix_odbc/
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;; * ASL 2.0:
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;; * ./c++/src/corelib/teamcity_*
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(license (list license:public-domain
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license:expat
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license:boost1.0
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license:lgpl2.0+
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license:asl2.0))))
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(define-public bowtie
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(package
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(name "bowtie")
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