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01/02: gnu: Add Blast+.
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From: |
Ricardo Wurmus |
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Subject: |
01/02: gnu: Add Blast+. |
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Date: |
Mon, 29 Jun 2015 14:13:35 +0000 |
rekado pushed a commit to branch master
in repository guix.
commit 82c370dea1c4711b70f129ffe598df149b08a82c
Author: Ricardo Wurmus <address@hidden>
Date: Tue Jun 16 16:24:24 2015 +0200
gnu: Add Blast+.
* gnu/packages/bioinformatics.scm (blast+): New variable.
---
gnu/packages/bioinformatics.scm | 148 +++++++++++++++++++++++++++++++++++++++
1 files changed, 148 insertions(+), 0 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4eac835..c7251c4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -33,6 +33,7 @@
#:use-module (gnu packages base)
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages cpio)
#:use-module (gnu packages file)
#:use-module (gnu packages java)
#:use-module (gnu packages linux)
@@ -260,6 +261,153 @@ into separate processes; and more.")
(inputs
`(("python2-numpy" ,python2-numpy)))))
+(define-public blast+
+ (package
+ (name "blast+")
+ (version "2.2.31")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/";
+ version "/ncbi-blast-" version "+-src.tar.gz"))
+ (sha256
+ (base32
+ "19gq6as4k1jrgsd26158ads6h7v4jca3h4r5dzg1y0m6ya50x5ph"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Remove bundled bzip2 and zlib
+ (delete-file-recursively "c++/src/util/compress/bzip2")
+ (delete-file-recursively "c++/src/util/compress/zlib")
+ (substitute* "c++/src/util/compress/Makefile.in"
+ (("bzip2 zlib api") "api"))
+ ;; Remove useless msbuild directory
+ (delete-file-recursively
+ "c++/src/build-system/project_tree_builder/msbuild")
+ #t))))
+ (build-system gnu-build-system)
+ (arguments
+ `(;; There are three(!) tests for this massive library, and all fail with
+ ;; "unparsable timing stats".
+ ;; ERR [127] -- [util/regexp] test_pcre.sh (unparsable timing
stats)
+ ;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing
stats)
+ ;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable
timing stats)
+ #:tests? #f
+ #:out-of-source? #t
+ #:parallel-build? #f ; not supported
+ #:phases
+ (modify-phases %standard-phases
+ (add-before
+ 'configure 'set-HOME
+ ;; $HOME needs to be set at some point during the configure phase
+ (lambda _ (setenv "HOME" "/tmp") #t))
+ (add-after
+ 'unpack 'enter-dir
+ (lambda _ (chdir "c++") #t))
+ (add-after
+ 'enter-dir 'fix-build-system
+ (lambda _
+ (define (which* cmd)
+ (cond ((string=? cmd "date")
+ ;; make call to "date" deterministic
+ "date -d @0")
+ ((which cmd)
+ => identity)
+ (else
+ (format (current-error-port)
+ "WARNING: Unable to find absolute path for ~s~%"
+ cmd)
+ #f)))
+
+ ;; Rewrite hardcoded paths to various tools
+ (substitute* (append '("src/build-system/configure.ac"
+ "src/build-system/configure"
+ "scripts/common/impl/if_diff.sh"
+ "scripts/common/impl/run_with_lock.sh"
+
"src/build-system/Makefile.configurables.real"
+ "src/build-system/Makefile.in.top"
+ "src/build-system/Makefile.meta.gmake=no"
+ "src/build-system/Makefile.meta.in"
+ "src/build-system/Makefile.meta_l"
+ "src/build-system/Makefile.meta_p"
+ "src/build-system/Makefile.meta_r"
+ "src/build-system/Makefile.mk.in"
+ "src/build-system/Makefile.requirements"
+
"src/build-system/Makefile.rules_with_autodep.in")
+ (find-files "scripts/common/check" "\\.sh$"))
+ (("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd)
+ (or (which* cmd) all)))
+
+ (substitute* (find-files "src/build-system" "^config.*")
+ (("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln")))
+ (("^PATH=.*") ""))
+
+ ;; rewrite "/var/tmp" in check script
+ (substitute* "scripts/common/check/check_make_unix.sh"
+ (("/var/tmp") "/tmp"))
+
+ ;; do not reset PATH
+ (substitute* (find-files "scripts/common/impl/" "\\.sh$")
+ (("^ *PATH=.*") "")
+ (("action=/bin/") "action=")
+ (("export PATH") ":"))
+ #t))
+ (replace
+ 'configure
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out"))
+ (lib (string-append (assoc-ref outputs "lib") "/lib"))
+ (include (string-append (assoc-ref outputs "include")
+ "/include/ncbi-tools++")))
+ ;; The 'configure' script doesn't recognize things like
+ ;; '--enable-fast-install'.
+ (zero? (system* "./configure.orig"
+ (string-append "--with-build-root=" (getcwd)
"/build")
+ (string-append "--prefix=" out)
+ (string-append "--libdir=" lib)
+ (string-append "--includedir=" include)
+ (string-append "--with-bz2="
+ (assoc-ref inputs "bzip2"))
+ (string-append "--with-z="
+ (assoc-ref inputs "zlib"))
+ ;; Each library is built twice by default, once
+ ;; with "-static" in its name, and again
+ ;; without.
+ "--without-static"
+ "--with-dll"))))))))
+ (outputs '("out" ; 19 MB
+ "lib" ; 203 MB
+ "include")) ; 32 MB
+ (inputs
+ `(("bzip2" ,bzip2)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("cpio" ,cpio)))
+ (home-page "http://blast.ncbi.nlm.nih.gov";)
+ (synopsis "Basic local alignment search tool")
+ (description
+ "BLAST is a popular method of performing a DNA or protein sequence
+similarity search, using heuristics to produce results quickly. It also
+calculates an “expect value” that estimates how many matches would have
+occurred at a given score by chance, which can aid a user in judging how much
+confidence to have in an alignment.")
+ ;; Most of the sources are in the public domain, with the following
+ ;; exceptions:
+ ;; * Expat:
+ ;; * ./c++/include/util/bitset/
+ ;; * ./c++/src/html/ncbi_menu*.js
+ ;; * Boost license:
+ ;; * ./c++/include/util/impl/floating_point_comparison.hpp
+ ;; * LGPL 2+:
+ ;; * ./c++/include/dbapi/driver/odbc/unix_odbc/
+ ;; * ASL 2.0:
+ ;; * ./c++/src/corelib/teamcity_*
+ (license (list license:public-domain
+ license:expat
+ license:boost1.0
+ license:lgpl2.0+
+ license:asl2.0))))
+
(define-public bowtie
(package
(name "bowtie")