gnu: Add Blast+.
* gnu/packages/bioinformatics.scm (blast+): New variable.
This commit is contained in:
Ricardo Wurmus
parent
11906b2c38
commit
82c370dea1
1 changed files with 148 additions and 0 deletions
|
|
@ -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")
|
||||
|
|
|
|||
Reference in a new issue