diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | 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 4eac8358a6..c7251c4c20 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") |