>From 81cbb9bfa523d56c68d5f9f4feed3676edb5a414 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wur...@mdc-berlin.de>
Date: Tue, 16 Jun 2015 16:24:24 +0200
Subject: [PATCH] gnu: Add Blast+.
* gnu/packages/bioinformatics.scm (blast+): New variable.
---
gnu/packages/bioinformatics.scm | 156 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 156 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ac4c50d..4a55040 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -31,6 +31,7 @@
#: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)
@@ -294,6 +295,161 @@ into separate processes; and more.")
(inputs
`(("python2-numpy" ,python2-numpy)))))
+(define-public blast+
+ (package
+ (name "blast+")
+ (version "2.2.30")
+ (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
+ "0h0fj5cpx6zpfwixgx5f5xbr4rn3cnai0x3j7grrg50vr18jvxr6"))))
+ (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
+ ;; $HOME needs to be set at some point during the configure phase
+ (lambda _ (setenv "HOME" "/tmp") #t))
+ (add-after
+ 'unpack 'enter-dir
+ (lambda _ (chdir "c++") #t))
+ (add-after
+ 'enter-dir 'fix-build-system
+ (lambda _
+ ;; Proceed even though the weird build system says that generated
+ ;; files are out of date
+ (setenv "NCBICXX_RECONF_POLICY" "warn")
+
+ ;; Remove bundled bzip2 and zlib
+ (delete-file-recursively "src/util/compress/bzip2")
+ (delete-file-recursively "src/util/compress/zlib")
+ (substitute* "src/util/compress/Makefile.in"
+ (("bzip2 zlib api") "api"))
+
+ ;; Remove useless msbuild directory
+ (delete-file-recursively "src/build-system/project_tree_builder/msbuild")
+
+ ;; Some of the files we're patching are
+ ;; ISO-8859-1-encoded, so choose it as the default
+ ;; encoding so the byte encoding is preserved.
+ (with-fluids ((%default-port-encoding #f))
+ (substitute* (find-files "src/build-system" "config.*")
+ (("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln")))
+ (("/bin/sh") (which "bash"))
+ (("^PATH=.*") "")))
+
+ ;; fix static and generated shebangs
+ (substitute* (find-files "scripts/common/check" "\\.sh")
+ (("/bin/sh") (which "bash")))
+
+ ;; rewrite "/var/tmp" in check script
+ (substitute* "scripts/common/check/check_make_unix.sh"
+ (("/var/tmp") (string-append (getcwd) "/build/build")))
+
+ ;; fix path to "echo"
+ (substitute* '("src/build-system/Makefile.rules_with_autodep.in"
+ "src/build-system/Makefile.meta.gmake=no"
+ "src/build-system/Makefile.meta_r"
+ "src/build-system/Makefile.requirements")
+ (("/bin/echo") (which "echo")))
+
+ ;; fix path to "basename"
+ (substitute* '("src/build-system/Makefile.in.top")
+ (("/usr/bin/basename") (which "basename")))
+
+ ;; fix path to "mv"
+ (substitute* '("src/build-system/Makefile.rules_with_autodep.in"
+ "src/build-system/Makefile.meta_p")
+ (("/bin/mv") (which "mv")))
+
+ ;; fix path to "rm"
+ (substitute* '("src/build-system/Makefile.mk.in"
+ "src/build-system/Makefile.meta.in"
+ "scripts/common/impl/run_with_lock.sh")
+ (("/bin/rm") (which "rm")))
+
+ ;; fix path to "cp"
+ (substitute* '("src/build-system/Makefile.configurables.real"
+ "src/build-system/Makefile.mk.in"
+ "src/build-system/configure"
+ "src/build-system/configure.ac"
+ "scripts/common/impl/if_diff.sh")
+ (("/bin/cp") (which "cp")))
+
+ ;; fix path to "mkdir"
+ (substitute* '("src/build-system/Makefile.mk.in"
+ "src/build-system/Makefile.meta.in")
+ (("/bin/mkdir") (which "mkdir")))
+
+ ;; fix path to "dirname"
+ (substitute* '("src/build-system/Makefile.configurables.real"
+ "src/build-system/Makefile.meta_p")
+ (("/usr/bin/dirname") (which "dirname")))
+
+ ;; make call to "date" deterministic
+ (substitute* "src/build-system/Makefile.meta_l"
+ (("/bin/date") "echo -n 0"))
+
+ ;; do not reset PATH
+ (substitute* (find-files "scripts/common/impl/" "\\.sh")
+ (("^ *PATH=.*") "")
+ (("action=/bin/") "action=")
+ (("export PATH") "echo -n 0"))
+ #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" ; 203MB
+ "include")) ; 32MB
+ (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.")
+ (license license:public-domain)))
+
(define-public bowtie
(package
(name "bowtie")
--
2.1.0
