aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--gnu/packages/bioinformatics.scm58
1 files changed, 58 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a2846f10eb..ff6c3379af 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -77,6 +77,64 @@ intervals from multiple files in widely-used genomic file formats such as BAM,
BED, GFF/GTF, VCF.")
(license license:gpl2)))
+(define-public bowtie
+ (package
+ (name "bowtie")
+ (version "2.2.4")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "15dnbqippwvhyh9zqjhaxkabk7lm1xbh1nvar1x4b5kwm117zijn"))
+ (modules '((guix build utils)))
+ (snippet
+ '(substitute* "Makefile"
+ (("^CC = .*$") "CC = gcc")
+ (("^CPP = .*$") "CPP = g++")
+ ;; replace BUILD_HOST and BUILD_TIME for deterministic build
+ (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
+ (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
+ (build-system gnu-build-system)
+ (inputs `(("perl" ,perl)
+ ("perl-clone" ,perl-clone)
+ ("perl-test-deep" ,perl-test-deep)
+ ("perl-test-simple" ,perl-test-simple)
+ ("python" ,python-2)))
+ (arguments
+ '(#:make-flags '("allall")
+ #:phases
+ (alist-delete
+ 'configure
+ (alist-replace
+ 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+ (mkdir-p bin)
+ (for-each (lambda (file)
+ (copy-file file (string-append bin file)))
+ (find-files "." "bowtie2.*"))))
+ (alist-replace
+ 'check
+ (lambda* (#:key outputs #:allow-other-keys)
+ (system* "perl"
+ "scripts/test/simple_tests.pl"
+ "--bowtie2=./bowtie2"
+ "--bowtie2-build=./bowtie2-build"))
+ %standard-phases)))))
+ (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
+ (synopsis "Fast and sensitive nucleotide sequence read aligner")
+ (description
+ "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing
+reads to long reference sequences. It is particularly good at aligning reads
+of about 50 up to 100s or 1,000s of characters, and particularly good at
+aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the
+genome with an FM Index to keep its memory footprint small: for the human
+genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports
+gapped, local, and paired-end alignment modes.")
+ (license license:gpl3+)))
+
(define-public samtools
(package
(name "samtools")