diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 116 |
1 files changed, 115 insertions, 1 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6f6178a3ff..ff6c3379af 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -28,6 +28,113 @@ #:use-module (gnu packages pkg-config) #:use-module (gnu packages python)) +(define-public bedtools + (package + (name "bedtools") + (version "2.22.0") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/arq5x/bedtools2/archive/v" + version ".tar.gz")) + (sha256 + (base32 + "16aq0w3dmbd0853j32xk9jin4vb6v6fgakfyvrsmsjizzbn3fpfl")))) + (build-system gnu-build-system) + (native-inputs `(("python" ,python-2))) + (inputs `(("samtools" ,samtools) + ("zlib" ,zlib))) + (arguments + '(#:test-target "test" + #:phases + (alist-cons-after + 'unpack 'patch-makefile-SHELL-definition + (lambda _ + ;; patch-makefile-SHELL cannot be used here as it does not + ;; yet patch definitions with `:='. Since changes to + ;; patch-makefile-SHELL result in a full rebuild, features + ;; of patch-makefile-SHELL are reimplemented here. + (substitute* "Makefile" + (("^SHELL := .*$") (string-append "SHELL := " (which "bash") " -e \n")))) + (alist-delete + 'configure + (alist-replace + 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) + (mkdir-p bin) + (for-each (lambda (file) + (copy-file file (string-append bin (basename file)))) + (find-files "bin" ".*")))) + %standard-phases))))) + (home-page "https://github.com/arq5x/bedtools2") + (synopsis "Tools for genome analysis and arithmetic") + (description + "Collectively, the bedtools utilities are a swiss-army knife of tools for +a wide-range of genomics analysis tasks. The most widely-used tools enable +genome arithmetic: that is, set theory on the genome. For example, bedtools +allows one to intersect, merge, count, complement, and shuffle genomic +intervals from multiple files in widely-used genomic file formats such as BAM, +BED, GFF/GTF, VCF.") + (license license:gpl2))) + +(define-public bowtie + (package + (name "bowtie") + (version "2.2.4") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v" + version ".tar.gz")) + (sha256 + (base32 + "15dnbqippwvhyh9zqjhaxkabk7lm1xbh1nvar1x4b5kwm117zijn")) + (modules '((guix build utils))) + (snippet + '(substitute* "Makefile" + (("^CC = .*$") "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") @@ -43,7 +150,14 @@ "1y5p2hs4gif891b4ik20275a8xf3qrr1zh9wpysp4g8m0g1jckf2")))) (build-system gnu-build-system) (arguments - '(#:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out"))) + `(;; There are 87 test failures when building on non-64-bit architectures + ;; due to invalid test data. This has since been fixed upstream (see + ;; <https://github.com/samtools/samtools/pull/307>), but as there has + ;; not been a new release we disable the tests for all non-64-bit + ;; systems. + #:tests? ,(string=? (or (%current-system) (%current-target-system)) + "x86_64-linux") + #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out"))) #:phases (alist-cons-after 'unpack |