diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 77 |
1 files changed, 40 insertions, 37 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c6531d669f..314d0ad322 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014, 2015 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2014, 2015, 2016 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2015 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> @@ -603,7 +603,7 @@ errors at the end of reads.") (define-public bowtie (package (name "bowtie") - (version "2.2.4") + (version "2.2.6") (source (origin (method url-fetch) (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v" @@ -611,42 +611,36 @@ errors at the end of reads.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "15dnbqippwvhyh9zqjhaxkabk7lm1xbh1nvar1x4b5kwm117zijn")) + "1ssfvymxfrap6f9pf86s9bvsbqdgka4abr2r7j3mgr4w1l289m86")) (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\\\"\""))) - (patches (list (search-patch "bowtie-fix-makefile.patch"))))) + (("-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))) + ("python" ,python-2) + ("tbb" ,tbb))) (arguments - '(#:make-flags '("allall") + '(#:make-flags + (list "allall" + "WITH_TBB=1" + (string-append "prefix=" (assoc-ref %outputs "out"))) #:phases (alist-delete 'configure (alist-replace - 'install + 'check (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) - (for-each (lambda (file) - (install-file file bin)) - (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))))) + (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 @@ -2079,7 +2073,7 @@ that a read originated from a particular isoform.") (define-public orfm (package (name "orfm") - (version "0.4.1") + (version "0.5.3") (source (origin (method url-fetch) (uri (string-append @@ -2087,12 +2081,16 @@ that a read originated from a particular isoform.") version "/orfm-" version ".tar.gz")) (sha256 (base32 - "05fmw145snk646ly076zby0fjav0k7ysbclck5d4s9pmgcfpijc2")))) + "0vb6d771gl4mix8bwx919x5ayy9pkj44n7ki336nz3rz2rx4c7gk")))) (build-system gnu-build-system) (inputs `(("zlib" ,zlib))) + (native-inputs + `(("ruby-bio-commandeer" ,ruby-bio-commandeer) + ("ruby-rspec" ,ruby-rspec) + ("ruby" ,ruby))) (synopsis "Simple and not slow open reading frame (ORF) caller") (description - "An ORF caller finds stretches of DNA that when translated are not + "An ORF caller finds stretches of DNA that, when translated, are not interrupted by stop codons. OrfM finds and prints these ORFs.") (home-page "https://github.com/wwood/OrfM") (license license:lgpl3+))) @@ -2458,18 +2456,21 @@ viewer.") (sha256 (base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h")))) (arguments - (substitute-keyword-arguments (package-arguments samtools) - ((#:tests? tests) #f) ;no "check" target - ((#:phases phases) - `(modify-phases ,phases - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append - (assoc-ref outputs "out") "/bin"))) - (mkdir-p bin) - (copy-file "samtools" - (string-append bin "/samtools"))))) - (delete 'patch-tests))))))) + `(#:tests? #f ;no "check" target + ,@(substitute-keyword-arguments (package-arguments samtools) + ((#:make-flags flags) + `(cons "LIBCURSES=-lncurses" ,flags)) + ((#:phases phases) + `(modify-phases ,phases + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append + (assoc-ref outputs "out") "/bin"))) + (mkdir-p bin) + (copy-file "samtools" + (string-append bin "/samtools"))))) + (delete 'patch-tests) + (delete 'configure)))))))) (define-public mosaik (let ((commit "5c25216d")) @@ -3841,6 +3842,8 @@ extracting the desired features in a convenient format.") (properties `((upstream-name . "GO.db"))) (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) (home-page "http://bioconductor.org/packages/GO.db") (synopsis "Annotation maps describing the entire Gene Ontology") (description |