diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 179 |
1 files changed, 121 insertions, 58 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6a90aa9456..04ed769cd8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3926,6 +3926,34 @@ clusters.") (home-page "https://sourceforge.net/projects/pardre/") (license license:gpl3+))) +(define-public ruby-bio-kseq + (package + (name "ruby-bio-kseq") + (version "0.0.2") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "bio-kseq" version)) + (sha256 + (base32 + "1xyaha46khb5jc6wzkbf7040jagac49jbimn0vcrzid0j8jdikrz")))) + (build-system ruby-build-system) + (arguments + `(#:test-target "spec")) + (native-inputs + `(("bundler" ,bundler) + ("ruby-rspec" ,ruby-rspec) + ("ruby-rake-compiler" ,ruby-rake-compiler))) + (inputs + `(("zlib" ,zlib))) + (synopsis "Ruby bindings for the kseq.h FASTA/Q parser") + (description + "@code{Bio::Kseq} provides ruby bindings to the @code{kseq.h} FASTA and +FASTQ parsing code. It provides a fast iterator over sequences and their +quality scores.") + (home-page "https://github.com/gusevfe/bio-kseq") + (license license:expat))) + (define-public bio-locus (package (name "bio-locus") @@ -4991,6 +5019,38 @@ by UCSC (hg19, February 2009) and stored in Biostrings objects.") provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") (license license:artistic2.0))) +(define-public r-bsgenome-mmusculus-ucsc-mm10 + (package + (name "r-bsgenome-mmusculus-ucsc-mm10") + (version "1.4.0") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/annotation/" instead of "bioc/". + (uri (string-append "http://www.bioconductor.org/packages/" + "release/data/annotation/src/contrib/" + "BSgenome.Mmusculus.UCSC.mm10_" + version ".tar.gz")) + (sha256 + (base32 + "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf")))) + (properties + `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) + (build-system r-build-system) + ;; As this package provides little more than a very large data file it + ;; doesn't make sense to build substitutes. + (arguments `(#:substitutable? #f)) + (propagated-inputs + `(("r-bsgenome" ,r-bsgenome))) + (home-page + "http://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") + (synopsis "Full genome sequences for Mouse") + (description + "This package provides full genome sequences for Mus +musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored +in Biostrings objects.") + (license license:artistic2.0))) + (define-public r-bsgenome-celegans-ucsc-ce6 (package (name "r-bsgenome-celegans-ucsc-ce6") @@ -5127,68 +5187,71 @@ libraries for systems that do not have these available via other means.") (license license:artistic2.0))) (define-public piranha - (package - (name "piranha") - (version "1.1.3") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/smithlabcode/piranha" - "/archive/svn/tags/piranha-" - version ".tar.gz")) - (sha256 - (base32 - "1lczxff01n4139w7xwqamlb36g9hgrcy93gh03nqszhwb8ivsrqd")))) - (build-system gnu-build-system) - (arguments - `(#:test-target "test" - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'copy-smithlab-cpp - (lambda* (#:key inputs #:allow-other-keys) - (mkdir "src/smithlab_cpp") - (for-each (lambda (file) - (install-file file "./src/smithlab_cpp/")) - (find-files (assoc-ref inputs "smithlab-cpp"))) - #t)) - (add-after 'install 'install-to-store - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin"))) - (mkdir-p bin) + ;; There is no release tarball for the latest version. The latest commit is + ;; older than one year at the time of this writing. + (let ((revision "1") + (commit "0466d364b71117d01e4471b74c514436cc281233")) + (package + (name "piranha") + (version (string-append "1.2.1-" revision "." (string-take commit 9))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/smithlabcode/piranha.git") + (commit commit))) + (sha256 + (base32 + "117dc0zf20c61jam69sk4abl57ah6yi6i7qra7d7y5zrbgk12q5n")))) + (build-system gnu-build-system) + (arguments + `(#:test-target "test" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'copy-smithlab-cpp + (lambda* (#:key inputs #:allow-other-keys) (for-each (lambda (file) - (install-file file bin)) - (find-files "bin" ".*"))) - #t))) - #:configure-flags - (list (string-append "--with-bam_tools_headers=" - (assoc-ref %build-inputs "bamtools") "/include/bamtools") - (string-append "--with-bam_tools_library=" - (assoc-ref %build-inputs "bamtools") "/lib/bamtools")))) - (inputs - `(("bamtools" ,bamtools) - ("samtools" ,samtools-0.1) - ("gsl" ,gsl) - ("smithlab-cpp" - ,(let ((commit "3723e2db438c51501d0423429ff396c3035ba46a")) - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/smithlabcode/smithlab_cpp.git") - (commit commit))) - (file-name (string-append "smithlab_cpp-" commit "-checkout")) - (sha256 - (base32 - "0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g"))))))) - (native-inputs - `(("python" ,python-2))) - (home-page "https://github.com/smithlabcode/piranha") - (synopsis "Peak-caller for CLIP-seq and RIP-seq data") - (description - "Piranha is a peak-caller for genomic data produced by CLIP-seq and + (install-file file "./src/smithlab_cpp/")) + (find-files (assoc-ref inputs "smithlab-cpp"))) + #t)) + (add-after 'install 'install-to-store + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (mkdir-p bin) + (for-each (lambda (file) + (install-file file bin)) + (find-files "bin" ".*"))) + #t))) + #:configure-flags + (list (string-append "--with-bam_tools_headers=" + (assoc-ref %build-inputs "bamtools") "/include/bamtools") + (string-append "--with-bam_tools_library=" + (assoc-ref %build-inputs "bamtools") "/lib/bamtools")))) + (inputs + `(("bamtools" ,bamtools) + ("samtools" ,samtools-0.1) + ("gsl" ,gsl) + ("smithlab-cpp" + ,(let ((commit "3723e2db438c51501d0423429ff396c3035ba46a")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/smithlabcode/smithlab_cpp.git") + (commit commit))) + (file-name (string-append "smithlab_cpp-" commit "-checkout")) + (sha256 + (base32 + "0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g"))))))) + (native-inputs + `(("python" ,python-2))) + (home-page "https://github.com/smithlabcode/piranha") + (synopsis "Peak-caller for CLIP-seq and RIP-seq data") + (description + "Piranha is a peak-caller for genomic data produced by CLIP-seq and RIP-seq experiments. It takes input in BED or BAM format and identifies regions of statistically significant read enrichment. Additional covariates may optionally be provided to further inform the peak-calling process.") - (license license:gpl3+))) + (license license:gpl3+)))) (define-public pepr (package |