diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 157 |
1 files changed, 156 insertions, 1 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 13572b0c75..cb3c4bc1fd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -720,7 +720,7 @@ e.g. microbiome samples, genomes, metagenomes.") (inputs inputs) (native-inputs `(("perl-test-most" ,perl-test-most))) - (home-page "http://search.cpan.org/dist/BioPerl") + (home-page "https://metacpan.org/release/BioPerl") (synopsis "Bioinformatics toolkit") (description "BioPerl is the product of a community effort to produce Perl code which @@ -13275,6 +13275,48 @@ cases include: @end enumerate\n") (license license:expat))) +(define-public r-circus + (package + (name "r-circus") + (version "0.1.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BIMSBbioinfo/ciRcus.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0jhjn3ilb057hbf6yzrihj13ifxxs32y7nkby8l3lkm28dg4p97h")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationhub" ,r-annotationhub) + ("r-biomart" ,r-biomart) + ("r-data-table" ,r-data-table) + ("r-dbi" ,r-dbi) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-hash" ,r-hash) + ("r-iranges" ,r-iranges) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rmysql" ,r-rmysql) + ("r-s4vectors" ,r-s4vectors) + ("r-stringr" ,r-stringr) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/BIMSBbioinfo/ciRcus") + (synopsis "Annotation, analysis and visualization of circRNA data") + (description "Circus is an R package for annotation, analysis and +visualization of circRNA data. Users can annotate their circRNA candidates +with host genes, gene featrues they are spliced from, and discriminate between +known and yet unknown splice junctions. Circular-to-linear ratios of circRNAs +can be calculated, and a number of descriptive plots easily generated.") + (license license:artistic2.0))) + (define-public r-loomr (let ((commit "df0144bd2bbceca6fadef9edc1bbc5ca672d4739") (revision "1")) @@ -13303,3 +13345,116 @@ cases include: (description "This package provides an R interface to access, create, and modify loom files. loomR aims to be completely compatible with loompy.") (license license:gpl3)))) + +(define-public gffread + ;; We cannot use the tagged release because it is not in sync with gclib. + ;; See https://github.com/gpertea/gffread/issues/26 + (let ((commit "ba7535fcb3cea55a6e5a491d916e93b454e87fd0") + (revision "1")) + (package + (name "gffread") + (version (git-version "0.9.12" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/gpertea/gffread.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1dl2nbcg96lxpd0drg48ssa8343nf7pw9s9mkrc4mjjmfwsin3ki")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no check target + #:make-flags + (list "GCLDIR=gclib") + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-after 'unpack 'copy-gclib-source + (lambda* (#:key inputs #:allow-other-keys) + (mkdir-p "gclib") + (copy-recursively (assoc-ref inputs "gclib-source") "gclib") + #t)) + ;; There is no install target + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (install-file "gffread" bin)) + #t))))) + (native-inputs + `(("gclib-source" + ,(let ((version "0.10.3") + (commit "54917d0849c1e83cfb057b5f712e5cb6a35d948f") + (revision "1")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/gpertea/gclib.git") + (commit commit))) + (file-name (git-file-name "gclib" version)) + (sha256 + (base32 + "0b51lc0b8syrv7186fd7n8f15rwnf264qgfmm2palrwks1px24mr"))))))) + (home-page "https://github.com/gpertea/gffread/") + (synopsis "Parse and convert GFF/GTF files") + (description + "This package provides a GFF/GTF file parsing utility providing format +conversions, region filtering, FASTA sequence extraction and more.") + ;; gffread is under Expat, but gclib is under Artistic 2.0 + (license (list license:expat + license:artistic2.0))))) + +(define-public find-circ + ;; The last release was in 2015. The license was clarified in 2017, so we + ;; take the latest commit. + (let ((commit "8655dca54970fcf7e92e22fbf57e1188724dda7d") + (revision "1")) + (package + (name "find-circ") + (version (git-version "1.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/marvin-jens/find_circ.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0p77pbqbclqr4srms34y1b9b4njybfpjiknc11ki84f3p8skb3cg")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are none + #:phases + ;; There is no actual build system. + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (path (getenv "PYTHONPATH"))) + (for-each (lambda (script) + (install-file script bin) + (wrap-program (string-append bin "/" script) + `("PYTHONPATH" ":" prefix (,path)))) + '("cmp_bed.py" + "find_circ.py" + "maxlength.py" + "merge_bed.py" + "unmapped2anchors.py"))) + #t))))) + (inputs + `(("python2" ,python-2) + ("python2-pysam" ,python2-pysam) + ("python2-numpy" ,python2-numpy))) + (home-page "https://github.com/marvin-jens/find_circ") + (synopsis "circRNA detection from RNA-seq reads") + (description "This package provides tools to detect head-to-tail +spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA) +in RNA-seq data.") + (license license:gpl3)))) |