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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 61 |
1 files changed, 61 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5184a2916a..dce8ab62f1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13345,3 +13345,64 @@ can be calculated, and a number of descriptive plots easily generated.") (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))))) |