gnu: Add gffread.

* gnu/packages/bioinformatics.scm (gffread): New variable.
This commit is contained in:
Ricardo Wurmus 2018-08-14 12:45:41 +02:00 committed by Ricardo Wurmus
parent a87ee0e41c
commit 689aacc12f
No known key found for this signature in database
GPG key ID: 197A5888235FACAC

View file

@ -13345,3 +13345,64 @@ (define-public r-loomr
(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)))))