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02/02: gnu: Add gffcompare.
From: |
Leo Famulari |
Subject: |
02/02: gnu: Add gffcompare. |
Date: |
Wed, 29 Aug 2018 14:14:02 -0400 (EDT) |
lfam pushed a commit to branch master
in repository guix.
commit 4f9355c3606ecbe83dce78e6d01fa974d912bd4a
Author: pimi <address@hidden>
Date: Tue Aug 28 22:26:13 2018 +0200
gnu: Add gffcompare.
gnu/packages/bioinformatics.scm (gffcompare): New variable.
Signed-off-by: Leo Famulari <address@hidden>
---
gnu/packages/bioinformatics.scm | 64 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 64 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3c300e4..22a0089 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11,6 +11,7 @@
;;; Copyright © 2017 Arun Isaac <address@hidden>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <address@hidden>
;;; Copyright © 2018 Gábor Boskovits <address@hidden>
+;;; Copyright © 2018 Mădălin Ionel Patrașcu <address@hidden>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -13494,3 +13495,66 @@ pseudotime and trajectory inference and differential
expression testing. The
Python-based implementation efficiently deals with datasets of more than one
million cells.")
(license license:bsd-3)))
+
+(define-public gffcompare
+ (let ((commit "be56ef4349ea3966c12c6397f85e49e047361c41")
+ (revision "1"))
+ (package
+ (name "gffcompare")
+ (version (git-version "0.10.15" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/gpertea/gffcompare/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0cp5qpxdhw4mxpya5dld8wi3jk00zyklm6rcri426wydinrnfmkg"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; no check target
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-before 'build 'copy-gclib-source
+ (lambda* (#:key inputs #:allow-other-keys)
+ (mkdir "../gclib")
+ (copy-recursively
+ (assoc-ref inputs "gclib-source") "../gclib")
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "gffcompare" bin)
+ #t))))))
+ (native-inputs
+ `(("gclib-source" ; see 'README.md' of gffcompare
+ ,(let ((commit "54917d0849c1e83cfb057b5f712e5cb6a35d948f")
+ (revision "1")
+ (name "gclib")
+ (version (git-version "0.10.3" revision commit)))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/gpertea/gclib/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
"0b51lc0b8syrv7186fd7n8f15rwnf264qgfmm2palrwks1px24mr")))))))
+ (home-page "https://github.com/gpertea/gffcompare/")
+ (synopsis "Tool for comparing or classifing transcripts of RNA-Seq")
+ (description
+ "@code{gffcompare} is a tool that can:
address@hidden
address@hidden compare and evaluate the accuracy of RNA-Seq transcript
assemblers
+(Cufflinks, Stringtie);
address@hidden collapse (merge) duplicate transcripts from multiple GTF/GFF3
files (e.g.
+resulted from assembly of different samples);
address@hidden classify transcripts from one or multiple GTF/GFF3 files as they
relate to
+reference transcripts provided in a annotation file (also in GTF/GFF3 format).
address@hidden enumerate")
+ (license
+ (list
+ license:expat ;license for gffcompare
+ license:artistic2.0))))) ;license for gclib