[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
[PATCH 4/4] gnu: Add python2-pbcommand.
From: |
Marius Bakke |
Subject: |
[PATCH 4/4] gnu: Add python2-pbcommand. |
Date: |
Sun, 25 Sep 2016 22:17:28 +0100 |
* gnu/packages/bioinformatics.scm (python2-pbcommand): New variable.
---
gnu/packages/bioinformatics.scm | 50 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 50 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1bf91a9..9343cc6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3373,6 +3373,56 @@ interrupted by stop codons. OrfM finds and prints these
ORFs.")
(home-page "https://github.com/wwood/OrfM")
(license license:lgpl3+)))
+(define-public python2-pbcommand
+ ;; Upstream does not tag git releases and PyPi is out of date.
+ ;; See https://github.com/PacificBiosciences/pbcommand/issues/116
+ (let ((revision "1")
+ (commit "e83a3443a1cd42b4da0d210201d711ede789917f"))
+ (package
+ (name "python2-pbcommand")
+ (version (string-append "0.4.11-" revision "." (string-take commit 7)))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url
"https://github.com/PacificBiosciences/pbcommand.git")
+ (commit commit)))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "1kwg84f23l7ik65qy7cxa6g5nipc2y23mppigd4j3vlzam18v52h"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2 ; Python-2 only.
+ #:configure-flags '("--single-version-externally-managed" "--root=/")
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'substitute-/bin/bash
+ (lambda _
+ ;; Fully qualify /bin/bash for running external commands.
+ (substitute* "pbcommand/engine/runner.py"
+ (("/bin/bash") (which "bash")))
+ #t))
+ (replace 'check
+ (lambda _ (zero? (system* "nosetests" "-v")))))))
+ (native-inputs
+ `(("python-nose" ,python2-nose)
+ ("python-sphinx-bootstrap-theme" ,python2-sphinx-bootstrap-theme)
+ ("python-sphinx-argparse" ,python2-sphinx-argparse)
+ ("python-tox" ,python2-tox)
+ ("python-setuptools" ,python2-setuptools)))
+ (propagated-inputs
+ `(("python-functools32" ,python2-functools32)
+ ("python-jsonschema" ,python2-jsonschema)
+ ("python-numpy" ,python2-numpy "out")
+ ("python-avro" ,python2-avro)
+ ("python-requests" ,python2-requests)
+ ("python-iso8601" ,python2-iso8601)))
+ (home-page "https://github.com/PacificBiosciences/pbcommand")
+ (synopsis "PacBio common models and CLI tool contract interface")
+ (description "PacBio library for common utils, models, and tools
+to interface with pbsmrtpipe workflow engine.")
+ (license license:bsd-3))))
+
(define-public python2-pbcore
(package
(name "python2-pbcore")
--
2.10.0