From 4d49796615cfbd8c34890835689eea74ddcfca60 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sun, 25 Sep 2016 21:11:58 +0100
Subject: [PATCH 4/4] gnu: Add python2-pbcommand.

* gnu/packages/bioinformatics.scm (python2-pbcommand): New variable.
---
 gnu/packages/bioinformatics.scm | 52 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 52 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1bf91a9..f5a5756 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3373,6 +3373,58 @@ 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+  ;; Upstream does not tag git releases and PyPi is out of date.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
+         ;; Without this flag, various artifacts from the build inputs may end up
+         ;; in the final output. It also works around https://bugs.gnu.org/20765 .
+         #: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