From 2c16316ef4420b462a1147e8eaee4680093616fd Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 20 Mar 2015 14:36:38 +0100
Subject: gnu: Add pbtranscript-tofu.

* gnu/packages/bioinformatics.scm (pbtranscript-tofu): New variable.
---
 gnu/packages/bioinformatics.scm | 55 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 55 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 744f8c2a4a..ca8dcb761a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -20,6 +20,7 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system python)
@@ -679,6 +680,60 @@ that a read originated from a particular isoform.")
 files and writing bioinformatics applications.")
     (license license:bsd-3)))
 
+(define-public pbtranscript-tofu
+  (let ((commit "c7bbd5472"))
+    (package
+      (name "pbtranscript-tofu")
+      (version (string-append "0.4.1." commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/PacificBiosciences/cDNA_primer.git")
+                      (commit commit)))
+                (file-name (string-append name "-" version ".tar.gz"))
+                (sha256
+                 (base32
+                  "148xkzi689c49g6fdhckp6mnmj2qhjdf1j4wifm6ja7ij95d7fxx"))))
+      (build-system python-build-system)
+      (arguments
+       `(#:python ,python-2
+         ;; With standard flags, the install phase attempts to create a zip'd
+         ;; egg file, and fails with an error: 'ZIP does not support timestamps
+         ;; before 1980'
+         #:configure-flags '("--single-version-externally-managed"
+                             "--record=pbtranscript-tofu.txt")
+         #:phases
+         (alist-cons-after
+          'unpack 'enter-directory-and-clean-up
+          (lambda _
+            (chdir "pbtranscript-tofu/pbtranscript/")
+            ;; Delete clutter
+            (delete-file-recursively "dist/")
+            (delete-file-recursively "setuptools_cython-0.2.1-py2.6.egg/")
+            (delete-file-recursively "pbtools.pbtranscript.egg-info")
+            (delete-file "Cython-0.20.1.tar.gz")
+            (delete-file "setuptools_cython-0.2.1-py2.7.egg")
+            (delete-file "setuptools_cython-0.2.1.tar.gz")
+            (delete-file "setup.cfg")
+            ;; files should be writable for install phase
+            (for-each (lambda (f) (chmod f #o755))
+                      (find-files "." "\\.py")))
+          %standard-phases)))
+      (inputs
+       `(("python-cython" ,python2-cython)
+         ("python-numpy" ,python2-numpy)
+         ("python-bx-python" ,python2-bx-python)
+         ("python-pbcore" ,python2-pbcore)))
+      (native-inputs
+       `(("python-nose" ,python2-nose)
+         ("python-setuptools" ,python2-setuptools)))
+      (home-page "https://github.com/PacificBiosciences/cDNA_primer")
+      (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol")
+      (description
+       "pbtranscript-tofu contains scripts to analyze transcriptome data
+generated using the PacBio Iso-Seq protocol.")
+      (license license:bsd-3))))
+
 (define-public rseqc
   (package
     (name "rseqc")
-- 
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