GNU bug report logs - #32781
[PATCH] gnu: Add poretools.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: pimi <madalinionel.patrascu <at> mdc-berlin.de>
Subject: bug#32781: closed (Re: [bug#32781] [PATCH] gnu: Add poretools.)
Date: Tue, 02 Oct 2018 20:06:02 +0000

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Your bug report

#32781: [PATCH] gnu: Add poretools.

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to 32781 <at> debbugs.gnu.org.

-- 
32781: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=32781
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

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From: Leo Famulari <leo <at> famulari.name>
To: pimi <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 32781-done <at> debbugs.gnu.org
Subject: Re: [bug#32781] [PATCH] gnu: Add poretools.
Date: Tue, 2 Oct 2018 16:05:42 -0400

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On Thu, Sep 20, 2018 at 12:22:58PM +0200, pimi wrote:
> * gnu/packages/bioinformatics.scm (poretools): New variable.

Thank you! Pushed as 3f0f49d70877df6c829b443830de99e0e1e1f6bc

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From: pimi <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Cc: pimi <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH] gnu: Add poretools.
Date: Thu, 20 Sep 2018 12:22:58 +0200

* gnu/packages/bioinformatics.scm (poretools): New variable.
---
 gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 67f24a617..fdc35e684 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13723,3 +13723,42 @@ juicer) and single-resolution or multi-resolution @code{.cool} files (for
 cooler).  Both @code{hic} and @code{cool} files describe Hi-C contact
 matrices.")
     (license license:expat)))
+
+(define-public poretools
+  ;; The latest release was in 2016 and the latest commit is from 2017
+  ;; the recommended way to install is to clone the git repository
+  ;; https://poretools.readthedocs.io/en/latest/content/installation.html
+  (let ((commit "e426b1f09e86ac259a00c261c79df91510777407")
+        (revision "1"))
+    (package
+      (name "poretools")
+      (version (git-version "0.6.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/arq5x/poretools.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0bglj833wxpp3cq430p1d3xp085ls221js2y90w7ir2x5ay8l7am"))))
+      (build-system python-build-system)
+      ;; requires python >=2.7, <3.0, and the same for python dependencies
+      (arguments `(#:python ,python-2))
+      (inputs
+       `(("hdf5" ,hdf5)))
+      (propagated-inputs
+       `(("python-dateutil" ,python2-dateutil)
+         ("python-h5py" ,python2-h5py)
+         ("python-matplotlib" ,python2-matplotlib)
+         ("python-pandas" ,python2-pandas)
+         ("python-seaborn" ,python2-seaborn)))
+      (home-page "https://poretools.readthedocs.io")
+      (synopsis "Toolkit for working with nanopore sequencing data")
+      (description
+       "The MinION from Oxford Nanopore Technologies is a nanopore sequencer.
+This @code{poretools} package is a flexible toolkit for exploring datasets
+generated by nanopore sequencing devices for the purposes of quality control and
+downstream analysis.  Poretools operates directly on the native FAST5, a variant
+of the Hierarchical Data Format (HDF5) standard.")
+      (license license:expat))))
-- 
2.17.1

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