pimi wrote 6 years ago
(address . guix-patches@gnu.org)(name . pimi)(address . madalinionel.patrascu@mdc-berlin.de)
20180920102258.17005-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioinformatics.scm (poretools): New variable.
---
gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++
1 file changed, 39 insertions(+)
Toggle diff (49 lines)
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