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| author | pimi <madalinionel.patrascu@mdc-berlin.de> | 2018-10-02 16:03:59 -0400 |
|---|---|---|
| committer | Leo Famulari <leo@famulari.name> | 2018-10-02 16:05:14 -0400 |
| commit | 3f0f49d70877df6c829b443830de99e0e1e1f6bc (patch) | |
| tree | 962afaa52b9adfe3b12e4378d68582ee23cc3c77 /gnu | |
| parent | d8d8844ec12c017480e83cd541e98b55e18a17f4 (diff) | |
| download | patches-3f0f49d70877df6c829b443830de99e0e1e1f6bc.tar patches-3f0f49d70877df6c829b443830de99e0e1e1f6bc.tar.gz | |
gnu: Add poretools.
* gnu/packages/bioinformatics.scm (poretools): New variable.
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 39 |
1 files changed, 39 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b84498d042..172832d148 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13899,3 +13899,42 @@ adapters, even at low sequence identity. Porechop also supports demultiplexing of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.") (license license:gpl3+)))) + +(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)))) |