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| author | Ben Woodcroft <donttrustben@gmail.com> | 2017-08-03 20:37:25 +1000 |
|---|---|---|
| committer | Ben Woodcroft <donttrustben@gmail.com> | 2017-08-03 21:02:30 +1000 |
| commit | 92971d68ac942cd4a38092b4ccb20a8192a56aaf (patch) | |
| tree | d551aed45228af4824c56b5ab6bc7b266254a53d /gnu/packages/bioinformatics.scm | |
| parent | a8ead6f91b74dbc5c776a5029a62e15bd84d7b0e (diff) | |
| download | patches-92971d68ac942cd4a38092b4ccb20a8192a56aaf.tar patches-92971d68ac942cd4a38092b4ccb20a8192a56aaf.tar.gz | |
gnu: htseq: Update to 0.9.1.
* gnu/packages/bioinformatics.scm (htseq): Update to 0.9.1.
[arguments]: Use python-3 by removing field.
[native-inputs]: Add 'python-cython'.
[propagated-inputs]: Use python3 numpy package.
[inputs]: Use python3 pysam package. Add 'python-matplotlib'.
(python2-htseq): New variable.
(clipper)[inputs]: Use it.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 17 |
1 files changed, 11 insertions, 6 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b47d13ea55..4de245abe6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1636,7 +1636,7 @@ databases.") (build-system python-build-system) (arguments `(#:python ,python-2)) ; only Python 2 is supported (inputs - `(("htseq" ,htseq) + `(("htseq" ,python2-htseq) ("python-pybedtools" ,python2-pybedtools) ("python-cython" ,python2-cython) ("python-scikit-learn" ,python2-scikit-learn) @@ -2981,7 +2981,7 @@ HMMs).") (define-public htseq (package (name "htseq") - (version "0.6.1") + (version "0.9.1") (source (origin (method url-fetch) (uri (string-append @@ -2989,14 +2989,16 @@ HMMs).") version ".tar.gz")) (sha256 (base32 - "1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv")))) + "11flgb1381xdhk43bzbfm3vhnszkpqg6jk76rpa5xd1zbrvvlnxg")))) (build-system python-build-system) - (arguments `(#:python ,python-2)) ; only Python 2 is supported + (native-inputs + `(("python-cython" ,python-cython))) ;; Numpy needs to be propagated when htseq is used as a Python library. (propagated-inputs - `(("python-numpy" ,python2-numpy))) + `(("python-numpy" ,python-numpy))) (inputs - `(("python-pysam" ,python2-pysam))) + `(("python-pysam" ,python-pysam) + ("python-matplotlib" ,python-matplotlib))) (home-page "http://www-huber.embl.de/users/anders/HTSeq/") (synopsis "Analysing high-throughput sequencing data with Python") (description @@ -3004,6 +3006,9 @@ HMMs).") from high-throughput sequencing assays.") (license license:gpl3+))) +(define-public python2-htseq + (package-with-python2 htseq)) + (define-public java-htsjdk (package (name "java-htsjdk") |