diff options
| author | Lars-Dominik Braun <lars@6xq.net> | 2021-07-20 11:50:31 +0200 |
|---|---|---|
| committer | Lars-Dominik Braun <lars@6xq.net> | 2021-07-21 13:36:08 +0200 |
| commit | 086c6800cfeb3db88bcd33badf5a6683ba4ce9db (patch) | |
| tree | f4ddd458f7da72842d9950bf6ab9693f3e984f66 /gnu/packages | |
| parent | 18a02fe7ca0c7be77d40e9953f7b07685cabd80d (diff) | |
gnu: checkm: Rename and update to 1.1.3.
Renamed from python2-checkm-genome to checkm to better reflect its
status as standalone-application and support for Python 3.
* gnu/packages/bioinformatics.scm (python2-checkm-genome): Redirect to…
(checkm): …here and update to 1.1.3.
[propagated-inputs]: Move to inputs.
[inputs]: Use Python 3 dependencies.
[home-page]: Point to real home-page.
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 33 |
1 files changed, 20 insertions, 13 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e418b2cefd..8aa21c4fd6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13061,28 +13061,32 @@ downstream analysis.") ("taxtastic" ,taxtastic))) (synopsis "Pplacer Python scripts"))) -(define-public python2-checkm-genome +(define-public checkm (package - (name "python2-checkm-genome") - (version "1.0.13") + (name "checkm") + (version "1.1.3") (source (origin (method url-fetch) (uri (pypi-uri "checkm-genome" version)) (sha256 (base32 - "0bm8gpxjmzxsxxl8lzwqhgx8g1dlnmp6znz7wv3hgb0gdjbf9dzz")))) + "0i2nnki639hgjag17wlva2x0ymn37b4krqsf6akxddykhfbkdnkz")))) (build-system python-build-system) (arguments - `(#:python ,python-2 - #:tests? #f)) ; some tests are interactive - (propagated-inputs - `(("python-dendropy" ,python2-dendropy) - ("python-matplotlib" ,python2-matplotlib) - ("python-numpy" ,python2-numpy) - ("python-pysam" ,python2-pysam) - ("python-scipy" ,python2-scipy))) - (home-page "https://pypi.org/project/Checkm/") + `(#:tests? #f ; Some tests fail for unknown reasons. + #:phases + (modify-phases %standard-phases + (add-before 'check 'set-HOME + (lambda _ + (setenv "HOME" "/tmp")))))) + (inputs + `(("python-dendropy" ,python-dendropy) + ("python-matplotlib" ,python-matplotlib) + ("python-numpy" ,python-numpy) + ("python-pysam" ,python-pysam) + ("python-scipy" ,python-scipy))) + (home-page "https://ecogenomics.github.io/CheckM/") (synopsis "Assess the quality of putative genome bins") (description "CheckM provides a set of tools for assessing the quality of genomes @@ -13097,6 +13101,9 @@ on marker set compatibility, similarity in genomic characteristics, and proximity within a reference genome.") (license license:gpl3+))) +(define-public python2-checkm-genome + (deprecated-package "python2-checkm-genome" checkm)) + (define-public umi-tools (package (name "umi-tools") |