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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 66 |
1 files changed, 66 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fc1f00a0b5..aae27ba0f5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4594,6 +4594,72 @@ for all the loaded RBPs across a given genomic sequence and draws a heatmap of the scores.") (license license:gpl3))) +(define-public python-splicekit + (package + (name "python-splicekit") + (version "0.7") + (home-page "https://github.com/bedapub/splicekit") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit "ded5dbec16b45e0df44750d9ae021ae2416ff921"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "04l244qagbplksqp81w2s60pkymyhjq389xmqwsyc0n4q6b054h2")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-beautifulsoup4 + python-dateutil + python-levenshtein + python-logomaker + python-numpy + python-pandas + python-plotly + python-psutil + python-pybio + python-pysam + python-rangehttpserver + python-requests + python-scanrbp)) + (native-inputs + (list python-setuptools + python-wheel + snakemake)) + (arguments + (list + #:tests? #false ;There are no tests. + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'adjust-requirements + (lambda _ + (substitute* "setup.py" + ;; bs4 is an alternative name for beautifulsoup4, only used to + ;; avoid name squatting on pypi. + (("bs4") "beautifulsoup4") + ;; levenshtein can only be found as python-levenshtein + (("levenshtein") "python-levenshtein")))) + ;; fireducks seems to be a binary-only python-panda replacement + (add-after 'unpack 'remove-fireducks + (lambda _ + (substitute* '("Snakefile" + "splicekit/core/delta_dar.py" + "splicekit/core/juan.py" + "splicekit/core/motifs.py" + "splicekit/judge/__init__.py") + (("import fireducks.pandas as pd") "import pandas as pd")) + (substitute* "splicekit.yaml" + ((".*fireducks.*") ""))))))) + (synopsis "Python toolkit for splicing analysis from short-read RNA-seq") + (description "Splicekit is a modular platform for splicing analysis from +short-read RNA-seq datasets. The platform also integrates pybio for genomic +operations and scanRBP for RNA-protein binding studies. The whole analysis is +self-contained (one single directory) and the platform is written in Python, +in a modular way.") + (license license:gpl3))) + (define-public python-fastalite (package (name "python-fastalite") |