diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 50 |
1 files changed, 50 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2593dc1f55..0059ed36ad 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1311,6 +1311,56 @@ relying on a complex dependency tree.") (define-public python2-fastalite (package-with-python2 python-fastalite)) +(define-public ciri-long + (package + (name "ciri-long") + (version "1.0.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/bioinfo-biols/CIRI-long") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "10k88i1fcqchrrjv82rmylwvbwqfba0n51palhig9hsg71xs0dbi")) + ;; Delete bundled binary + (snippet '(delete-file "libs/ccs")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "setup.py" + (("'argparse[^']*',") "") ; only for python2 + (("==") ">=")))) + (add-before 'build 'build-libssw + (lambda _ + (with-directory-excursion "libs/striped_smith_waterman" + (invoke "make" "libssw.so"))))))) + (inputs + `(("python-biopython" ,python-biopython) + ("python-bwapy" ,python-bwapy) + ("python-cython" ,python-cython) + ("python-levenshtein" ,python-levenshtein) + ("python-mappy" ,python-mappy) + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-pysam" ,python-pysam) + ("python-pyspoa" ,python-pyspoa) + ("python-scikit-learn" ,python-scikit-learn) + ("python-scipy" ,python-scipy))) + (native-inputs + `(("python-nose" ,python-nose) + ("python-setuptools" ,python-setuptools))) + (home-page "https://ciri-cookbook.readthedocs.io/") + (synopsis "Circular RNA identification for Nanopore sequencing") + (description "CIRI-long is a package for circular RNA identification using +long-read sequencing data.") + (license license:expat))) + (define-public bpp-core ;; The last release was in 2014 and the recommended way to install from source ;; is to clone the git repository, so we do this. |