diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 45 |
1 files changed, 45 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 5262615..4ed6b54 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -3429,6 +3429,51 @@ extension for metagenomic datasets, QUAST-LG, the extension for large genomes (license:non-copyleft "http://topaz.gatech.edu/GeneMark/license_download.cgi"))))) +(define-public blobtools + (let ((commit "6ed1ccf06617a0997f99cc2b28ffc82766c9a763") + (revision "2")) ;; 2022-10-02 + (package + (name "blobtools") + (version (git-version "1.1.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/DRL/blobtools") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "03a8n0s8qq6il5650basz4mlfp25743ii239jd0xsiirk5mmr8h7")) + (patches (search-patches "blobtools-setup-py.patch")) + )) + (build-system python-build-system) + (arguments + (list #:tests? #f ; No tests in repo. + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-setup.py + (lambda _ + (substitute* "setup.py" + (("^reqs = .*") + (string-append "with open ('requirements.txt') as f:\n" + " reqs = f.read().splitlines()\n")) + (("cmdclass.*") + "entry_points={'console_scripts': [\"blobtools=lib.interface:main\"]},\n"))))))) + (inputs + (list python-docopt + python-matplotlib + python-tqdm + python-pysam + python-pyyaml)) + (home-page "https://blobtools.readme.io/") + (synopsis + "Modular command-line solution for partitioning of genome datasets") + (description "Blobtools is a modular command-line solution for +visualisation, quality control and taxonomic partitioning of genome datasets. +BlobTools takes the information from HITS files and sums up bitscores by +taxonomic group at each taxonomic rank.") + (license license:gpl3)))) + ;; TODO: Regenerate or remove docs folder. (define-public python-pixy (package |