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authorEfraim Flashner2022-09-20 15:26:30 +0300
committerEfraim Flashner2022-09-20 15:26:30 +0300
commitee15e19b68607d6b715ee5a0afec284812047f5b (patch)
tree8d6c4c09b31bf87bb9248ff9f41254575d54239d /gn/packages
parentc76d239f93e5bef315a719b3eee3cef5452e6bda (diff)
downloadguix-bioinformatics-ee15e19b68607d6b715ee5a0afec284812047f5b.tar.gz
gn: Add blobtools.
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/bioinformatics.scm45
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