diff options
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 16 |
1 files changed, 11 insertions, 5 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4c49b00252..f63ae5f324 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12,7 +12,7 @@ ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> ;;; Copyright © 2018, 2019, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> -;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com> +;;; Copyright © 2019, 2020 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com> ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org> ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de> @@ -1894,7 +1894,7 @@ multiple sequence alignments.") (define-public python-pysam (package (name "python-pysam") - (version "0.15.1") + (version "0.16.0.1") (source (origin (method git-fetch) ;; Test data is missing on PyPi. @@ -1904,7 +1904,7 @@ multiple sequence alignments.") (file-name (git-file-name name version)) (sha256 (base32 - "1vj367w6xbn9bpmksm162l1aipf7cj97h1q83y7jcpm33ihwpf7x")) + "168bwwm8c2k22m7paip8q0yajyl7xdxgnik0bgjl7rhqg0majz0f")) (modules '((guix build utils))) (snippet '(begin ;; Drop bundled htslib. TODO: Also remove samtools @@ -1934,8 +1934,13 @@ multiple sequence alignments.") ;; This file contains tests that require a connection to the ;; internet. (delete-file "tests/tabix_test.py") - ;; FIXME: This test fails + ;; These tests fail (see: + ;; https://github.com/pysam-developers/pysam/issues/939). + (delete-file "tests/compile_test.py") (delete-file "tests/AlignmentFile_test.py") + (delete-file "tests/AlignmentFileHeader_test.py") + (delete-file "tests/StreamFiledescriptors_test.py") + (delete-file "tests/VariantRecord_test.py") ;; Add first subdirectory of "build" directory to PYTHONPATH. (setenv "PYTHONPATH" (string-append @@ -1965,7 +1970,8 @@ multiple sequence alignments.") ;; Dependencies below are are for tests only. ("samtools" ,samtools) ("bcftools" ,bcftools) - ("python-nose" ,python-nose))) + ("python-nose" ,python-nose) + ("python-pytest" ,python-pytest))) (home-page "https://github.com/pysam-developers/pysam") (synopsis "Python bindings to the SAMtools C API") (description |