diff options
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 51 |
1 files changed, 26 insertions, 25 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0b19b02f46..d324424a58 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -404,10 +404,10 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") ;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1. (license (list license:gpl3+ license:expat)))) -(define-public bcftools-1.9 +(define-public bcftools-1.10 (package (inherit bcftools) (name "bcftools") - (version "1.9") + (version "1.10") (source (origin (method url-fetch) (uri (string-append "https://github.com/samtools/bcftools/" @@ -415,15 +415,15 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") version "/bcftools-" version ".tar.bz2")) (sha256 (base32 - "1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg")) + "10xgwfdgqb6dsmr3ndnpb77mc3a38dy8kh2c6czn6wj7jhdp4dra")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled htslib. - (delete-file-recursively "htslib-1.9") + (delete-file-recursively "htslib-1.10") #t)))) (build-system gnu-build-system) (native-inputs - `(("htslib" ,htslib-1.9) + `(("htslib" ,htslib-1.10) ("perl" ,perl))))) (define-public bedops @@ -2071,7 +2071,7 @@ has several key features: (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. @@ -2081,7 +2081,7 @@ has several key features: (file-name (git-file-name name version)) (sha256 (base32 - "1vj367w6xbn9bpmksm162l1aipf7cj97h1q83y7jcpm33ihwpf7x")) + "168bwwm8c2k22m7paip8q0yajyl7xdxgnik0bgjl7rhqg0majz0f")) (modules '((guix build utils))) (snippet '(begin ;; Drop bundled htslib. TODO: Also remove samtools @@ -2108,10 +2108,7 @@ has several key features: #t)) (replace 'check (lambda* (#:key inputs outputs #:allow-other-keys) - ;; This file contains tests that require a connection to the - ;; internet. - (delete-file "tests/tabix_test.py") - ;; FIXME: This test fails + ;; Failing test removed in the next release. (delete-file "tests/AlignmentFile_test.py") ;; Add first subdirectory of "build" directory to PYTHONPATH. (setenv "PYTHONPATH" @@ -2125,23 +2122,27 @@ has several key features: (setenv "HOME" "/tmp") (invoke "make" "-C" "pysam_data") (invoke "make" "-C" "cbcf_data") - ;; Running nosetests without explicitly asking for a single - ;; process leads to a crash. Running with multiple processes - ;; fails because the tests are not designed to run in parallel. - - ;; FIXME: tests keep timing out on some systems. - (invoke "nosetests" "-v" "--processes" "1"))))))) + (invoke "pytest" "-k" + (string-append + ;; requires network access. + "not FileHTTP" + ;; bug in test suite with samtools update + ;; https://github.com/pysam-developers/pysam/issues/961 + " and not TestHeaderBAM" + " and not TestHeaderCRAM" + " and not test_text_processing")))))))) (propagated-inputs - `(("htslib" ,htslib-1.9))) ; Included from installed header files. + `(("htslib" ,htslib-1.10))) ; Included from installed header files. (inputs `(("ncurses" ,ncurses) ("curl" ,curl) ("zlib" ,zlib))) (native-inputs `(("python-cython" ,python-cython) + ("python-pytest" ,python-pytest) ;; Dependencies below are are for tests only. - ("samtools" ,samtools-1.9) - ("bcftools" ,bcftools-1.9) + ("samtools" ,samtools-1.10) + ("bcftools" ,bcftools-1.10) ("python-nose" ,python-nose))) (home-page "https://github.com/pysam-developers/pysam") (synopsis "Python bindings to the SAMtools C API") @@ -6111,10 +6112,10 @@ variant calling (in conjunction with bcftools), and a simple alignment viewer.") (license license:expat))) -(define-public samtools-1.9 +(define-public samtools-1.10 (package (inherit samtools) (name "samtools") - (version "1.9") + (version "1.10") (source (origin (method url-fetch) @@ -6123,14 +6124,14 @@ viewer.") version "/samtools-" version ".tar.bz2")) (sha256 (base32 - "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8")) + "119ms0dpydw8dkh3zc4yyw9zhdzgv12px4l2kayigv31bpqcb7kv")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled htslib. - (delete-file-recursively "htslib-1.9") + (delete-file-recursively "htslib-1.10") #t)))) (inputs - `(("htslib" ,htslib-1.9) + `(("htslib" ,htslib-1.10) ("ncurses" ,ncurses) ("perl" ,perl) ("python" ,python) |