diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 41 |
1 files changed, 29 insertions, 12 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5b9413f181..24467166c7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15,6 +15,7 @@ ;;; Copyright © 2019 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> ;;; ;;; This file is part of GNU Guix. ;;; @@ -784,13 +785,13 @@ intended to behave exactly the same as the original BWK awk.") (define-public python-pybedtools (package (name "python-pybedtools") - (version "0.8.0") + (version "0.8.1") (source (origin (method url-fetch) (uri (pypi-uri "pybedtools" version)) (sha256 (base32 - "1xl454ijvd4dzfvqgfahad49b49j7qy710fq9xh1rvk42z6x5ssf")))) + "14w5i40gi25clrr7h4wa2pcpnyipya8hrqi7nq77553zc5wf0df0")))) (build-system python-build-system) (arguments `(#:modules ((ice-9 ftw) @@ -817,6 +818,10 @@ intended to behave exactly the same as the original BWK awk.") ;; (see: https://github.com/daler/pybedtools/issues/192). (("def test_getting_example_beds") "def _do_not_test_getting_example_beds")) + ;; This issue still occurs on python2 + (substitute* "pybedtools/test/test_issues.py" + (("def test_issue_303") + "def _test_issue_303")) #t)) ;; TODO: Remove phase after it's part of PYTHON-BUILD-SYSTEM. ;; build system. @@ -885,7 +890,12 @@ Python.") (license license:gpl2+))) (define-public python2-pybedtools - (package-with-python2 python-pybedtools)) + (let ((pybedtools (package-with-python2 python-pybedtools))) + (package + (inherit pybedtools) + (native-inputs + `(("python2-pathlib" ,python2-pathlib) + ,@(package-native-inputs pybedtools)))))) (define-public python-biom-format (package @@ -2745,7 +2755,7 @@ quantitative phenotypes.") (define-public edirect (package (name "edirect") - (version "12.1.20190829") + (version "13.3.20200128") (source (origin (method url-fetch) (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect" @@ -2753,7 +2763,10 @@ quantitative phenotypes.") "/edirect-" version ".tar.gz")) (sha256 (base32 - "1xb330z28dgp7slrvp8r7rgncsasv9lpcpqim571yg728dq7xdik")))) + "093zp7klv81ph0y8mm8d78a9hnpfxbv2kdym70gzdf3vz176rw33")) + (modules '((guix build utils))) + (snippet + '(begin (delete-file "Mozilla-CA.tar.gz") #t)))) (build-system perl-build-system) (arguments `(#:phases @@ -8278,7 +8291,7 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-qtl (package (name "r-qtl") - (version "1.45-11") + (version "1.46-2") (source (origin (method url-fetch) @@ -8286,7 +8299,7 @@ throughput genetic sequencing data sets using regression methods.") version ".tar.gz")) (sha256 (base32 - "1d6qgj602fm6zia3djl4hmca0ri4v57ffp3g93p2yc3cabx2hq90")))) + "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a")))) (build-system r-build-system) (home-page "https://rqtl.org/") (synopsis "R package for analyzing QTL experiments in genetics") @@ -12140,8 +12153,8 @@ reading, writing, and exporting phylogenetic trees.") (version "1.005") (source (origin (method url-fetch) - (uri (string-append "http://search.maven.org/remotecontent?" - "filepath=org/biojava/thirdparty/forester/" + (uri (string-append "https://repo1.maven.org/maven2/" + "org/biojava/thirdparty/forester/" version "/forester-" version "-sources.jar")) (file-name (string-append name "-" version ".jar")) (sha256 @@ -12217,7 +12230,8 @@ reading, writing, and exporting phylogenetic trees.") (method url-fetch) (uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/" "29e04321615da6b35c1e15c60e52caf3f21d8e6a/" - "forester/java/classes/resources/synth_look_and_feel_1.xml")) + "forester/java/classes/resources/" + "synth_look_and_feel_1.xml")) (file-name (string-append name "-synth-look-and-feel-" version ".xml")) (sha256 (base32 @@ -13509,14 +13523,14 @@ bgzipped text file that contains a pair of genomic coordinates per line.") (define-public python-pyfaidx (package (name "python-pyfaidx") - (version "0.5.7") + (version "0.5.8") (source (origin (method url-fetch) (uri (pypi-uri "pyfaidx" version)) (sha256 (base32 - "02jvdx3ksy6w5gd29i1d0g0zsabbz7c14qg482ff7pza6sdl0b2i")))) + "038xi3a6zvrxbyyfpp64ka8pcjgsdq4fgw9cl5lpxbvmm1bzzw2q")))) (build-system python-build-system) (propagated-inputs `(("python-six" ,python-six))) @@ -13527,6 +13541,9 @@ bgzipped text file that contains a pair of genomic coordinates per line.") fasta subsequences.") (license license:bsd-3))) +(define-public python2-pyfaidx + (package-with-python2 python-pyfaidx)) + (define-public python-cooler (package (name "python-cooler") |