diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 112 |
1 files changed, 85 insertions, 27 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cfa0263e46..550c0387e9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -475,20 +475,6 @@ BED, GFF/GTF, VCF.") (find-files "bin" ".*"))) #t))))))) -;; Needed for pybedtools. -(define-public bedtools-2.26 - (package (inherit bedtools) - (name "bedtools") - (version "2.26.0") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/arq5x/bedtools2/releases/" - "download/v" version "/" - "bedtools-" version ".tar.gz")) - (sha256 - (base32 - "0jhavwifnf7lmkb11h9y7dynr8d699h0rd2l52j1pfgircr2zwv5")))))) - (define-public pbbam (package (name "pbbam") @@ -806,12 +792,13 @@ intended to behave exactly the same as the original BWK awk.") ;; See https://github.com/daler/pybedtools/issues/192 #:phases (modify-phases %standard-phases - ;; See https://github.com/daler/pybedtools/issues/261 (add-after 'unpack 'disable-broken-tests (lambda _ - ;; This test (pybedtools.test.test_scripts.test_venn_mpl) needs a - ;; graphical environment. (substitute* "pybedtools/test/test_scripts.py" + ;; This test freezes. + (("def test_intron_exon_reads") + "def _do_not_test_intron_exon_reads") + ;; This test fails in the Python 2 build. (("def test_venn_mpl") "def _do_not_test_venn_mpl")) (substitute* "pybedtools/test/test_helpers.py" @@ -868,7 +855,7 @@ intended to behave exactly the same as the original BWK awk.") (mkdir-p "/tmp/test") (copy-recursively "pybedtools/test" "/tmp/test") (with-directory-excursion "/tmp/test" - (invoke "pytest"))))))) + (invoke "pytest" "-v" "--doctest-modules"))))))) (propagated-inputs `(("bedtools" ,bedtools) ("samtools" ,samtools) @@ -985,6 +972,64 @@ e.g. microbiome samples, genomes, metagenomes.") (("install_requires.append\\(\"pyqi\"\\)") "pass")) #t))))))))) +(define-public python-pairtools + (package + (name "python-pairtools") + (version "0.3.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mirnylab/pairtools") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0gr8y13q7sd6yai6df4aavl2470n1f9s3cib6r473z4hr8hcbwmc")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-references + (lambda _ + (substitute* '("pairtools/pairtools_merge.py" + "pairtools/pairtools_sort.py") + (("/bin/bash") (which "bash"))) + #t)) + (replace 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (with-directory-excursion "/tmp" + (invoke "pytest" "-v"))))))) + (native-inputs + `(("python-cython" ,python-cython) + ("python-nose" ,python-nose) + ("python-pytest" ,python-pytest))) + (inputs + `(("python" ,python-wrapper))) + (propagated-inputs + `(("htslib" ,htslib) ; for bgzip, looked up in PATH + ("samtools" ,samtools) ; looked up in PATH + ("lz4" ,lz4) ; for lz4c + ("python-click" ,python-click) + ("python-numpy" ,python-numpy))) + (home-page "https://github.com/mirnylab/pairtools") + (synopsis "Process mapped Hi-C data") + (description "Pairtools is a simple and fast command-line framework to +process sequencing data from a Hi-C experiment. Process pair-end sequence +alignments and perform the following operations: + +@itemize +@item detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end + sequences of Hi-C DNA molecules +@item sort @code{.pairs} files for downstream analyses +@item detect, tag and remove PCR/optical duplicates +@item generate extensive statistics of Hi-C datasets +@item select Hi-C pairs given flexibly defined criteria +@item restore @code{.sam} alignments from Hi-C pairs. +@end itemize +") + (license license:expat))) + (define-public bioperl-minimal (let* ((inputs `(("perl-module-build" ,perl-module-build) ("perl-data-stag" ,perl-data-stag) @@ -8702,9 +8747,9 @@ library implementing most of the pipeline's features.") (inputs `(("r-minimal" ,r-minimal) ("r-rcas" ,r-rcas) - ("guile-next" ,guile-2.2) + ("guile" ,guile-2.2) ("guile-json" ,guile-json-1) - ("guile-redis" ,guile-redis))) + ("guile-redis" ,guile2.2-redis))) (native-inputs `(("pkg-config" ,pkg-config))) (home-page "https://github.com/BIMSBbioinfo/rcas-web") @@ -13743,18 +13788,31 @@ bound.") (define-public python-pypairix (package (name "python-pypairix") - (version "0.3.6") + (version "0.3.7") + ;; The tarball on pypi does not include the makefile to build the + ;; programs. (source (origin - (method url-fetch) - (uri (pypi-uri "pypairix" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/4dn-dcic/pairix.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0zs92b74s5v4xy2h16s15f3z6l4nnbw8x8zyif7xx5xpafjn0xss")))) + "1snr3lrmsld8sy77ng6ba6wcmd33xjccf1l2f3m6pi29xis9nd6p")))) (build-system python-build-system) - ;; FIXME: the tests fail because test.support cannot be loaded: - ;; ImportError: cannot import name 'support' - (arguments '(#:tests? #f)) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'build 'build-programs + (lambda _ (invoke "make"))) + (add-after 'install 'install-programs + (lambda* (#:key outputs #:allow-other-keys) + (copy-recursively "bin" (string-append + (assoc-ref outputs "out") + "/bin")) + #t))))) (inputs `(("zlib" ,zlib))) (home-page "https://github.com/4dn-dcic/pairix") |