diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 90 |
1 files changed, 61 insertions, 29 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0c12e7c874..035a7bb808 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6536,31 +6536,56 @@ Cuffdiff or Ballgown programs.") (define-public taxtastic (package (name "taxtastic") - (version "0.8.5") + (version "0.8.11") (source (origin - (method url-fetch) - (uri (pypi-uri "taxtastic" version)) + ;; The Pypi version does not include tests. + (method git-fetch) + (uri (git-reference + (url "https://github.com/fhcrc/taxtastic.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "03pysw79lsrvz4lwzis88j15067ffqbi4cid5pqhrlxmd6bh8rrk")))) + "1sv8mkg64jn7zdwf1jj71c16686yrwxk0apb1l8sjszy9p166g0p")))) (build-system python-build-system) (arguments - `(#:python ,python-2 - #:phases + `(#:phases (modify-phases %standard-phases + (add-after 'unpack 'prepare-directory + (lambda _ + ;; The git checkout must be writable for tests. + (for-each make-file-writable (find-files ".")) + ;; This test fails, but the error is not caught by the test + ;; framework, so the tests fail... + (substitute* "tests/test_taxit.py" + (("self.cmd_fails\\(''\\)") + "self.cmd_fails('nothing')")) + ;; This version file is expected to be created with git describe. + (mkdir-p "taxtastic/data") + (with-output-to-file "taxtastic/data/ver" + (lambda () (display ,version))) + #t)) + (add-after 'unpack 'python37-compatibility + (lambda _ + (substitute* "taxtastic/utils.py" + (("import csv") "import csv, errno") + (("os.errno") "errno")) + #t)) (replace 'check - (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t))))) + ;; Note, this fails to run with "-v" as it tries to write to a + ;; closed output stream. + (lambda _ (invoke "python" "-m" "unittest") #t))))) (propagated-inputs - `(("python-sqlalchemy" ,python2-sqlalchemy) - ("python-decorator" ,python2-decorator) - ("python-biopython" ,python2-biopython) - ("python-pandas" ,python2-pandas) - ("python-psycopg2" ,python2-psycopg2) - ("python-fastalite" ,python2-fastalite) - ("python-pyyaml" ,python2-pyyaml) - ("python-six" ,python2-six) - ("python-jinja2" ,python2-jinja2) - ("python-dendropy" ,python2-dendropy))) + `(("python-sqlalchemy" ,python-sqlalchemy) + ("python-decorator" ,python-decorator) + ("python-biopython" ,python-biopython) + ("python-pandas" ,python-pandas) + ("python-psycopg2" ,python-psycopg2) + ("python-fastalite" ,python-fastalite) + ("python-pyyaml" ,python-pyyaml) + ("python-six" ,python-six) + ("python-jinja2" ,python-jinja2) + ("python-dendropy" ,python-dendropy))) (home-page "https://github.com/fhcrc/taxtastic") (synopsis "Tools for taxonomic naming and annotation") (description @@ -9091,6 +9116,8 @@ number detection tools.") ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes (inputs `(("zlib" ,zlib))) (home-page "https://github.com/al2na/methylKit") @@ -9360,6 +9387,8 @@ analysis.") ("r-ggplot2" ,r-ggplot2) ("r-lattice" ,r-lattice) ("r-limma" ,r-limma))) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html") (synopsis "Variance stabilization and calibration for microarray data") (description @@ -13238,18 +13267,14 @@ in RNA-seq data.") (define-public python-scanpy (package (name "python-scanpy") - (version "1.4") - ;; Fetch from git because the pypi tarball does not include tests. + (version "1.4.5.1") (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/theislab/scanpy.git") - (commit version))) - (file-name (git-file-name name version)) + (method url-fetch) + (uri (pypi-uri "scanpy" version)) (sha256 (base32 - "0zn6x6c0cnm1a20i6isigwb51g3pr9zpjk8r1minjqnxi5yc9pm4")))) + "14kh1ji70xxhmri5q8sgcibsidhr6f221wxrcw8a5xvibj5da17j")))) (build-system python-build-system) (arguments `(#:phases @@ -13276,18 +13301,23 @@ in RNA-seq data.") ("python-igraph" ,python-igraph) ("python-joblib" ,python-joblib) ("python-louvain" ,python-louvain) + ("python-legacy-api-wrap" ,python-legacy-api-wrap) ("python-matplotlib" ,python-matplotlib) ("python-natsort" ,python-natsort) ("python-networkx" ,python-networkx) ("python-numba" ,python-numba) + ("python-packaging" ,python-packaging) ("python-pandas" ,python-pandas) + ("python-patsy" ,python-patsy) ("python-scikit-learn" ,python-scikit-learn) ("python-scipy" ,python-scipy) ("python-seaborn" ,python-seaborn) ("python-statsmodels" ,python-statsmodels) - ("python-tables" ,python-tables))) + ("python-tables" ,python-tables) + ("python-umap-learn" ,python-umap-learn))) (native-inputs - `(("python-pytest" ,python-pytest))) + `(("python-pytest" ,python-pytest) + ("python-setuptools-scm" ,python-setuptools-scm))) (home-page "https://github.com/theislab/scanpy") (synopsis "Single-Cell Analysis in Python.") (description "Scanpy is a scalable toolkit for analyzing single-cell gene @@ -13953,7 +13983,7 @@ datasets.") (define-public ngless (package (name "ngless") - (version "1.0.1") + (version "1.1.0") (source (origin (method git-fetch) @@ -13963,7 +13993,7 @@ datasets.") (file-name (git-file-name name version)) (sha256 (base32 - "06ygv8q2zjqsnrid1302yrlhhvb8ik48nq6n0higk3i1mdc8r0dg")))) + "1wim8wpqyff080dfcazynrmjwqas38m24m0v350w245mmhrapdma")))) (build-system haskell-build-system) (arguments `(#:haddock? #f ; The haddock phase fails with: NGLess/CmdArgs.hs:20:1: @@ -14423,6 +14453,8 @@ repeated areas between contigs.") (base32 "0fgygyzqgrq32dv6a00biq1p1cwi6kbl5iqblxq1kklj6b2mzmhs")))) (build-system python-build-system) + (native-inputs + `(("python-joblib" ,python-joblib))) (propagated-inputs `(("python-click" ,python-click) ("python-cython" ,python-cython) |