diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 68 |
1 files changed, 44 insertions, 24 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 73cca16717..849225bd78 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -767,6 +767,29 @@ into separate processes; and more.") (define-public python2-biopython (package-with-python2 python-biopython)) +(define-public python-fastalite + (package + (name "python-fastalite") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "fastalite" version)) + (sha256 + (base32 + "1qli6pxp77i9xn2wfciq2zaxhl82bdxb33cpzqzj1z25yd036wqj")))) + (build-system python-build-system) + (arguments + `(#:tests? #f)) ; Test data is not distributed. + (home-page "https://github.com/nhoffman/fastalite") + (synopsis "Simplest possible FASTA parser") + (description "This library implements a FASTA and a FASTQ parser without +relying on a complex dependency tree.") + (license license:expat))) + +(define-public python2-fastalite + (package-with-python2 python-fastalite)) + (define-public bpp-core ;; The last release was in 2014 and the recommended way to install from source ;; is to clone the git repository, so we do this. @@ -1948,15 +1971,18 @@ accessing bigWig files.") (define-public python-dendropy (package (name "python-dendropy") - (version "4.2.0") + (version "4.4.0") (source (origin (method url-fetch) - (uri (pypi-uri "DendroPy" version)) + ;; Source from GitHub so that tests are included. + (uri + (string-append "https://github.com/jeetsukumaran/DendroPy/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p")) - (patches (search-patches "python-dendropy-fix-tests.patch")))) + "0v2fccny5xjaah546bsch1mw4kh61qq5frz2ibllxs9mp6ih9bsn")))) (build-system python-build-system) (home-page "http://packages.python.org/DendroPy/") (synopsis "Library for phylogenetics and phylogenetic computing") @@ -1964,23 +1990,10 @@ accessing bigWig files.") "DendroPy is a library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.") - (license license:bsd-3) - (properties `((python2-variant . ,(delay python2-dendropy)))))) + (license license:bsd-3))) (define-public python2-dendropy - (let ((base (package-with-python2 (strip-python2-variant python-dendropy)))) - (package - (inherit base) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (replace 'check - ;; There is currently a test failure that only happens on some - ;; systems, and only using "setup.py test" - (lambda _ (zero? (system* "nosetests"))))))) - (native-inputs `(("python2-nose" ,python2-nose) - ,@(package-native-inputs base)))))) + (package-with-python2 python-dendropy)) (define-public python-py2bit (package @@ -6046,7 +6059,13 @@ Cuffdiff or Ballgown programs.") `(("python-sqlalchemy" ,python2-sqlalchemy) ("python-decorator" ,python2-decorator) ("python-biopython" ,python2-biopython) - ("python-pandas" ,python2-pandas))) + ("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))) (home-page "https://github.com/fhcrc/taxtastic") (synopsis "Tools for taxonomic naming and annotation") (description @@ -12833,11 +12852,12 @@ once. This package provides tools to perform Drop-seq analyses.") (lambda _ (substitute* "Makefile.in" (("(^ tests/test_trim_galore/test.sh).*" _ m) m) + (("^ tests/test_multiqc/test.sh") "") (("^ test.sh") "")) #t))))) (inputs `(("gzip" ,gzip) - ("snakemake" ,snakemake) + ("snakemake" ,snakemake-4) ("fastqc" ,fastqc) ("multiqc" ,multiqc) ("star" ,star) @@ -12931,7 +12951,7 @@ expression report comparing samples in an easily configurable manner.") ("fastqc" ,fastqc) ("bowtie" ,bowtie) ("idr" ,idr) - ("snakemake" ,snakemake) + ("snakemake" ,snakemake-4) ("samtools" ,samtools) ("bedtools" ,bedtools) ("kentutils" ,kentutils))) @@ -12992,7 +13012,7 @@ in an easily configurable manner.") ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml) - ("snakemake" ,snakemake) + ("snakemake" ,snakemake-4) ("bismark" ,bismark) ("fastqc" ,fastqc) ("bowtie" ,bowtie) @@ -13041,7 +13061,7 @@ methylation and segmentation.") ("python-loompy" ,python-loompy) ("ghc-pandoc" ,ghc-pandoc-1) ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) - ("snakemake" ,snakemake) + ("snakemake" ,snakemake-4) ("star" ,star) ("r-minimal" ,r-minimal) ("r-argparser" ,r-argparser) |