diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 49 |
1 files changed, 17 insertions, 32 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8377e811db..e90281fb5f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -215,8 +215,7 @@ structure of the predicted RNA.") ("libtool" ,libtool) ("zlib" ,zlib) ("python-nose" ,python2-nose) - ("python-pysam" ,python2-pysam) - ("python-setuptools" ,python2-setuptools))) + ("python-pysam" ,python2-pysam))) (inputs `(("htslib" ,htslib) ("samtools" ,samtools) @@ -530,8 +529,7 @@ intended to behave exactly the same as the original BWK awk.") ("samtools" ,samtools))) (native-inputs `(("python-pyyaml" ,python2-pyyaml) - ("python-nose" ,python2-nose) - ("python-setuptools" ,python2-setuptools))) + ("python-nose" ,python2-nose))) (home-page "https://pythonhosted.org/pybedtools/") (synopsis "Python wrapper for BEDtools programs") (description @@ -1342,8 +1340,7 @@ well as many of the command line options.") `(("python-numpy" ,python2-numpy) ("zlib" ,zlib))) (native-inputs - `(("python-nose" ,python2-nose) - ("python-setuptools" ,python2-setuptools))) + `(("python-nose" ,python2-nose))) (home-page "http://bitbucket.org/james_taylor/bx-python/") (synopsis "Tools for manipulating biological data") (description @@ -1407,7 +1404,6 @@ multiple sequence alignments.") ("zlib" ,zlib))) (native-inputs `(("python-cython" ,python-cython) - ("python-setuptools" ,python-setuptools) ;; Dependencies below are are for tests only. ("samtools" ,samtools) ("bcftools" ,bcftools) @@ -1583,9 +1579,8 @@ databases.") ("python-numpy" ,python2-numpy) ("python-scipy" ,python2-scipy))) (native-inputs - `(("python-mock" ,python2-mock) ; for tests - ("python-pytz" ,python2-pytz) ; for tests - ("python-setuptools" ,python2-setuptools))) + `(("python-mock" ,python2-mock) ; for tests + ("python-pytz" ,python2-pytz))) ; for tests (home-page "https://github.com/YeoLab/clipper") (synopsis "CLIP peak enrichment recognition") (description @@ -1758,8 +1753,7 @@ time.") ("zlib" ,zlib))) (native-inputs `(("python-cython" ,python2-cython) - ("python-nose" ,python2-nose) - ("python-setuptools" ,python2-setuptools))) + ("python-nose" ,python2-nose))) (home-page "http://crossmap.sourceforge.net/") (synopsis "Convert genome coordinates between assemblies") (description @@ -1857,8 +1851,7 @@ preparation protocols.") (alist-delete 'check %standard-phases)))) (native-inputs `(("python-cython" ,python-cython) - ("python-nose" ,python-nose) - ("python-setuptools" ,python-setuptools))) + ("python-nose" ,python-nose))) (home-page "https://code.google.com/p/cutadapt/") (synopsis "Remove adapter sequences from nucleotide sequencing reads") (description @@ -2000,8 +1993,7 @@ trees (phylogenies) and characters.") ;; 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-setuptools" ,python2-setuptools) - ("python2-nose" ,python2-nose) + (native-inputs `(("python2-nose" ,python2-nose) ,@(package-native-inputs base)))))) @@ -2029,9 +2021,8 @@ trees (phylogenies) and characters.") ("python-pysam" ,python2-pysam) ("python-pybigwig" ,python2-pybigwig))) (native-inputs - `(("python-mock" ,python2-mock) ;for tests - ("python-pytz" ,python2-pytz) ;for tests - ("python-setuptools" ,python2-setuptools))) + `(("python-mock" ,python2-mock) ;for tests + ("python-pytz" ,python2-pytz))) ;for tests (home-page "https://github.com/fidelram/deepTools") (synopsis "Tools for normalizing and visualizing deep-sequencing data") (description @@ -2687,8 +2678,7 @@ comment or quality sections.") ("python-pysam" ,python2-pysam) ("python-networkx" ,python2-networkx))) (native-inputs - `(("python-cython" ,python2-cython) - ("python-setuptools" ,python2-setuptools))) + `(("python-cython" ,python2-cython))) (home-page "http://grit-bio.org") (synopsis "Tool for integrative analysis of RNA-seq type assays") (description @@ -2934,8 +2924,7 @@ data. It also provides the bgzip, htsfile, and tabix utilities.") ("python-numpy" ,python-numpy) ("python-matplotlib" ,python-matplotlib))) (native-inputs - `(("python-cython" ,python-cython) - ("python-setuptools" ,python-setuptools))) + `(("python-cython" ,python-cython))) (home-page "https://github.com/nboley/idr") (synopsis "Tool to measure the irreproducible discovery rate (IDR)") (description @@ -3423,9 +3412,8 @@ linker_so='gcc -shared'); defines"))))) ("python-scipy" ,python2-scipy) ("python-matplotlib" ,python2-matplotlib))) (native-inputs - `(("python-mock" ,python2-mock) ;for tests - ("python-pytz" ,python2-pytz) ;for tests - ("python-setuptools" ,python2-setuptools))) + `(("python-mock" ,python2-mock) ;for tests + ("python-pytz" ,python2-pytz))) ;for tests (home-page "http://genes.mit.edu/burgelab/miso/index.html") (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation") (description @@ -3562,8 +3550,7 @@ files and writing bioinformatics applications.") ("python-pandas" ,python2-pandas) ("python-pysnptools" ,python2-pysnptools))) (native-inputs - `(("python-setuptools" ,python2-setuptools) - ("python-mock" ,python2-mock) + `(("python-mock" ,python2-mock) ("python-nose" ,python2-nose) ("unzip" ,unzip))) (home-page "https://github.com/PMBio/warpedLMM") @@ -3625,8 +3612,7 @@ the phenotype as it models the data.") ("python-h5py" ,python2-h5py))) (native-inputs `(("python-cython" ,python2-cython) - ("python-nose" ,python2-nose) - ("python-setuptools" ,python2-setuptools))) + ("python-nose" ,python2-nose))) (home-page "https://github.com/PacificBiosciences/cDNA_primer") (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol") (description @@ -4750,8 +4736,7 @@ bioinformatics file formats, sequence alignment, and more.") ;; should be removed. `(("python-biopython" ,python2-biopython-1.66))) (native-inputs - `(("python-setuptools" ,python2-setuptools) - ("python-nose" ,python2-nose))) + `(("python-nose" ,python2-nose))) (home-page "http://github.com/fhcrc/seqmagick") (synopsis "Tools for converting and modifying sequence files") (description |