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-rw-r--r--gnu/packages/bioinformatics.scm400
1 files changed, 286 insertions, 114 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 773b5909b6..415024fadc 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -50,6 +50,7 @@
#:use-module (gnu packages documentation)
#:use-module (gnu packages datastructures)
#:use-module (gnu packages file)
+ #:use-module (gnu packages flex)
#:use-module (gnu packages gawk)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gd)
@@ -215,8 +216,7 @@ 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)
@@ -523,15 +523,14 @@ intended to behave exactly the same as the original BWK awk.")
(build-system python-build-system)
(arguments `(#:python ,python-2)) ; no Python 3 support
(inputs
- `(("python-cython" ,python2-cython)
- ("python-matplotlib" ,python2-matplotlib)))
+ `(("python-matplotlib" ,python2-matplotlib)))
(propagated-inputs
`(("bedtools" ,bedtools)
("samtools" ,samtools)))
(native-inputs
- `(("python-pyyaml" ,python2-pyyaml)
- ("python-nose" ,python2-nose)
- ("python-setuptools" ,python2-setuptools)))
+ `(("python-cython" ,python2-cython)
+ ("python-pyyaml" ,python2-pyyaml)
+ ("python-nose" ,python2-nose)))
(home-page "https://pythonhosted.org/pybedtools/")
(synopsis "Python wrapper for BEDtools programs")
(description
@@ -586,9 +585,7 @@ e.g. microbiome samples, genomes, metagenomes.")
(substitute* "setup.py"
(("install_requires.append\\(\"pyqi\"\\)") "pass"))
#t)))
- ,@(package-arguments base)))
- (native-inputs `(("python2-setuptools" ,python2-setuptools)
- ,@(package-native-inputs base))))))
+ ,@(package-arguments base))))))
(define-public bioperl-minimal
(let* ((inputs `(("perl-module-build" ,perl-module-build)
@@ -673,7 +670,7 @@ provide a coordinated and extensible framework to do computational biology.")
(add-before 'check 'set-home
;; Some tests require a home directory to be set.
(lambda _ (setenv "HOME" "/tmp") #t)))))
- (inputs
+ (propagated-inputs
`(("python-numpy" ,python-numpy)))
(home-page "http://biopython.org/")
(synopsis "Tools for biological computation in Python")
@@ -684,15 +681,10 @@ bioinformatics programs; a standard sequence class and tools for performing
common operations on them; code to perform data classification; code for
dealing with alignments; code making it easy to split up parallelizable tasks
into separate processes; and more.")
- (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE"))
- (properties `((python2-variant . ,(delay python2-biopython))))))
+ (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE"))))
(define-public python2-biopython
- (let ((base (package-with-python2 (strip-python2-variant python-biopython))))
- (package
- (inherit base)
- (native-inputs `(("python2-setuptools" ,python2-setuptools)
- ,@(package-native-inputs base))))))
+ (package-with-python2 python-biopython))
;; An outdated version of biopython is required for seqmagick, see
;; https://github.com/fhcrc/seqmagick/issues/59
@@ -1339,8 +1331,7 @@ 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
@@ -1404,7 +1395,6 @@ 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)
@@ -1430,7 +1420,6 @@ also includes an interface for tabix.")
(sha256
(base32
"1q8wnj2kga9nz1lwc4w7qv52smfm536hp6mc8w6s53lhyj0mpi22"))))
- (properties `((python2-variant . ,(delay python2-twobitreader))))
(build-system python-build-system)
(arguments
'(;; Tests are not distributed in the PyPi release.
@@ -1447,11 +1436,7 @@ UCSC genome browser.")
(license license:artistic2.0)))
(define-public python2-twobitreader
- (let ((base (package-with-python2 (strip-python2-variant python-twobitreader))))
- (package
- (inherit base)
- (native-inputs `(("python2-setuptools" ,python2-setuptools)
- ,@(package-native-inputs base))))))
+ (package-with-python2 python-twobitreader))
(define-public python-plastid
(package
@@ -1463,7 +1448,6 @@ UCSC genome browser.")
(sha256
(base32
"1sqkz5d3b9kf688mp7k771c87ins42j7j0whmkb49cb3fsg8s8lj"))))
- (properties `((python2-variant . ,(delay python2-plastid))))
(build-system python-build-system)
(arguments
;; Some test files are not included.
@@ -1488,12 +1472,7 @@ high-throughput sequencing data – with an emphasis on simplicity.")
(license license:bsd-3)))
(define-public python2-plastid
- (let ((base (package-with-python2 (strip-python2-variant python-plastid))))
- (package
- (inherit base)
- ;; setuptools is required at runtime
- (propagated-inputs `(("python2-setuptools" ,python2-setuptools)
- ,@(package-propagated-inputs base))))))
+ (package-with-python2 python-plastid))
(define-public cd-hit
(package
@@ -1580,9 +1559,8 @@ 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
@@ -1755,8 +1733,7 @@ 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
@@ -1854,8 +1831,7 @@ 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
@@ -1945,10 +1921,7 @@ accessing bigWig files.")
(license license:expat)))
(define-public python2-pybigwig
- (let ((pybigwig (package-with-python2 python-pybigwig)))
- (package (inherit pybigwig)
- (native-inputs
- `(("python-setuptools" ,python2-setuptools))))))
+ (package-with-python2 python-pybigwig))
(define-public python-dendropy
(package
@@ -1997,8 +1970,7 @@ 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))))))
@@ -2026,9 +1998,8 @@ 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
@@ -2683,8 +2654,7 @@ 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
@@ -2810,8 +2780,6 @@ HMMs).")
`(("python-numpy" ,python2-numpy)))
(inputs
`(("python-pysam" ,python2-pysam)))
- (native-inputs
- `(("python-setuptools" ,python2-setuptools)))
(home-page "http://www-huber.embl.de/users/anders/HTSeq/")
(synopsis "Analysing high-throughput sequencing data with Python")
(description
@@ -2932,8 +2900,7 @@ 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
@@ -3090,8 +3057,6 @@ data.")
#:tests? #f)) ; no test target
(inputs
`(("python-numpy" ,python2-numpy)))
- (native-inputs
- `(("python-setuptools" ,python2-setuptools)))
(home-page "http://github.com/taoliu/MACS/")
(synopsis "Model based analysis for ChIP-Seq data")
(description
@@ -3423,9 +3388,8 @@ 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
@@ -3472,6 +3436,45 @@ program for nucleotide and protein sequences.")
;; License information found in 'muscle -h' and usage.cpp.
(license license:public-domain)))
+(define-public newick-utils
+ ;; There are no recent releases so we package from git.
+ (let ((commit "da121155a977197cab9fbb15953ca1b40b11eb87"))
+ (package
+ (name "newick-utils")
+ (version (string-append "1.6-1." (string-take commit 8)))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/tjunier/newick_utils.git")
+ (commit commit)))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'autoconf
+ (lambda _ (zero? (system* "autoreconf" "-vif")))))))
+ (inputs
+ ;; XXX: TODO: Enable Lua and Guile bindings.
+ ;; https://github.com/tjunier/newick_utils/issues/13
+ `(("libxml2" ,libxml2)
+ ("flex" ,flex)
+ ("bison" ,bison)))
+ (native-inputs
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("libtool" ,libtool)))
+ (synopsis "Programs for working with newick format phylogenetic trees")
+ (description
+ "Newick-utils is a suite of utilities for processing phylogenetic trees
+in Newick format. Functions include re-rooting, extracting subtrees,
+trimming, pruning, condensing, drawing (ASCII graphics or SVG).")
+ (home-page "https://github.com/tjunier/newick_utils")
+ (license license:bsd-3))))
+
(define-public orfm
(package
(name "orfm")
@@ -3509,18 +3512,15 @@ interrupted by stop codons. OrfM finds and prints these ORFs.")
"1kjmv891d6qbpp4shhhvkl02ff4q5xlpnls2513sm2cjcrs52f1i"))))
(build-system python-build-system)
(arguments `(#:python ,python-2)) ; pbcore requires Python 2.7
- (inputs
+ (propagated-inputs
`(("python-cython" ,python2-cython)
("python-numpy" ,python2-numpy)
("python-pysam" ,python2-pysam)
("python-h5py" ,python2-h5py)))
(native-inputs
- `(("python-docutils" ,python2-docutils)
- ("python-nose" ,python2-nose)
- ("python-setuptools" ,python2-setuptools)
- ("python-sphinx" ,python2-sphinx)))
- (propagated-inputs
- `(("python-pyxb" ,python2-pyxb)))
+ `(("python-nose" ,python2-nose)
+ ("python-sphinx" ,python2-sphinx)
+ ("python-pyxb" ,python2-pyxb)))
(home-page "http://pacificbiosciences.github.io/pbcore/")
(synopsis "Library for reading and writing PacBio data files")
(description
@@ -3543,18 +3543,7 @@ files and writing bioinformatics applications.")
"1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j"))))
(build-system python-build-system)
(arguments
- `(#:python ,python-2 ; requires Python 2.7
- #:phases
- (modify-phases %standard-phases
- (add-after
- 'install 'remove-bin-directory
- (lambda* (#:key outputs #:allow-other-keys)
- ;; The "bin" directory only contains wrappers for running
- ;; the module tests. They are not needed after the
- ;; "check" phase.
- (delete-file-recursively
- (string-append (assoc-ref outputs "out") "/bin"))
- #t)))))
+ `(#:python ,python-2)) ; requires Python 2.7
(propagated-inputs
`(("python-scipy" ,python2-scipy)
("python-numpy" ,python2-numpy)
@@ -3563,8 +3552,7 @@ 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")
@@ -3598,11 +3586,6 @@ the phenotype as it models the data.")
(build-system python-build-system)
(arguments
`(#:python ,python-2
- ;; With standard flags, the install phase attempts to create a zip'd
- ;; egg file, and fails with an error: 'ZIP does not support timestamps
- ;; before 1980'
- #:configure-flags '("--single-version-externally-managed"
- "--record=pbtranscript-tofu.txt")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'enter-directory
@@ -3626,8 +3609,7 @@ 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
@@ -3693,6 +3675,58 @@ for sequences to be aligned and then, simultaneously with the alignment,
predicts the locations of structural units in the sequences.")
(license license:gpl2+)))
+(define-public proteinortho
+ (package
+ (name "proteinortho")
+ (version "5.15")
+ (source
+ (origin
+ (method url-fetch)
+ (uri
+ (string-append
+ "http://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v"
+ version "_src.tar.gz"))
+ (sha256
+ (base32
+ "05wacnnbx56avpcwhzlcf6b7s77swcpv3qnwz5sh1z54i51gg2ki"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:test-target "test"
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'configure
+ ;; There is no configure script, so we modify the Makefile directly.
+ (lambda* (#:key outputs #:allow-other-keys)
+ (substitute* "Makefile"
+ (("INSTALLDIR=.*")
+ (string-append
+ "INSTALLDIR=" (assoc-ref outputs "out") "/bin\n")))
+ #t))
+ (add-before 'install 'make-install-directory
+ ;; The install directory is not created during 'make install'.
+ (lambda* (#:key outputs #:allow-other-keys)
+ (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
+ #t))
+ (add-after 'install 'wrap-programs
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((path (getenv "PATH"))
+ (out (assoc-ref outputs "out"))
+ (binary (string-append out "/bin/proteinortho5.pl")))
+ (wrap-program binary `("PATH" ":" prefix (,path))))
+ #t)))))
+ (inputs
+ `(("perl" ,perl)
+ ("python" ,python-2)
+ ("blast+" ,blast+)))
+ (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho")
+ (synopsis "Detect orthologous genes across species")
+ (description
+ "Proteinortho is a tool to detect orthologous genes across different
+species. For doing so, it compares similarities of given gene sequences and
+clusters them to find significant groups. The algorithm was designed to handle
+large-scale data and can be applied to hundreds of species at once.")
+ (license license:gpl2+)))
+
(define-public pyicoteo
(package
(name "pyicoteo")
@@ -3765,7 +3799,7 @@ partial genes, and identifies translation initiation sites.")
(define-public roary
(package
(name "roary")
- (version "3.6.8")
+ (version "3.7.0")
(source
(origin
(method url-fetch)
@@ -3774,7 +3808,7 @@ partial genes, and identifies translation initiation sites.")
version ".tar.gz"))
(sha256
(base32
- "0g0pzcv8y7n2w8q7c9q0a7s2ghkwci6w8smg9mjw4agad5cd7yaw"))))
+ "0x2hpb3nfsc6x2nq1788w0fhqfzc7cn2dp4xwyva9m3k6xlz0m43"))))
(build-system perl-build-system)
(arguments
`(#:phases
@@ -4024,7 +4058,6 @@ BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.")
`(("python-cython" ,python2-cython)
("python-pysam" ,python2-pysam)
("python-numpy" ,python2-numpy)
- ("python-setuptools" ,python2-setuptools)
("zlib" ,zlib)))
(native-inputs
`(("python-nose" ,python2-nose)))
@@ -4586,11 +4619,7 @@ sequence itself can be retrieved from these databases.")
(license license:bsd-3)))
(define-public python2-screed
- (let ((base (package-with-python2 (strip-python2-variant python-screed))))
- (package
- (inherit base)
- (native-inputs `(("python2-setuptools" ,python2-setuptools)
- ,@(package-native-inputs base))))))
+ (package-with-python2 python-screed))
(define-public sra-tools
(package
@@ -4752,8 +4781,7 @@ 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
@@ -7246,6 +7274,29 @@ two-dimensional genome scans.")
libraries for systems that do not have these available via other means.")
(license license:artistic2.0)))
+(define-public r-r4rna
+ (package
+ (name "r-r4rna")
+ (version "0.1.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "http://www.e-rna.org/r-chie/files/R4RNA_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1p0i78wh76jfgmn9jphbwwaz6yy6pipzfg08xs54cxavxg2j81p5"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-optparse" ,r-optparse)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (home-page "http://www.e-rna.org/r-chie/index.cgi")
+ (synopsis "Analysis framework for RNA secondary structure")
+ (description
+ "The R4RNA package aims to be a general framework for the analysis of RNA
+secondary structure and comparative analysis in R.")
+ (license license:gpl3+)))
+
(define-public r-rhtslib
(package
(name "r-rhtslib")
@@ -7426,6 +7477,141 @@ characterization and visualization of a wide range of mutational patterns
in SNV base substitution data.")
(license license:expat)))
+(define-public r-wgcna
+ (package
+ (name "r-wgcna")
+ (version "1.51")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "WGCNA" version))
+ (sha256
+ (base32
+ "0hzvnhw76vwg8bl8x368f0c5szpwb8323bmrb3bir93i5bmfjsxx"))))
+ (properties `((upstream-name . "WGCNA")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-doparallel" ,r-doparallel)
+ ("r-dynamictreecut" ,r-dynamictreecut)
+ ("r-fastcluster" ,r-fastcluster)
+ ("r-foreach" ,r-foreach)
+ ("r-go-db" ,r-go-db)
+ ("r-hmisc" ,r-hmisc)
+ ("r-impute" ,r-impute)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-preprocesscore" ,r-preprocesscore)))
+ (home-page
+ "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
+ (synopsis "Weighted correlation network analysis")
+ (description
+ "This package provides functions necessary to perform Weighted
+Correlation Network Analysis on high-dimensional data. It includes functions
+for rudimentary data cleaning, construction and summarization of correlation
+networks, module identification and functions for relating both variables and
+modules to sample traits. It also includes a number of utility functions for
+data manipulation and visualization.")
+ (license license:gpl2+)))
+
+(define-public r-chipkernels
+ (let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372")
+ (revision "1"))
+ (package
+ (name "r-chipkernels")
+ (version (string-append "1.1-" revision "." (string-take commit 9)))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ManuSetty/ChIPKernels.git")
+ (commit commit)))
+ (file-name (string-append name "-" version))
+ (sha256
+ (base32
+ "14bj5qhjm1hsm9ay561nfbqi9wxsa7y487df2idsaaf6z10nw4v0"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-iranges" ,r-iranges)
+ ("r-xvector" ,r-xvector)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-gtools" ,r-gtools)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-sfsmisc" ,r-sfsmisc)
+ ("r-kernlab" ,r-kernlab)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-biocgenerics" ,r-biocgenerics)))
+ (home-page "https://github.com/ManuSetty/ChIPKernels")
+ (synopsis "Build string kernels for DNA Sequence analysis")
+ (description "ChIPKernels is an R package for building different string
+kernels used for DNA Sequence analysis. A dictionary of the desired kernel
+must be built and this dictionary can be used for determining kernels for DNA
+Sequences.")
+ (license license:gpl2+))))
+
+(define-public r-seqgl
+ (package
+ (name "r-seqgl")
+ (version "1.1.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/ManuSetty/SeqGL/"
+ "archive/" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0pnk1p3sci5yipyc8xnb6jbmydpl80fld927xgnbcv104hy8h8yh"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-chipkernels" ,r-chipkernels)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-spams" ,r-spams)
+ ("r-wgcna" ,r-wgcna)
+ ("r-fastcluster" ,r-fastcluster)))
+ (home-page "https://github.com/ManuSetty/SeqGL")
+ (synopsis "Group lasso for Dnase/ChIP-seq data")
+ (description "SeqGL is a group lasso based algorithm to extract
+transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles.
+This package presents a method which uses group lasso to discriminate between
+bound and non bound genomic regions to accurately identify transcription
+factors bound at the specific regions.")
+ (license license:gpl2+)))
+
+(define-public r-gkmsvm
+ (package
+ (name "r-gkmsvm")
+ (version "0.71.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "gkmSVM" version))
+ (sha256
+ (base32
+ "1zpxgxmf2nd5j5wn00ps6kfxr8wxh7d1swr1rr4spq7sj5z5z0k0"))))
+ (properties `((upstream-name . "gkmSVM")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-kernlab" ,r-kernlab)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rocr" ,r-rocr)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-seqinr" ,r-seqinr)))
+ (home-page "http://cran.r-project.org/web/packages/gkmSVM")
+ (synopsis "Gapped-kmer support vector machine")
+ (description
+ "This R package provides tools for training gapped-kmer SVM classifiers
+for DNA and protein sequences. This package supports several sequence
+kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
+ (license license:gpl2+)))
+
(define-public emboss
(package
(name "emboss")
@@ -7615,19 +7801,7 @@ may optionally be provided to further inform the peak-calling process.")
(build-system python-build-system)
(arguments
`(#:python ,python-2 ; python2 only
- #:tests? #f ; no tests included
- #:phases
- (modify-phases %standard-phases
- ;; When setuptools is used a ".egg" archive is generated and
- ;; installed. This makes it hard to actually run PePr. This issue
- ;; has been reported upstream:
- ;; https://github.com/shawnzhangyx/PePr/issues/9
- (add-after 'unpack 'disable-egg-generation
- (lambda _
- (substitute* "setup.py"
- (("from setuptools import setup")
- "from distutils.core import setup"))
- #t)))))
+ #:tests? #f)) ; no tests included
(propagated-inputs
`(("python2-numpy" ,python2-numpy)
("python2-scipy" ,python2-scipy)
@@ -7689,8 +7863,6 @@ replacement for strverscmp.")
("python-click" ,python-click)
("python-matplotlib" ,python-matplotlib)
("python-numpy" ,python-numpy)))
- (native-inputs
- `(("python-setuptools" ,python-setuptools)))
(home-page "http://multiqc.info")
(synopsis "Aggregate bioinformatics analysis reports")
(description