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-rw-r--r--gnu/packages/bioinformatics.scm179
1 files changed, 121 insertions, 58 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6a90aa9456..04ed769cd8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3926,6 +3926,34 @@ clusters.")
(home-page "https://sourceforge.net/projects/pardre/")
(license license:gpl3+)))
+(define-public ruby-bio-kseq
+ (package
+ (name "ruby-bio-kseq")
+ (version "0.0.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (rubygems-uri "bio-kseq" version))
+ (sha256
+ (base32
+ "1xyaha46khb5jc6wzkbf7040jagac49jbimn0vcrzid0j8jdikrz"))))
+ (build-system ruby-build-system)
+ (arguments
+ `(#:test-target "spec"))
+ (native-inputs
+ `(("bundler" ,bundler)
+ ("ruby-rspec" ,ruby-rspec)
+ ("ruby-rake-compiler" ,ruby-rake-compiler)))
+ (inputs
+ `(("zlib" ,zlib)))
+ (synopsis "Ruby bindings for the kseq.h FASTA/Q parser")
+ (description
+ "@code{Bio::Kseq} provides ruby bindings to the @code{kseq.h} FASTA and
+FASTQ parsing code. It provides a fast iterator over sequences and their
+quality scores.")
+ (home-page "https://github.com/gusevfe/bio-kseq")
+ (license license:expat)))
+
(define-public bio-locus
(package
(name "bio-locus")
@@ -4991,6 +5019,38 @@ by UCSC (hg19, February 2009) and stored in Biostrings objects.")
provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
(license license:artistic2.0)))
+(define-public r-bsgenome-mmusculus-ucsc-mm10
+ (package
+ (name "r-bsgenome-mmusculus-ucsc-mm10")
+ (version "1.4.0")
+ (source (origin
+ (method url-fetch)
+ ;; We cannot use bioconductor-uri here because this tarball is
+ ;; located under "data/annotation/" instead of "bioc/".
+ (uri (string-append "http://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "BSgenome.Mmusculus.UCSC.mm10_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
+ (properties
+ `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
+ (build-system r-build-system)
+ ;; As this package provides little more than a very large data file it
+ ;; doesn't make sense to build substitutes.
+ (arguments `(#:substitutable? #f))
+ (propagated-inputs
+ `(("r-bsgenome" ,r-bsgenome)))
+ (home-page
+ "http://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
+ (synopsis "Full genome sequences for Mouse")
+ (description
+ "This package provides full genome sequences for Mus
+musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
+in Biostrings objects.")
+ (license license:artistic2.0)))
+
(define-public r-bsgenome-celegans-ucsc-ce6
(package
(name "r-bsgenome-celegans-ucsc-ce6")
@@ -5127,68 +5187,71 @@ libraries for systems that do not have these available via other means.")
(license license:artistic2.0)))
(define-public piranha
- (package
- (name "piranha")
- (version "1.1.3")
- (source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/smithlabcode/piranha"
- "/archive/svn/tags/piranha-"
- version ".tar.gz"))
- (sha256
- (base32
- "1lczxff01n4139w7xwqamlb36g9hgrcy93gh03nqszhwb8ivsrqd"))))
- (build-system gnu-build-system)
- (arguments
- `(#:test-target "test"
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'copy-smithlab-cpp
- (lambda* (#:key inputs #:allow-other-keys)
- (mkdir "src/smithlab_cpp")
- (for-each (lambda (file)
- (install-file file "./src/smithlab_cpp/"))
- (find-files (assoc-ref inputs "smithlab-cpp")))
- #t))
- (add-after 'install 'install-to-store
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (bin (string-append out "/bin")))
- (mkdir-p bin)
+ ;; There is no release tarball for the latest version. The latest commit is
+ ;; older than one year at the time of this writing.
+ (let ((revision "1")
+ (commit "0466d364b71117d01e4471b74c514436cc281233"))
+ (package
+ (name "piranha")
+ (version (string-append "1.2.1-" revision "." (string-take commit 9)))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/smithlabcode/piranha.git")
+ (commit commit)))
+ (sha256
+ (base32
+ "117dc0zf20c61jam69sk4abl57ah6yi6i7qra7d7y5zrbgk12q5n"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:test-target "test"
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'copy-smithlab-cpp
+ (lambda* (#:key inputs #:allow-other-keys)
(for-each (lambda (file)
- (install-file file bin))
- (find-files "bin" ".*")))
- #t)))
- #:configure-flags
- (list (string-append "--with-bam_tools_headers="
- (assoc-ref %build-inputs "bamtools") "/include/bamtools")
- (string-append "--with-bam_tools_library="
- (assoc-ref %build-inputs "bamtools") "/lib/bamtools"))))
- (inputs
- `(("bamtools" ,bamtools)
- ("samtools" ,samtools-0.1)
- ("gsl" ,gsl)
- ("smithlab-cpp"
- ,(let ((commit "3723e2db438c51501d0423429ff396c3035ba46a"))
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/smithlabcode/smithlab_cpp.git")
- (commit commit)))
- (file-name (string-append "smithlab_cpp-" commit "-checkout"))
- (sha256
- (base32
- "0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g")))))))
- (native-inputs
- `(("python" ,python-2)))
- (home-page "https://github.com/smithlabcode/piranha")
- (synopsis "Peak-caller for CLIP-seq and RIP-seq data")
- (description
- "Piranha is a peak-caller for genomic data produced by CLIP-seq and
+ (install-file file "./src/smithlab_cpp/"))
+ (find-files (assoc-ref inputs "smithlab-cpp")))
+ #t))
+ (add-after 'install 'install-to-store
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin")))
+ (mkdir-p bin)
+ (for-each (lambda (file)
+ (install-file file bin))
+ (find-files "bin" ".*")))
+ #t)))
+ #:configure-flags
+ (list (string-append "--with-bam_tools_headers="
+ (assoc-ref %build-inputs "bamtools") "/include/bamtools")
+ (string-append "--with-bam_tools_library="
+ (assoc-ref %build-inputs "bamtools") "/lib/bamtools"))))
+ (inputs
+ `(("bamtools" ,bamtools)
+ ("samtools" ,samtools-0.1)
+ ("gsl" ,gsl)
+ ("smithlab-cpp"
+ ,(let ((commit "3723e2db438c51501d0423429ff396c3035ba46a"))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/smithlabcode/smithlab_cpp.git")
+ (commit commit)))
+ (file-name (string-append "smithlab_cpp-" commit "-checkout"))
+ (sha256
+ (base32
+ "0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g")))))))
+ (native-inputs
+ `(("python" ,python-2)))
+ (home-page "https://github.com/smithlabcode/piranha")
+ (synopsis "Peak-caller for CLIP-seq and RIP-seq data")
+ (description
+ "Piranha is a peak-caller for genomic data produced by CLIP-seq and
RIP-seq experiments. It takes input in BED or BAM format and identifies
regions of statistically significant read enrichment. Additional covariates
may optionally be provided to further inform the peak-calling process.")
- (license license:gpl3+)))
+ (license license:gpl3+))))
(define-public pepr
(package