diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 313 |
1 files changed, 311 insertions, 2 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a5c28afc6e..b47f136935 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -85,6 +85,7 @@ #:use-module (gnu packages ruby) #:use-module (gnu packages serialization) #:use-module (gnu packages statistics) + #:use-module (gnu packages swig) #:use-module (gnu packages tbb) #:use-module (gnu packages tex) #:use-module (gnu packages texinfo) @@ -2093,7 +2094,7 @@ identify enrichments with functional annotations of the genome.") (define-public diamond (package (name "diamond") - (version "0.9.3") + (version "0.9.6") (source (origin (method url-fetch) (uri (string-append @@ -2102,7 +2103,7 @@ identify enrichments with functional annotations of the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1fs5ilvda50vfdg9wll35w8hcpq3jlkp8q2kim4llkwljkj8bls3")))) + "1y8a10b695pvgn7kk2s87jdwbdf7iszpnr6139pw8ina1ajs4w8y")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target @@ -9223,3 +9224,311 @@ working with SAM and BAM files. Current parallelised functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth.") (license license:gpl2+))) + +(define-public ritornello + (package + (name "ritornello") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/KlugerLab/" + "Ritornello/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "02nik86gq9ljjriv6pamwlmqnfky3ads1fpklx6mc3hx6k40pg38")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are no tests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-samtools-references + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("src/SamStream.h" + "src/BufferedGenomeReader.h") + (("<sam.h>") "<samtools/sam.h>")) + #t)) + (delete 'configure) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin/"))) + (mkdir-p bin) + (install-file "bin/Ritornello" bin) + #t)))))) + (inputs + `(("samtools" ,samtools-0.1) + ("fftw" ,fftw) + ("boost" ,boost) + ("zlib" ,zlib))) + (home-page "https://github.com/KlugerLab/Ritornello") + (synopsis "Control-free peak caller for ChIP-seq data") + (description "Ritornello is a ChIP-seq peak calling algorithm based on +signal processing that can accurately call binding events without the need to +do a pair total DNA input or IgG control sample. It has been tested for use +with narrow binding events such as transcription factor ChIP-seq.") + (license license:gpl3+))) + +(define-public trim-galore + (package + (name "trim-galore") + (version "0.4.2") + (source + (origin + (method url-fetch) + (uri (string-append "http://www.bioinformatics.babraham.ac.uk/" + "projects/trim_galore/trim_galore_v" + version ".zip")) + (sha256 + (base32 + "0b9qdxi4521gsrjvbhgky8g7kry9b5nx3byzaxkgxz7p4k8bn1mn")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no tests + #:phases + (modify-phases %standard-phases + ;; The archive contains plain files. + (replace 'unpack + (lambda* (#:key source #:allow-other-keys) + (zero? (system* "unzip" source)))) + (delete 'configure) + (delete 'build) + (add-after 'unpack 'hardcode-tool-references + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "trim_galore" + (("\\$path_to_cutadapt = 'cutadapt'") + (string-append "$path_to_cutadapt = '" + (assoc-ref inputs "cutadapt") + "/bin/cutadapt'")) + (("\\| gzip") + (string-append "| " + (assoc-ref inputs "gzip") + "/bin/gzip")) + (("\"gunzip") + (string-append "\"" + (assoc-ref inputs "gzip") + "/bin/gunzip"))) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") + "/bin"))) + (mkdir-p bin) + (install-file "trim_galore" bin) + #t)))))) + (inputs + `(("gzip" ,gzip) + ("perl" ,perl) + ("cutadapt" ,cutadapt))) + (native-inputs + `(("unzip" ,unzip))) + (home-page "http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/") + (synopsis "Wrapper around Cutadapt and FastQC") + (description "Trim Galore! is a wrapper script to automate quality and +adapter trimming as well as quality control, with some added functionality to +remove biased methylation positions for RRBS sequence files.") + (license license:gpl3+))) + +(define-public gess + (package + (name "gess") + (version "1.0") + (source (origin + (method url-fetch) + (uri (string-append "http://compbio.uthscsa.edu/" + "GESS_Web/files/" + "gess-" version ".src.tar.gz")) + (sha256 + (base32 + "0hyk403kxscclzfs24pvdgiv0wm03kjcziqdrp5w46cb049gz0d7")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no tests + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((python (assoc-ref inputs "python")) + (out (assoc-ref outputs "out")) + (bin (string-append out "/bin/")) + (target (string-append + out "/lib/python2.7/site-packages/gess/"))) + (mkdir-p target) + (copy-recursively "." target) + ;; Make GESS.py executable + (chmod (string-append target "GESS.py") #o555) + ;; Add Python shebang to the top and make Matplotlib + ;; usable. + (substitute* (string-append target "GESS.py") + (("\"\"\"Description:" line) + (string-append "#!" (which "python") " +import matplotlib +matplotlib.use('Agg') +" line))) + ;; Make sure GESS has all modules in its path + (wrap-program (string-append target "GESS.py") + `("PYTHONPATH" ":" prefix (,target ,(getenv "PYTHONPATH")))) + (mkdir-p bin) + (symlink (string-append target "GESS.py") + (string-append bin "GESS.py")) + #t)))))) + (inputs + `(("python" ,python-2) + ("python2-pysam" ,python2-pysam) + ("python2-scipy" ,python2-scipy) + ("python2-numpy" ,python2-numpy) + ("python2-networkx" ,python2-networkx) + ("python2-biopython" ,python2-biopython))) + (home-page "http://compbio.uthscsa.edu/GESS_Web/") + (synopsis "Detect exon-skipping events from raw RNA-seq data") + (description + "GESS is an implementation of a novel computational method to detect de +novo exon-skipping events directly from raw RNA-seq data without the prior +knowledge of gene annotation information. GESS stands for the graph-based +exon-skipping scanner detection scheme.") + (license license:bsd-3))) + +(define-public phylip + (package + (name "phylip") + (version "3.696") + (source + (origin + (method url-fetch) + (uri (string-append "http://evolution.gs.washington.edu/phylip/" + "download/phylip-" version ".tar.gz")) + (sha256 + (base32 + "01jar1rayhr2gba2pgbw49m56rc5z4p5wn3ds0m188hrlln4a2nd")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no check target + #:make-flags (list "-f" "Makefile.unx" "install") + #:parallel-build? #f ; not supported + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'enter-dir + (lambda _ (chdir "src") #t)) + (delete 'configure) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((target (string-append (assoc-ref outputs "out") + "/bin"))) + (mkdir-p target) + (for-each (lambda (file) + (install-file file target)) + (find-files "../exe" ".*"))) + #t))))) + (home-page "http://evolution.genetics.washington.edu/phylip/") + (synopsis "Tools for inferring phylogenies") + (description "PHYLIP (the PHYLogeny Inference Package) is a package of +programs for inferring phylogenies (evolutionary trees).") + (license license:bsd-2))) + +(define-public imp + (package + (name "imp") + (version "2.6.2") + (source + (origin + (method url-fetch) + (uri (string-append "https://integrativemodeling.org/" + version "/download/imp-" version ".tar.gz")) + (sha256 + (base32 + "0lxqx7vh79d771svr611dkilp6sn30qrbw8zvscbrm37v38d2j6h")))) + (build-system cmake-build-system) + (arguments + `(;; FIXME: Some tests fail because they produce warnings, others fail + ;; because the PYTHONPATH does not include the modeller's directory. + #:tests? #f + ;; Do not place libraries in an architecture-specific directory. + #:configure-flags + (list "-DCMAKE_INSTALL_LIBDIR=lib"))) + (inputs + `(("boost" ,boost) + ("gsl" ,gsl) + ("swig" ,swig) + ("hdf5" ,hdf5) + ("fftw" ,fftw) + ("python" ,python-2))) + (propagated-inputs + `(("python2-numpy" ,python2-numpy) + ("python2-scipy" ,python2-scipy) + ("python2-pandas" ,python2-pandas) + ("python2-scikit-learn" ,python2-scikit-learn) + ("python2-networkx" ,python2-networkx))) + (home-page "https://integrativemodeling.org") + (synopsis "Integrative modeling platform") + (description "IMP's broad goal is to contribute to a comprehensive +structural characterization of biomolecules ranging in size and complexity +from small peptides to large macromolecular assemblies, by integrating data +from diverse biochemical and biophysical experiments. IMP provides a C++ and +Python toolbox for solving complex modeling problems, and a number of +applications for tackling some common problems in a user-friendly way.") + ;; IMP is largely available under the GNU Lesser GPL; see the file + ;; COPYING.LGPL for the full text of this license. Some IMP modules are + ;; available under the GNU GPL (see the file COPYING.GPL). + (license (list license:lgpl2.1+ + license:gpl3+)))) + +(define-public tadbit + (package + (name "tadbit") + (version "0.2") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/3DGenomes/TADbit/" + "archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1cnfqrl4685zar4nnw94j94nhvl2h29jm448nadqi1h05z6fdk4f")))) + (build-system python-build-system) + (arguments + `(;; Tests are included and must be run after installation, but + ;; they are incomplete and thus cannot be run. + #:tests? #f + #:python ,python-2 + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-problems-with-setup.py + (lambda* (#:key outputs #:allow-other-keys) + ;; setup.py opens these files for writing + (chmod "_pytadbit/_version.py" #o664) + (chmod "README.rst" #o664) + + ;; Don't attempt to install the bash completions to + ;; the home directory. + (rename-file "extras/.bash_completion" + "extras/tadbit") + (substitute* "setup.py" + (("\\(path.expanduser\\('~'\\)") + (string-append "(\"" + (assoc-ref outputs "out") + "/etc/bash_completion.d\"")) + (("extras/\\.bash_completion") + "extras/tadbit")) + #t))))) + (inputs + ;; TODO: add Chimera for visualization + `(("imp" ,imp) + ("mcl" ,mcl) + ("python2-scipy" ,python2-scipy) + ("python2-numpy" ,python2-numpy) + ("python2-matplotlib" ,python2-matplotlib) + ("python2-pysam" ,python2-pysam))) + (home-page "http://3dgenomes.github.io/TADbit/") + (synopsis "Analyze, model, and explore 3C-based data") + (description + "TADbit is a complete Python library to deal with all steps to analyze, +model, and explore 3C-based data. With TADbit the user can map FASTQ files to +obtain raw interaction binned matrices (Hi-C like matrices), normalize and +correct interaction matrices, identify adn compare the so-called +@dfn{Topologically Associating Domains} (TADs), build 3D models from the +interaction matrices, and finally, extract structural properties from the +models. TADbit is complemented by TADkit for visualizing 3D models.") + (license license:gpl3+))) |