diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 254 |
1 files changed, 252 insertions, 2 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 959a7ac2fd..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) @@ -3435,6 +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") @@ -3635,6 +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") @@ -3707,7 +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) @@ -3716,7 +3808,7 @@ partial genes, and identifies translation initiation sites.") version ".tar.gz")) (sha256 (base32 - "0g0pzcv8y7n2w8q7c9q0a7s2ghkwci6w8smg9mjw4agad5cd7yaw")))) + "0x2hpb3nfsc6x2nq1788w0fhqfzc7cn2dp4xwyva9m3k6xlz0m43")))) (build-system perl-build-system) (arguments `(#:phases @@ -7182,6 +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") @@ -7362,6 +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") |