From 31a9d653ad37c9f00b601cfe4a95d90c35c09223 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sat, 26 Nov 2016 14:59:30 +1000 Subject: gnu: Add proteinortho. * gnu/packages/bioinformatics.scm (proteinortho): New variable. --- gnu/packages/bioinformatics.scm | 52 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 773b5909b6..308931f3d8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3693,6 +3693,58 @@ (define-public prank 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") -- cgit v1.2.3 From 5e0a0f4226b1f146fe74c8347fc983ef9ac0d271 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sat, 26 Nov 2016 19:00:17 +1000 Subject: gnu: roary: Update to 3.7.0. * gnu/packages/bioinformatics.scm (roary): Update to 3.7.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 308931f3d8..8d2cb93c7c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3817,7 +3817,7 @@ (define-public prodigal (define-public roary (package (name "roary") - (version "3.6.8") + (version "3.7.0") (source (origin (method url-fetch) @@ -3826,7 +3826,7 @@ (define-public roary version ".tar.gz")) (sha256 (base32 - "0g0pzcv8y7n2w8q7c9q0a7s2ghkwci6w8smg9mjw4agad5cd7yaw")))) + "0x2hpb3nfsc6x2nq1788w0fhqfzc7cn2dp4xwyva9m3k6xlz0m43")))) (build-system perl-build-system) (arguments `(#:phases -- cgit v1.2.3 From 9926875572cf2936b7f23fb291328bfa68c038c6 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sun, 27 Nov 2016 13:11:46 +1000 Subject: gnu: Add newick-utils. * gnu/packages/bioinformatics.scm (newick-utils): New variable. --- gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8d2cb93c7c..f04acc0a5c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -50,6 +50,7 @@ (define-module (gnu packages bioinformatics) #: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) @@ -3472,6 +3473,45 @@ (define-public muscle ;; 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") -- cgit v1.2.3 From e619a5c245d76c559ff98b4f5dc070c571d90574 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2016 15:04:18 +0100 Subject: gnu: Add r-r4rna. * gnu/packages/bioinformatics.scm (r-r4rna): New variable. --- gnu/packages/bioinformatics.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f04acc0a5c..0b6fbe5df2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7338,6 +7338,29 @@ (define-public r-zlibbioc 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") -- cgit v1.2.3 From d71605294fff1a12f3145fa4788da1556284c91c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2016 15:15:45 +0100 Subject: gnu: Add r-wgcna. * gnu/packages/bioinformatics.scm (r-wgcna): New variable. --- gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0b6fbe5df2..0b10b1b6e7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7541,6 +7541,42 @@ (define-public r-mutationalpatterns 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 emboss (package (name "emboss") -- cgit v1.2.3 From c827f2028629c43f73aee99600d34fc97fca4208 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2016 15:22:03 +0100 Subject: gnu: Add r-chipkernels. * gnu/packages/bioinformatics.scm (r-chipkernels): New variable. --- gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0b10b1b6e7..73e1d09b89 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7577,6 +7577,42 @@ (define-public r-wgcna 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 emboss (package (name "emboss") -- cgit v1.2.3 From 2d9fb1702fb0d142e83cfbf949f9330981ed9687 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2016 15:24:25 +0100 Subject: gnu: Add r-seqgl. * gnu/packages/bioinformatics.scm (r-seqgl): New variable. --- gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 73e1d09b89..5f63707bf8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7613,6 +7613,36 @@ (define-public r-chipkernels 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 emboss (package (name "emboss") -- cgit v1.2.3 From bd3be46e7fd148eef4b4ba81ee5cd4d159e9c20c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 24 Nov 2016 15:42:22 +0100 Subject: gnu: Add r-gkmsvm. * gnu/packages/bioinformatics.scm (r-gkmsvm): New variable. --- gnu/packages/bioinformatics.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5f63707bf8..4b848535dc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7643,6 +7643,39 @@ (define-public r-seqgl 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") -- cgit v1.2.3