Merge branch 'master' into python-build-system

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")