Merge pull request #10 from roelj/master

Added contra and delly.

2 files changed, 425 insertions, 5 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 11a624f..a4d14b0 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -62,6 +62,113 @@
   #:use-module (gnu packages bootstrap)
   #:use-module (srfi srfi-1))
 
+(define-public contra
+  (package
+    (name "contra")
+    (version "2.0.6")
+    (source (origin
+      (method url-fetch)
+      (uri (string-append
+            "mirror://sourceforge/contra-cnv/CONTRA.v" version ".tar.gz"))
+      (sha256
+       (base32
+        "0agpcm2xh5f0i9n9sx1kvln6mzdksddmh11bvzj6bh76yw5pnw91"))))
+    (build-system gnu-build-system)
+    (propagated-inputs
+     `(("python" ,python-2)
+       ("r" ,r)
+       ("r-dnacopy" ,r-dnacopy)
+       ("bedtools" ,bedtools)
+       ("samtools" ,samtools)))
+    (arguments
+     `(#:tests? #f ; There are no tests.
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (delete 'build) ; We can use Guix's BEDtools instead.
+         (replace 'install
+           (lambda _
+             (let* ((out (assoc-ref %outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (doc (string-append out "/share/doc/contra")))
+               (mkdir-p bin)
+               (mkdir-p doc)
+               (and
+                (zero? (system* "cp" "--recursive" "scripts" bin))
+                (zero? (system* "cp" "contra.py" bin))
+                (zero? (system* "cp" "baseline.py" bin))
+                ;; There's only a pre-built PDF available.
+                (zero? (system* "cp" "CONTRA_User_Guide.2.0.pdf" doc)))))))))
+    (home-page "http://contra-cnv.sourceforge.net/")
+    (synopsis "Tool for copy number variation (CNV) detection for targeted
+resequencing data")
+    (description "CONTRA is a tool for copy number variation (CNV) detection
+for targeted resequencing data such as those from whole-exome capture data.
+CONTRA calls copy number gains and losses for each target region with key
+strategies including the use of base-level log-ratios to remove GC-content
+bias, correction for an imbalanced library size effect on log-ratios, and the
+estimation of log-ratio variations via binning and interpolation.  It takes
+standard alignment formats (BAM/SAM) and outputs in variant call format
+(VCF 4.0) for easy integration with other next generation sequencing analysis
+package.")
+    (license license:gpl3+)))
+
+(define boost-delly
+  (package (inherit boost)
+    (name "boost-delly")
+    (version "1.57.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "mirror://sourceforge/boost/boost_"
+                    (string-map (lambda (x) (if (eq? x #\.) #\_ x)) version)
+                    ".tar.bz2"))
+              (sha256
+               (base32
+                "0rs94vdmg34bwwj23fllva6mhrml2i7mvmlb11zyrk1k5818q34i"))))))
+
+(define-public delly
+  (package
+    (name "delly")
+    (version "0.7.2")
+    (source (origin
+      (method url-fetch)
+      (uri (string-append "https://github.com/tobiasrausch/delly/archive/v"
+            version ".tar.gz"))
+      (sha256
+       (base32 "173mmg43dbxqkyq0kiffz63xbmggr2kzd55mwxci9yfh5md1zprn"))
+      (patches (list (search-patch "delly-use-system-libraries.patch")))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("python" ,python-2)))
+    (inputs
+     `(("boost" ,boost-delly) ; Use version 1.57.0 instead.
+       ("htslib" ,htslib)
+       ("zlib" ,zlib)
+       ("bzip2" ,bzip2)))
+    (arguments
+     `(#:tests? #f ; There are no tests to run.
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure) ; There is no configure phase.
+         (replace 'install
+           (lambda _
+             (let ((bin (string-append (assoc-ref %outputs "out") "/bin")))
+               (install-file "src/cov" bin)
+               (install-file "src/delly" bin)
+               (install-file "src/extract" bin)
+               (install-file "src/iover" bin)
+               (install-file "src/stats" bin)))))))
+    (home-page "https://github.com/tobiasrausch/delly")
+    (synopsis "Integrated structural variant prediction method")
+    (description "Delly is an integrated structural variant prediction method
+that can discover and genotype deletions, tandem duplications, inversions and
+translocations at single-nucleotide resolution in short-read massively parallel
+sequencing data.  It uses paired-ends and split-reads to sensitively and
+accurately delineate genomic rearrangements throughout the genome.  Structural
+variants can be visualized using Delly-maze and Delly-suave.")
+    (license license:gpl3)))
+
 (define-public freec
   (package
     (name "control-freec")
@@ -1141,15 +1248,19 @@ manipulations on VCF files.")
       ("python" ,python-2)
       ("perl" ,perl)))
    (arguments
-    `(#:tests? #f
-      #:phases
+    `(#:phases
       (modify-phases %standard-phases
         (delete 'configure) ; There is no configure phase.
+        ;; The build phase needs to run 'make' twice for the reasons described
+        ;; below.
         (replace 'build
           (lambda* (#:key inputs #:allow-other-keys)
-            ;; The first run creates a Makefile.local file.
+            ;; The first run creates a Makefile.local file.  Make will report
+            ;; the failure to find Makefile.local, but we can ignore this error.
             (system* "make" (string-append "SAMTOOLS=" (assoc-ref inputs "samtools")))
-            ;; The second run actually compiles the program.
+            ;; The second run actually compiles the program.  Now Makefile.local
+            ;; is available, and we should treat an exiting make with an error as
+            ;; a true error.
             (zero? (system* "make"))))
         (replace 'install
           (lambda* (#:key outputs #:allow-other-keys)
@@ -1157,7 +1268,17 @@ manipulations on VCF files.")
               (install-file "src/pindel" bin)
               (install-file "src/pindel2vcf" bin)
               (install-file "src/pindel2vcf4tcga" bin)
-              (install-file "src/sam2pindel" bin)))))))
+              (install-file "src/sam2pindel" bin))))
+        ;; There are multiple test targets, so in order to run all
+        ;; tests, we must run the separate make targets.
+        (replace 'check
+          (lambda* (#:key inputs #:allow-other-keys)
+            (and
+             (zero? (system* "make" "acceptance-tests"))
+             (zero? (system* "make" "coverage-tests"))
+             (zero? (system* "make" "cppcheck"))
+             (zero? (system* "make" "functional-tests"))
+             (zero? (system* "make" "regression-tests"))))))))
    (home-page "https://github.com/genome/pindel")
    (synopsis "Structural variants detector for next-gen sequencing data")
    (description "Pindel can detect breakpoints of large deletions, medium sized
diff --git a/gn/packages/java.scm b/gn/packages/java.scm
new file mode 100644
index 0000000..3fce390
--- /dev/null
+++ b/gn/packages/java.scm
@@ -0,0 +1,299 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages java)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix utils)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix svn-download)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix build-system ant)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages autotools)
+  #:use-module (gnu packages bioinformatics)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages gcc)
+  #:use-module (gnu packages java)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages certs)
+  #:use-module (gnu packages zip))
+
+;; ----------------------------------------------------------------------------
+;; WORKING PACKAGES
+;; ----------------------------------------------------------------------------
+
+(define-public xz-java
+  (package
+   (name "xz-java")
+   (version "1.5")
+   (source (origin
+     (method url-fetch)
+     (uri (string-append "http://tukaani.org/xz/"
+                         name "-" version ".zip"))
+     (sha256
+      (base32 "0x6vn9dp9kxk83x2fp3394n95dk8fx9yg8jns9371iqsn0vy8ih1"))))
+   (build-system ant-build-system)
+   (arguments
+    `(#:tests? #f ; There's no test target.
+      #:jdk ,icedtea-7
+      #:phases
+      (modify-phases %standard-phases
+        (replace 'unpack
+          (lambda _
+            (mkdir-p "source")
+            (chdir "source")
+            (zero? (system* "unzip" (assoc-ref %build-inputs "source")))))
+        (replace 'install
+          (lambda _
+            (let ((out (string-append (assoc-ref %outputs "out")
+                                      "/share/java/xz/")))
+              (mkdir-p out)
+              (copy-file "build/jar/xz.jar" (string-append out "/xz-1.5.jar"))))))))
+   (native-inputs
+    `(("unzip" ,unzip)))
+   (home-page "http://tukaani.org/xz/java.html")
+   (synopsis "Implementation of XZ data compression in pure Java")
+   (description "This aims to be a complete implementation of XZ data
+compression in pure Java.  Single-threaded streamed compression and
+decompression and random access decompression have been fully implemented.")
+   (license license:public-domain)))
+
+(define-public jakarta-oro
+  (package
+    (name "jakarta-oro")
+    (version "2.0.8")
+    (source (origin
+      (method url-fetch)
+      (uri (string-append "http://archive.apache.org/dist/jakarta/oro/"
+                          name "-" version ".tar.gz"))
+      (sha256
+       (base32 "0rpmnsskiwmsy8r0sckz5n5dbvh3vkxx8hpm177c754r8xy3qksc"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:tests? #f ; There is no 'check' target
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'install
+           (lambda _
+             (let ((out (string-append (assoc-ref %outputs "out")
+                                       "/share/java/oro/")))
+               (mkdir-p out)
+               (copy-file "jakarta-oro-2.0.8.jar" (string-append out "/oro-2.0.8.jar"))))))
+                ))
+    (home-page "http://jakarta.apache.org/oro/")
+    (synopsis "Set of text-processing Java classes")
+    (description "The Jakarta-ORO Java classes are a set of text-processing
+Java classes that provide Perl5 compatible regular expressions, AWK-like regular
+expressions, glob expressions, and utility classes for performing substitutions,
+splits, filtering filenames, etc.")
+    (license license:asl1.1)))
+
+;; ----------------------------------------------------------------------------
+;; IN PROGRESS
+;; ----------------------------------------------------------------------------
+
+(define-public jsch
+  (package
+    (name "jsch")
+    (version "0.1.53")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://sourceforge.net/jsch/" name "/"
+                                  version "/" name "-" version ".zip"))
+              (sha256
+               (base32 "1729j7khwj6yvkr26fjaf273i3krhz2n1m3mbv5ms4x00qrhrxdn"))))
+    (build-system ant-build-system)
+    (home-page "http://www.jcraft.com/jsch/")
+    (synopsis "JSch is a pure Java implementation of SSH2")
+    (description "JSch is a pure Java implementation of SSH2.  JSch allows you
+to connect to an sshd server and use port forwarding, X11 forwarding, file
+transfer, etc., and you can integrate its functionality into your own Java
+programs.")
+    (license license:bsd-3)))
+
+(define-public commons-vfs
+  (package
+    (name "commons-vfs")
+    (version "2.0")
+    (source (origin
+      (method url-fetch)
+      (uri (string-append
+            "http://mirrors.supportex.net/apache/commons/vfs/source/"
+            name "-" version "-src.tar.gz"))
+      (sha256
+       (base32 "1gkfg9g14kjkh2kf041ssdz9xnw7hpfmdsyrs1bbhyzikwg4s3d9"))))
+    (build-system ant-build-system)
+    (home-page "https://commons.apache.org/proper/commons-vfs/")
+    (synopsis "Commons Virtual File System API for Java")
+    (description "Commons VFS provides a single API for accessing various
+different file systems.  It presents a uniform view of the files from various
+different sources, such as the files on local disk, on an HTTP server, or
+inside a Zip archive. ")
+    (license license:asl2.0)))
+
+(define-public ivy
+;; Ivy tries to download the following packages:
+;; - https://repo1.maven.org/maven2/org/apache/ant/ant/1.7.1/ant-1.7.1.jar               => We have ant-1.9.6
+;; - https://repo1.maven.org/maven2/org/apache/ant/ant-nodeps/1.7.1/ant-nodeps-1.7.1.jar => Probably not needed
+;; - https://repo1.maven.org/maven2/org/apache/ant/ant-trax/1.7.1/ant-trax-1.7.1.jar     => Classes moved to ant.jar
+;; - https://repo1.maven.org/maven2/commons-httpclient/commons-httpclient/3.0/commons-httpclient-3.0.jar
+;; - https://repo1.maven.org/maven2/oro/oro/2.0.8/oro-2.0.8.jar                          => Packaged
+;; - https://repo1.maven.org/maven2/commons-vfs/commons-vfs/1.0/commons-vfs-1.0.jar
+;; - https://repo1.maven.org/maven2/com/jcraft/jsch/0.1.50/jsch-0.1.50.jar
+;; - https://repo1.maven.org/maven2/com/jcraft/jsch.agentproxy/0.0.6/jsch.agentproxy-0.0.6.jar
+;; - https://repo1.maven.org/maven2/com/jcraft/jsch.agentproxy.connector-factory/0.0.6/jsch.agentproxy.connector-factory-0.0.6.jar
+;; - https://repo1.maven.org/maven2/com/jcraft/jsch.agentproxy.jsch/0.0.6/jsch.agentproxy.jsch-0.0.6.jar
+;; - https://repo1.maven.org/maven2/org/bouncycastle/bcpg-jdk14/1.45/bcpg-jdk14-1.45.jar
+;; - https://repo1.maven.org/maven2/org/bouncycastle/bcprov-jdk14/1.45/bcprov-jdk14-1.45.jar
+;; - https://repo1.maven.org/maven2/junit/junit/3.8.2/junit-3.8.2.jar
+;; - https://repo1.maven.org/maven2/commons-lang/commons-lang/2.6/commons-lang-2.6.jar
+;; - https://repo1.maven.org/maven2/org/apache/ant/ant-testutil/1.7.0/ant-testutil-1.7.0.jar
+;; - https://repo1.maven.org/maven2/ant/ant-launcher/1.6.2/ant-launcher-1.6.2.jar
+;; - https://repo1.maven.org/maven2/ant-contrib/ant-contrib/1.0b3/ant-contrib-1.0b3.jar
+;; - https://repo1.maven.org/maven2/xerces/xercesImpl/2.6.2/xercesImpl-2.6.2.jar
+;; - https://repo1.maven.org/maven2/xerces/xmlParserAPIs/2.6.2/xmlParserAPIs-2.6.2.jar
+  (package
+    (name "ivy")
+    (version "2.4.0")
+    (source (origin
+      (method url-fetch)
+      (uri (string-append "http://ftp.nluug.nl/internet/apache/ant/" name "/"
+                          version "/apache-" name "-" version "-src.tar.gz"))
+      (sha256
+       (base32 "1xkfn57g2m7l6y0xdq75x5rnrgk52m9jx2xah70g3ggl8750hbr0"))))
+    (build-system ant-build-system)
+    (inputs
+     `(("nss-certs" ,nss-certs)))
+    (home-page "http://ant.apache.org/ivy/")
+    (synopsis "Dependency manager for Ant")
+    (description "Apache Ivy is a popular dependency manager focusing on
+flexibility and simplicity.")
+    (license license:asl2.0)))
+
+
+;; ----------------------------------------------------------------------------
+;; ON HOLD: WAITING FOR MAVEN PACKAGES
+;; ----------------------------------------------------------------------------
+
+;; TODO: Needs commons-compress
+;; (define-public ant-compress
+;;   (package
+;;     (name "ant-compress")
+;;     (version "1.4")
+;;     (source (origin
+;;               (method url-fetch)
+;;               (uri "https://www.apache.org/dist/ant/antlibs/compress/source/apache-ant-compress-1.4-src.tar.gz"))
+;;             (sha256
+;;              (base32 "17v5i11srmi12ckgrvhlwn0gvapgizs5672x252h143r0ya4c04d")))
+;;       ))
+
+;; TODO: Needs Maven.
+;; (define-public commons-compress
+;;   (package
+;;     (name "apache-commons-compress")
+;;     (version "1.10")
+;;     (source (origin
+;;               (method url-fetch)
+;;               (uri ("http://ftp.tudelft.nl/apache//commons/compress/source/commons-compress-1.10-src.tar.gz")))
+;;             (sha256
+;;              (base32 "06b40k9dmgqkga3qmfpgzq87jf3fkcxnwaiyczclh58yibg19604")))
+;;     ))
+
+;; TODO: Needs Maven.
+;; (define-public jcommander
+;;   (package
+;;     (name "jcommander")
+;;     (version "1.48")
+;;     (source (origin
+;;       (method url-fetch)
+;;       (uri (string-append "https://github.com/cbeust/jcommander/archive/"
+;;                           name "-" version ".tar.gz"))
+;;       (sha256
+;;        (base32 "1qn56hd6sxkfdv9j6pwf8c7ia00n39zry236a6achc87wq2kmfnw"))))
+;;     (build-system ant-build-system)
+;;     (home-page "http://jcommander.org/")
+;;     (synopsis "Java framework for parsing command line parameters")
+;;     (description "JCommander is a very small Java framework that makes it
+;; trivial to parse command line parameters. ")
+;;     (license license:asl2.0)))
+
+;; TODO: Needs Maven.
+;; (define-public maven-remote-resources-plugin
+;;   (package
+;;     (name "maven-remote-resources-plugin")
+;;     (version "1.5")
+;;     (source (origin
+;;       (method svn-fetch)
+;;       (uri (svn-reference
+;;             (url (string-append "http://svn.apache.org/viewvc/maven/plugins/tags/"
+;;                                 name "-" version))
+;;             (revision 1513840)))
+;;       (file-name (string-append name "-" version "-checkout"))
+;;       (sha256
+;;        (base32 "1g0iavyb34kvs3jfrx2hfnr8lr11m39sj852cy7528wva1glfl4i"))))
+;;     (build-system ant-build-system)
+;;     (home-page "https://maven.apache.org/plugins/maven-remote-resources-plugin/")
+;;     (synopsis "")
+;;     (description "")
+;;     (license license:asl2.0)))
+
+;; TODO: Needs Maven.
+;; (define-public junit
+;;   (package
+;;     (name "junit")
+;;     (version "4.12")
+;;     (source (origin
+;;       (method url-fetch)
+;;       (uri (string-append "https://github.com/junit-team/"
+;;                           name "/archive/r" version ".tar.gz"))
+;;       (sha256
+;;        (base32 "1r6ww2y3jpbpqh03r0966xxiz2vs8n72g6n6l0sjs3aspy56v8b1"))))
+;;     (build-system ant-build-system)
+;;     (home-page "http://junit.org/")
+;;     (synopsis "Framework to write repeatable tests")
+;;     (description "JUnit is a simple framework to write repeatable tests.  It is
+;; an instance of the xUnit architecture for unit testing frameworks.")
+;;     (license license:asl2.0)))
+
+(define-public maven
+  (package
+    (name "maven")
+    (version "3.3.9")
+    (source (origin
+      (method url-fetch)
+      (uri (string-append "http://apache.proserve.nl/maven/maven-3/"
+                          version "/source/apache-maven-" version "-src.tar.gz"))
+      (sha256
+       (base32 "1g0iavyb34kvs3jfrx2hfnr8lr11m39sj852cy7528wva1glfl4i"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:make-flags "-Dmaven.home=build/"
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'set-m2-variable
+           (lambda _
+             (setenv "M2_HOME" (string-append (assoc-ref %outputs "out") "/maven-3.3.9")))))))
+    (home-page "https://maven.apache.org/")
+    (synopsis "")
+    (description "Apache Maven is a software project management and
+comprehension tool. Based on the concept of a project object model (POM),
+Maven can manage a project's build, reporting and documentation from a central
+piece of information.")
+    (license license:asl2.0)))