From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:42606) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1erAOO-0003cQ-8J for guix-patches@gnu.org; Wed, 28 Feb 2018 17:40:10 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1erAOM-0005S3-2V for guix-patches@gnu.org; Wed, 28 Feb 2018 17:40:08 -0500 Received: from debbugs.gnu.org ([208.118.235.43]:58369) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1erAOL-0005RE-PX for guix-patches@gnu.org; Wed, 28 Feb 2018 17:40:05 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1erAOI-0000AL-TW for guix-patches@gnu.org; Wed, 28 Feb 2018 17:40:05 -0500 Subject: [bug#30658] [PATCH 4/4] gnu: Add fastqc. Resent-Message-ID: From: Ricardo Wurmus Date: Wed, 28 Feb 2018 23:38:54 +0100 Message-Id: <20180228223854.31118-4-rekado@elephly.net> In-Reply-To: <20180228223854.31118-1-rekado@elephly.net> References: <20180228223854.31118-1-rekado@elephly.net> List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: 30658@debbugs.gnu.org Cc: Ricardo Wurmus * gnu/packages/bioinformatics.scm (fastqc): New variable. --- gnu/packages/bioinformatics.scm | 79 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 79 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c427a6d03..99fcf34f1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3211,6 +3211,85 @@ VCF.") ("jdk" ,icedtea-8 "jdk") ("jdk-src" ,(car (assoc-ref (package-native-inputs icedtea-8) "jdk-drop"))))))) +(define-public fastqc + (package + (name "fastqc") + (version "0.11.5") + (source + (origin + (method url-fetch) + (uri (string-append "http://www.bioinformatics.babraham.ac.uk/" + "projects/fastqc/fastqc_v" + version "_source.zip")) + (sha256 + (base32 + "18rrlkhcrxvvvlapch4dpj6xc6mpayzys8qfppybi8jrpgx5cc5f")))) + (build-system ant-build-system) + (arguments + `(#:tests? #f ; there are no tests + #:build-target "build" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-dependencies + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "build.xml" + (("jbzip2-0.9.jar") + (string-append (assoc-ref inputs "java-jbzip2") + "/share/java/jbzip2.jar")) + (("sam-1.103.jar") + (string-append (assoc-ref inputs "java-picard-1.113") + "/share/java/sam-1.112.jar")) + (("cisd-jhdf5.jar") + (string-append (assoc-ref inputs "java-cisd-jhdf5") + "/share/java/sis-jhdf5.jar"))) + #t)) + ;; There is no installation target + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (share (string-append out "/share/fastqc/")) + (exe (string-append share "/fastqc"))) + (for-each mkdir-p (list bin share)) + (copy-recursively "bin" share) + (substitute* exe + (("my \\$java_bin = 'java';") + (string-append "my $java_bin = '" + (assoc-ref inputs "java") + "/bin/java';"))) + (chmod exe #o555) + (symlink exe (string-append bin "/fastqc")) + #t)))))) + (inputs + `(("java" ,icedtea) + ("perl" ,perl) ; needed for the wrapper script + ("java-cisd-jhdf5" ,java-cisd-jhdf5) + ("java-picard-1.113" ,java-picard-1.113) + ("java-jbzip2" ,java-jbzip2))) + (native-inputs + `(("unzip" ,unzip))) + (home-page "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/") + (synopsis "Quality control tool for high throughput sequence data") + (description + "FastQC aims to provide a simple way to do some quality control +checks on raw sequence data coming from high throughput sequencing +pipelines. It provides a modular set of analyses which you can use to +give a quick impression of whether your data has any problems of which +you should be aware before doing any further analysis. + +The main functions of FastQC are: + +@itemize +@item Import of data from BAM, SAM or FastQ files (any variant); +@item Providing a quick overview to tell you in which areas there may + be problems; +@item Summary graphs and tables to quickly assess your data; +@item Export of results to an HTML based permanent report; +@item Offline operation to allow automated generation of reports + without running the interactive application. +@end itemize\n") + (license license:gpl3+))) + (define-public htslib (package (name "htslib") -- 2.16.2