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[bug#30658] [PATCH 4/4] gnu: Add fastqc.
From: |
Ricardo Wurmus |
Subject: |
[bug#30658] [PATCH 4/4] gnu: Add fastqc. |
Date: |
Wed, 28 Feb 2018 23:38:54 +0100 |
* 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:
+
address@hidden
address@hidden Import of data from BAM, SAM or FastQ files (any variant);
address@hidden Providing a quick overview to tell you in which areas there may
+ be problems;
address@hidden Summary graphs and tables to quickly assess your data;
address@hidden Export of results to an HTML based permanent report;
address@hidden Offline operation to allow automated generation of reports
+ without running the interactive application.
address@hidden itemize\n")
+ (license license:gpl3+)))
+
(define-public htslib
(package
(name "htslib")
--
2.16.2