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[bug#30658] [PATCH 0/4] Add FastQC

From: Ricardo Wurmus
Subject: [bug#30658] [PATCH 0/4] Add FastQC
Date: Wed, 28 Feb 2018 23:14:35 +0100

Hi Guix,

this patch adds fastqc, a very popular bioinformatics tool.

This has been in my staging repo for a very long time because it is written in
Java and bundled pre-built third-party jars.  I finally managed to build the
last few dependencies from source.  These java-cisd-* packages were really not
easy to build and you can tell by how complicated they are.

Both java-cisd-base and java-cisd-jhdf5 include native libraries, which I'm
building from the included C sources.  The packages include tests, but unlike
other Java packages these tests are in the form of an application that needs
to be executed.  Hence the extra build phase after "check" to actually run the

FastQC seems to work, but I haven't performed any comprehensive tests yet.

Ricardo Wurmus (4):
  gnu: Add java-cisd-base.
  gnu: Add java-cisd-args4j.
  gnu: Add java-cisd-jhdf5.
  gnu: Add fastqc.

 gnu/packages/bioinformatics.scm |  79 ++++++++
 gnu/packages/java.scm           | 439 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 518 insertions(+)


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