[gentoo-commits] proj/sci:master commit in: sci-biology/fastqc/files/, sci-biology/fastqc/

[gentoo-commits] proj/sci:master commit in: sci-biology/fastqc/files/, sci-biology/fastqc/

[Aisha Tammy]

commit:     727e16a722a057469a4ea348ef4a896c978cd961
Author:     Anton Molyboha <anton.stay.connected <AT> gmail <DOT> com>
AuthorDate: Sat Nov 14 00:07:53 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Sat Nov 14 18:51:15 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=727e16a7

sci-biology/fastqc: correctly install the package.

Based on local testing, the program now works for .fastq files, but does
not work for .fast5 files. This is also not the latest version. However,
this is a step forward from "not working at all". The issues will need
to be solved in the future.

Signed-off-by: Anton Molyboha <anton.stay.connected <AT> gmail.com>
Closes: https://github.com/gentoo/sci/pull/834
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>

 sci-biology/fastqc/fastqc-0.11.3.ebuild | 54 +++++++++++++++------------------
 sci-biology/fastqc/files/00fastqc       |  1 +
 sci-biology/fastqc/metadata.xml         |  4 +++
 3 files changed, 29 insertions(+), 30 deletions(-)

diff --git a/sci-biology/fastqc/fastqc-0.11.3.ebuild b/sci-biology/fastqc/fastqc-0.11.3.ebuild
index f30dd8e2e..4be2ae23b 100644
--- a/sci-biology/fastqc/fastqc-0.11.3.ebuild
+++ b/sci-biology/fastqc/fastqc-0.11.3.ebuild
@@ -1,31 +1,27 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit java-pkg-2 eutils java-ant-2
+inherit java-pkg-2 eutils java-ant-2 prefix
 
 DESCRIPTION="Quality control FASTA/FASTQ sequence files"
-HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
-SRC_URI="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v"${PV}"_source.zip"
+HOMEPAGE="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
+SRC_URI="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v"${PV}"_source.zip"
 
 LICENSE="GPL-3+"
 SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
 
-DEPEND="sci-biology/picard
-	sci-libs/jhdf5
-	>=virtual/jre-1.5:*"
-RDEPEND="${DEPEND}
-	dev-lang/perl
-	>=virtual/jdk-1.5:*
-	dev-java/ant-core"
+RDEPEND="dev-lang/perl"
+DEPEND="${RDEPEND} >=virtual/jdk-1.5:*"
+BDEPEND="app-arch/unzip"
 
 S="${WORKDIR}"/FastQC
 
 src_prepare(){
 	cp "${FILESDIR}"/build.xml . || die
+	default
 }
 
 src_compile(){
@@ -33,22 +29,20 @@ src_compile(){
 }
 
 src_install(){
-	dobin fastqc run_fastqc.bat
+	insinto "opt/${PN}"
+	doins -r bin
+	chmod a+x "${ED}/opt/${PN}/bin/fastqc"
+	# Add the package's bin directory to the PATH.
+	doenvd "${FILESDIR}/00fastqc"
+	if use prefix ; then
+		hprefixify "${ED}/etc/env.d/00fastqc"
+	fi
+
 	dodoc README.txt RELEASE_NOTES.txt
+}
 
-	# There is no fastqc.jar.  The output from the compilation is the set of
-	# .class files (a jar file is just a zip file full of .class files).  All
-	# you need to copy out is the contents of the bin subdirectory, the rest of
-	# the download you can discard.
-	#
-	# jbzip2-0.9.jar comes from https://code.google.com/p/jbzip2
-	#
-	# ignore the sam-1.103.jar and rely on /usr/share/picard/lib/sam.jar from sci-biology/picard
-	# The sam-1.103.jar library comes from
-	# http://sourceforge.net/projects/picard/files/sam-jdk/.  Note that there is
-	# a newer version of this codebase at https://github.com/samtools/htsjdk but
-	# that FastQC is NOT yet compatible with the updated API (this will probably
-	# happen in a future release).  This library is needed to read SAM/BAM
-	# format files.
-	# cisd-jhdf5.jar should be provided by sci-libs/jhdf5
+pkg_postinst() {
+	ewarn "Remember to run: env-update && source \"${EPREFIX}/etc/profile\" if you plan"
+	ewarn "to use this tool in a shell before logging out (or restarting"
+	ewarn "your login manager)"
 }

diff --git a/sci-biology/fastqc/files/00fastqc b/sci-biology/fastqc/files/00fastqc
new file mode 100644
index 000000000..021de8bb0
--- /dev/null
+++ b/sci-biology/fastqc/files/00fastqc
@@ -0,0 +1 @@
+PATH="/opt/fastqc/bin"

diff --git a/sci-biology/fastqc/metadata.xml b/sci-biology/fastqc/metadata.xml
index 138cb7705..7c86089a2 100644
--- a/sci-biology/fastqc/metadata.xml
+++ b/sci-biology/fastqc/metadata.xml
@@ -5,6 +5,10 @@
 		<email>mmokrejs@fold.natur.cuni.cz</email>
 		<name>Martin Mokrejs</name>
 	</maintainer>
+	<maintainer type="person">
+		<email>anton.stay.connected@gmail.com</email>
+		<name>Anton Molyboha</name>
+	</maintainer>
 	<maintainer type="project">
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>