sci-biology/ICC: initial ebuild, perl installation steps need to be fixed

4 files changed, 80 insertions, 0 deletions

diff --git a/sci-biology/ICC/ChangeLog b/sci-biology/ICC/ChangeLog
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+++ b/sci-biology/ICC/ChangeLog
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+# ChangeLog for sci-biology/ICC
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*ICC-2.0.1 (07 Jan 2015)
+
+  07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +ICC-2.0.1.ebuild:
+  initial ebuild, perl installation steps need to be fixed
+
diff --git a/sci-biology/ICC/ICC-2.0.1.ebuild b/sci-biology/ICC/ICC-2.0.1.ebuild
new file mode 100644
index 000000000..5e5fb5cbd
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+++ b/sci-biology/ICC/ICC-2.0.1.ebuild
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+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit perl-module
+
+DESCRIPTION="Error corrector for Roche/454 and IonTorrent data with indel and carryforward, SNP and haplotype calling"
+HOMEPAGE="http://indra.mullins.microbiol.washington.edu/ICC"
+SRC_URI="http://indra.mullins.microbiol.washington.edu/cgi-bin/ICC/info.cgi?ID=ICC_v2.0.1.zip -> ICC_v2.0.1.zip"
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="dev-lang/perl
+	sci-biology/ncbi-tools++"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"
+
+src_install(){
+	dobin Scripts/*.pl
+	dodoc README.txt
+
+	# BUG: does not work
+	cd Scripts/lib || die
+	perl-module_src_install DESTDIR="${D}" *.pm Parallel/ForkManager.pm # install into @INC path
+
+}
+
+#    testing: Blast/Linux/LICENSE      OK
+#    testing: Example/exampleReads.fas   OK
+#    testing: Example/exampleReads.qual   OK
+#    testing: Example/exampleReference.fas   OK
+#    testing: README.md                OK
+#    testing: README.txt               OK
+#    testing: Scripts/                 OK
+#    testing: Scripts/CC.pl            OK
+#    testing: Scripts/HIC.pl           OK
+#    testing: Scripts/IC.pl            OK
+#    testing: Scripts/alignRegion.pl   OK
+#    testing: Scripts/config.pl        OK
+#    testing: Scripts/lib/             OK
+#    testing: Scripts/lib/.DS_Store    OK
+#    testing: Scripts/lib/Parallel/    OK
+#    testing: Scripts/lib/Parallel/ForkManager.pm   OK
+#    testing: Scripts/lib/paths.pm     OK
+#    testing: Scripts/lib/seqAlign.pm   OK
+#    testing: Scripts/lib/utils.pm     OK
+#    testing: Scripts/ntFreq.pl        OK
+#    testing: Scripts/readQualFilter.pl   OK
+#    testing: Scripts/retrieveRegion.pl   OK
+#    testing: Scripts/retrieveWindows.pl   OK
+#    testing: Scripts/runBLAST.pl      OK
+#    testing: Scripts/runICC.pl        OK
+#    testing: Scripts/uniqueReads.pl   OK
+#    testing: VersionHistory.txt       OK
+
diff --git a/sci-biology/ICC/Manifest b/sci-biology/ICC/Manifest
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--- /dev/null
+++ b/sci-biology/ICC/Manifest
@@ -0,0 +1 @@
+DIST ICC_v2.0.1.zip 63756669 SHA256 475eb33c8a9c49babc746823a988494f645f2d437ddb46c6988fbd14df39b833 SHA512 2952c5489e81f0702d3854a5a6f9591c4674b559a58be647bcd24c9837e8208ed1187721063a95abc120dffd860e13bd996a4f89f5e90de2d56ccd3750cce42e WHIRLPOOL 23bad2bf3daef731a5ffe967fe99e2dac698131f6b5e7becc2e9f4eaf3e9aa791f34b346382c84247f08e6717c07977c2e0104b1adb6877db6f29129ea4b4b43
diff --git a/sci-biology/ICC/metadata.xml b/sci-biology/ICC/metadata.xml
new file mode 100644
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--- /dev/null
+++ b/sci-biology/ICC/metadata.xml
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+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>