[gentoo-commits] proj/sci:master commit in: sci-biology/Atlas2/

[Martin Mokrejs]

commit:     9eb2c98e084ad39a175118774bad2e0fd587057d
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 21:13:39 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 21:13:39 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9eb2c98e

sci-biology/Atlas2: a skeleton for a new package, needs help from ruby team

---
 sci-biology/Atlas2/Atlas2-1.4.3.ebuild | 41 ++++++++++++++++++++++++++++++++++
 sci-biology/Atlas2/ChangeLog           | 10 +++++++++
 sci-biology/Atlas2/metadata.xml        |  9 ++++++++
 3 files changed, 60 insertions(+)

diff --git a/sci-biology/Atlas2/Atlas2-1.4.3.ebuild b/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
new file mode 100644
index 0000000..7e2049d
--- /dev/null
+++ b/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+USE_RUBY="ruby19 ruby20"
+
+inherit ruby-fakegem
+
+DESCRIPTION="Variant analysis tools (true SNPs, insertions, deletions) from whole exome capture sequencing (WECS)"
+HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas2"
+SRC_URI="http://downloads.sourceforge.net/project/atlas2/Atlas2_v1.4.3.zip"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="dev-lang/ruby
+	sci-biology/samtools
+	sci-biology/blat
+	sci-biology/phrap
+	sci-biology/ucsc-genome-browser" # that provides bigWig.h and jkweb.a, aka Jim Kent's src
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/all/"${PN}"_v"${PV}"
+
+src_compile(){
+	cd SOLiD-SNP-caller || die
+	emake
+
+	cd ../vcfPrinter
+	# TODO: install the *.rb files
+
+	cd ../Atlas-Indel2
+	# TODO: install the *.rb and files in lib/
+
+	cd ../Atlas-SNP2
+	# TODO: install
+}

diff --git a/sci-biology/Atlas2/ChangeLog b/sci-biology/Atlas2/ChangeLog
new file mode 100644
index 0000000..65bee22
--- /dev/null
+++ b/sci-biology/Atlas2/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/Atlas2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*Atlas2-1.4.3 (23 Mar 2014)
+
+  23 Mar 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
+  +Atlas2-1.4.3.ebuild, +metadata.xml:
+  a skeleton for a new package, needs help from ruby team
+

diff --git a/sci-biology/Atlas2/metadata.xml b/sci-biology/Atlas2/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/Atlas2/metadata.xml
@@ -0,0 +1,9 @@
+<?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@×××××××××××××××.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>