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

[Martin Mokrejs]

commit:     27b9edadf33754b1305771c3b657ed21c05b1267
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 24 01:20:53 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 24 01:20:53 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=27b9edad

sci-biology/pileup: new package; a pileup pipeline used along SSAHA2

---
 sci-biology/pileup/ChangeLog         | 10 ++++++
 sci-biology/pileup/metadata.xml      |  9 +++++
 sci-biology/pileup/pileup-0.6.ebuild | 66 ++++++++++++++++++++++++++++++++++++
 3 files changed, 85 insertions(+)

diff --git a/sci-biology/pileup/ChangeLog b/sci-biology/pileup/ChangeLog
new file mode 100644
index 0000000..ea30368
--- /dev/null
+++ b/sci-biology/pileup/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/pileup
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*pileup-0.6 (24 Mar 2014)
+
+  24 Mar 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> +pileup-0.6.ebuild,
+  +metadata.xml:
+  new package; a pileup pipeline used along SSAHA2
+

diff --git a/sci-biology/pileup/metadata.xml b/sci-biology/pileup/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/pileup/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>

diff --git a/sci-biology/pileup/pileup-0.6.ebuild b/sci-biology/pileup/pileup-0.6.ebuild
new file mode 100644
index 0000000..e78d5de
--- /dev/null
+++ b/sci-biology/pileup/pileup-0.6.ebuild
@@ -0,0 +1,66 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+DESCRIPTION="Pipeline to align reads into the format also understood by samtools, maq, pipeline maybe using ssaha2?"
+HOMEPAGE="http://www.sanger.ac.uk/resources/software/ssaha2/"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/pileup.tgz"
+
+# http://samtools.sourceforge.net/pileup.shtml
+# 
+LICENSE=""
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/pileup_v"${PV}"
+
+src_prepare(){
+	sed -i "s/^CC= gcc/#CC= gcc/" ssaha_pileup/ssaha_pileup/makefile || die "sed failed to fix makefile"
+	sed -i "s/^CFLAGS= -O2/#CFLAGS= -O2/" ssaha_pileup/ssaha_pileup/makefile || die "sed failed to fix makefile"
+
+	for d in get_seqreads ssaha_split; do
+		sed -i "s/^CC = cc/#CC = cc/" ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
+		sed -i "s/^CFLAGS = -O4/#CFLAGS = -O4/" ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
+	done
+
+	for d in search_read ssaha_parseSNP; do
+		sed -i "s/^CC = gcc/#CC = gcc/" ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
+		sed -i "s/^CFLAGS = -Wall -O4/#CFLAGS = -Wall -O4/" ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
+	done
+}
+
+src_compile(){
+	cd ssaha_pileup/ssaha_pileup || die "Cannot cd to "${S}"ssaha_pileup/ssaha_pileup"
+	emake || die "emake failed"
+
+	for d in get_seqreads ssaha_split ssaha_parseSNP search_read; do
+		cd "${S}"/ssaha_pileup/other_codes/$d  || die "Cannot cd to "${S}"ssaha_pileup/other_codes/"$d
+		make clean
+		emake || die "emake failed"
+	done
+}
+
+src_install(){
+	cd ssaha_pileup/ssaha_pileup || die "Cannot cd to "${S}"ssaha_pileup/ssaha_pileup"
+	dobin ssaha_pileup ssaha_solexa ssaha_pairs ssaha_clean ssaha_mates ssaha_cigar ssaha_indel view_pileup ssaha_reads ssaha_merge ssaha_check-cigar || die "dobin failed"
+
+	cd "${S}" || die
+	for f in ssaha_pileup/other_codes/get_seqreads/get_seqreads \
+		ssaha_pileup/other_codes/ssaha_split/ssaha_split \
+		ssaha_pileup/other_codes/ssaha_parseSNP/ssaha_parseSNP \
+		ssaha_pileup/other_codes/search_read/search_read; do
+			dobin $f || die "dobin failed"
+	done
+
+	# TODO:
+	# pileup_v0.6/ssaha_pileup/tag.pl
+
+	# Finally, a tcsh shell script has to be created with full paths to ssaha2 binaries
+	# convert the awk line from install.csh to a proper shellscript based on pileup.csh_src
+}