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 <[email protected]> +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>[email protected]</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 +}
