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author | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 13:49:04 -0700 |
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committer | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 17:38:18 -0700 |
commit | 56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch) | |
tree | 3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-biology/allpathslg | |
download | gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.gz gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.bz2 gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.zip |
proj/gentoo: Initial commit
This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.
This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.
Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed
Diffstat (limited to 'sci-biology/allpathslg')
-rw-r--r-- | sci-biology/allpathslg/Manifest | 3 | ||||
-rw-r--r-- | sci-biology/allpathslg/allpathslg-42337.ebuild | 35 | ||||
-rw-r--r-- | sci-biology/allpathslg/allpathslg-47093.ebuild | 36 | ||||
-rw-r--r-- | sci-biology/allpathslg/allpathslg-52415.ebuild | 54 | ||||
-rw-r--r-- | sci-biology/allpathslg/files/allpathslg-47093-gcc4.9.patch | 16 | ||||
-rw-r--r-- | sci-biology/allpathslg/metadata.xml | 5 |
6 files changed, 149 insertions, 0 deletions
diff --git a/sci-biology/allpathslg/Manifest b/sci-biology/allpathslg/Manifest new file mode 100644 index 000000000000..8209935b6d9e --- /dev/null +++ b/sci-biology/allpathslg/Manifest @@ -0,0 +1,3 @@ +DIST allpathslg-42337.tar.gz 2739498 SHA256 a2c8f64f6ba1705b2331ca07761d189183c6745f8717ffc67ee98e9e3ca3dba6 SHA512 7595fbe14a5029578b57d16f781cbb2a0f0ad6b1af2dd770e2274f8fe2e11d0013fdff12cc85c1be748e769ffb23b7d5fe30920feef38e0e8b947d05b8bda31c WHIRLPOOL 79bda55d49877641eb55630950472a06d8f25db467dbfecde8b4d04c3ce16c071d32dd312fa9a0f72723bf4caa8f9b1d0346acf438b9671b4bed2c0672c788b9 +DIST allpathslg-47093.tar.gz 3057279 SHA256 493e21ae727250ea632b73b61545c32de2d8fb31e6a92605393ebb4af251f828 SHA512 499d23de52cad666fac663eb4a7d770b2129c4f9622f6c808ce30283429b6f67fb343f8712b07c7cb062c429117a0855da960ffc1d2ffb4e7ec2f544ba5a6314 WHIRLPOOL a3bc58dc140be3cddbd44c7035e628c4425bf86bc38592004df21d4dc91958ced9f08d667b43c15c214e53e3098805f368a856e66e5c2049b0e03d043b098ebc +DIST allpathslg-52415.tar.gz 3129266 SHA256 3c62024a0eacdc223bc727be4718da644fb302f785c7c7347a09ff422ce96362 SHA512 afe25b07d2e07dee3ced2283ffe858f24acfb35d53e9c11fcbcc47373594453d798c344d5604eb24d5c8d3685a185a3b8807bb3547d8066cbaab8d8cf927d1d6 WHIRLPOOL de15dfeddeca2f64fd8780839c45096c28cb47ec219d781f6754f9cf65ad6dfc39b8a48aaa2c36f777282fb08ac78ef8cd04c2e1d79f4f797710d3bb38792785 diff --git a/sci-biology/allpathslg/allpathslg-42337.ebuild b/sci-biology/allpathslg/allpathslg-42337.ebuild new file mode 100644 index 000000000000..9fb44dfcc905 --- /dev/null +++ b/sci-biology/allpathslg/allpathslg-42337.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit autotools flag-o-matic + +DESCRIPTION="De novo assembly of whole-genome shotgun microreads" +HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd" +SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +IUSE="" +KEYWORDS="amd64 -x86" + +DEPEND=" + dev-libs/boost + !sci-biology/allpaths + sci-biology/vaal" +RDEPEND="" + +src_prepare() { + sed -i 's/-ggdb3//' configure.ac || die + eautoreconf +} + +src_install() { + einstall || die + # Provided by sci-biology/vaal + for i in QueryLookupTable ScaffoldAccuracy MakeLookupTable Fastb ShortQueryLookup; do + rm "${D}/usr/bin/$i" || die + done +} diff --git a/sci-biology/allpathslg/allpathslg-47093.ebuild b/sci-biology/allpathslg/allpathslg-47093.ebuild new file mode 100644 index 000000000000..ab971ec46c89 --- /dev/null +++ b/sci-biology/allpathslg/allpathslg-47093.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit autotools eutils flag-o-matic + +DESCRIPTION="De novo assembly of whole-genome shotgun microreads" +HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd" +SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 -x86" + +DEPEND=" + dev-libs/boost + !sci-biology/allpaths + sci-biology/vaal" +RDEPEND="" + +src_prepare() { + epatch "${FILESDIR}"/${P}-gcc4.9.patch + sed -i 's/-ggdb//' configure.ac || die + eautoreconf +} + +src_install() { + default + # Provided by sci-biology/vaal + for i in QueryLookupTable ScaffoldAccuracy MakeLookupTable Fastb ShortQueryLookup; do + rm "${ED}/usr/bin/$i" || die + done +} diff --git a/sci-biology/allpathslg/allpathslg-52415.ebuild b/sci-biology/allpathslg/allpathslg-52415.ebuild new file mode 100644 index 000000000000..29de20e37670 --- /dev/null +++ b/sci-biology/allpathslg/allpathslg-52415.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils flag-o-matic + +DESCRIPTION="De novo assembly of whole-genome shotgun microreads" +# see also http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12 +HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd" +SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="openmp" + +DEPEND=" + dev-libs/boost + !sci-biology/allpaths + sci-biology/vaal" +RDEPEND="" + +pkg_pretend() { + # as of release 44849, GCC 4.7.0 (or higher) is required + # seems pre gcc-4.7 users must stay with: + # ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-01/allpathslg-44837.tar.gz + if [[ ${MERGE_TYPE} != binary ]]; then + [[ $(tc-getCC) == *gcc* ]] && [[ $(gcc-version) < 4.7 ]] && \ + die "You need to use gcc >4.7" + fi +} + +src_prepare() { + local i + sed \ + -e 's/-ggdb//' \ + -e 's:CEHCK:CHECK:g' \ + -i configure.ac || die + for i in QueryLookupTable ScaffoldAccuracy MakeLookupTable Fastb ShortQueryLookup; do + sed -e "/bin_PROGRAMS/s: ${i} : :g" -i src/Makefile.am || die + done + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + $(use_enable openmp) + ) + autotools-utils_src_configure +} diff --git a/sci-biology/allpathslg/files/allpathslg-47093-gcc4.9.patch b/sci-biology/allpathslg/files/allpathslg-47093-gcc4.9.patch new file mode 100644 index 000000000000..46e5493d28ce --- /dev/null +++ b/sci-biology/allpathslg/files/allpathslg-47093-gcc4.9.patch @@ -0,0 +1,16 @@ + src/paths/long/VariantCallTools.cc | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/paths/long/VariantCallTools.cc b/src/paths/long/VariantCallTools.cc +index dfe2787..725878b 100644 +--- a/src/paths/long/VariantCallTools.cc ++++ b/src/paths/long/VariantCallTools.cc +@@ -1674,7 +1674,7 @@ void EdgesOnRef::FindAllPathsNoLoop(const GraphT& dg, int entrace_edge, int exit + int n1 = to_right2[entrace_edge]; + int n2 = to_left2[exit_edge]; + +- PartialPath start = {{n1},{}}; ++ PartialPath start{{n1},vec<int>{}}; + stack<PartialPath> visited; + visited.push(start); + while (! visited.empty()) { diff --git a/sci-biology/allpathslg/metadata.xml b/sci-biology/allpathslg/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/allpathslg/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> |