From 56bd759df1d0c750a065b8c845e93d5dfa6b549d Mon Sep 17 00:00:00 2001 From: "Robin H. Johnson" Date: Sat, 8 Aug 2015 13:49:04 -0700 Subject: proj/gentoo: Initial commit MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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 X-Thanks: Alec Warner - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring - wrote much python to improve cvs2svn X-Thanks: Rich Freeman - validation scripts X-Thanks: Patrick Lauer - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed --- sci-biology/dialign-tx/Manifest | 1 + sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild | 44 ++++++++++++++++++++++ .../files/dialign-tx-1.0.2-implicits.patch | 18 +++++++++ sci-biology/dialign-tx/metadata.xml | 5 +++ 4 files changed, 68 insertions(+) create mode 100644 sci-biology/dialign-tx/Manifest create mode 100644 sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild create mode 100644 sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch create mode 100644 sci-biology/dialign-tx/metadata.xml (limited to 'sci-biology/dialign-tx') diff --git a/sci-biology/dialign-tx/Manifest b/sci-biology/dialign-tx/Manifest new file mode 100644 index 00000000000..de90a59afc9 --- /dev/null +++ b/sci-biology/dialign-tx/Manifest @@ -0,0 +1 @@ +DIST DIALIGN-TX_1.0.2.tar.gz 1765296 SHA256 fb3940a48a12875332752a298f619f0da62593189cd257d28932463c7cebcb8f SHA512 ff43f1f2900bdd12b7a8ba382a4d6ad68e6c2e6d7ceb1a65f0e571bb891cc2dc2661fb6ce698aaabf0e20c14565b5927ae0076a7170c8611679f936851a00c43 WHIRLPOOL 70565aa507f23a4f79affd8bda64e1b2698680e2288718c7518bd1d3782ca51ab747f8860e5513e7b1d480efd065702cc407c8137e96c47c3aad28ecdd345277 diff --git a/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild b/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild new file mode 100644 index 00000000000..c73d043742b --- /dev/null +++ b/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils multilib toolchain-funcs + +MY_P=DIALIGN-TX_${PV} + +DESCRIPTION="Greedy and progressive approaches for segment-based multiple sequence alignment" +HOMEPAGE="http://dialign-tx.gobics.de/" +SRC_URI="http://dialign-tx.gobics.de/${MY_P}.tar.gz" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="" + +S=${WORKDIR}/${MY_P} + +src_prepare() { + sed -e "s/\$(CC) -o/\$(CC) \$(LDFLAGS) -o/" \ + -i source/Makefile || die #336533 + epatch "${FILESDIR}"/${P}-implicits.patch +} + +src_compile() { + emake -C source clean + emake -C source CC="$(tc-getCC)" \ + CPPFLAGS="" +} + +src_install() { + dobin "${S}"/source/dialign-tx + insinto /usr/$(get_libdir)/${PN}/conf + doins "${S}"/conf/* +} + +pkg_postinst() { + einfo "The configuration directory is" + einfo "${ROOT}usr/$(get_libdir)/${PN}/conf" + einfo "You will need to pass this to ${PN} on every run." +} diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch new file mode 100644 index 00000000000..a8388d03232 --- /dev/null +++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch @@ -0,0 +1,18 @@ +--- source/museq.c ++++ source/museq.c +@@ -38,6 +38,7 @@ + //extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, + // struct prob_dist *pdist); + //extern struct diag_col *create_diag_col(int seq_amount); ++extern void free_diag(struct diag* dg); + extern void free_diag_col(struct diag_col* dcol); + extern struct diag_col *find_all_diags(struct scr_matrix *smatrix, + struct prob_dist *pdist, +@@ -52,6 +53,7 @@ + + // alig.c + extern struct alignment* create_empty_alignment(struct seq_col *scol); ++extern void free_alignment(struct alignment *algn); + //extern char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); + extern int simple_aligner(struct seq_col *scol, struct diag_col *dcol, + struct scr_matrix* smatrix, diff --git a/sci-biology/dialign-tx/metadata.xml b/sci-biology/dialign-tx/metadata.xml new file mode 100644 index 00000000000..f17a827e310 --- /dev/null +++ b/sci-biology/dialign-tx/metadata.xml @@ -0,0 +1,5 @@ + + + + sci-biology + -- cgit v1.2.1