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authorJakov Smolić <jsmolic@gentoo.org>2022-01-16 18:33:16 +0100
committerJakov Smolić <jsmolic@gentoo.org>2022-01-16 18:33:16 +0100
commit2fd2b0673fc4a3a7c35c9cd18f45216fb1c488c4 (patch)
tree26917d40cc4e961e541e8643431cfc7397c3f052 /sci-biology
parentdev-java/gnu-jaf: Stabilize 1.1.2 amd64, #831312 (diff)
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sci-biology/gibbs: treeclean
Bug: https://bugs.gentoo.org/829216 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org>
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/gibbs/Manifest1
-rw-r--r--sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch11
-rw-r--r--sci-biology/gibbs/gibbs-3.1.ebuild47
-rw-r--r--sci-biology/gibbs/metadata.xml13
4 files changed, 0 insertions, 72 deletions
diff --git a/sci-biology/gibbs/Manifest b/sci-biology/gibbs/Manifest
deleted file mode 100644
index 24b52453c962..000000000000
--- a/sci-biology/gibbs/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST gibbs-3.1.tar.gz 563300 BLAKE2B 74b97407ccdac49d19dd2fa5fe3a5384b52a3ae871f197c1212e818fb7ce2307f2d04a91cf8a1d14c82d57b6f7266bbae849091bec9e580b8d473b595a836212 SHA512 b1ffc0d0c7debaced3c3d850eb7d2c42e13358d1e7c6ff5e6be0273446edc50bd655c52c5ae904a9054d47d7a48abd54a7684534ba7681375b657ad77fb8cb52
diff --git a/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch b/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch
deleted file mode 100644
index 6eaad637cfc8..000000000000
--- a/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/configure.in
-+++ b/configure.in
-@@ -51,7 +51,7 @@
- fi
- ])
-
--CFLAGS="$OPTFLAGS $MPIFLAGS -Wall -Werror $MACFLAG"
-+CFLAGS="$CFLAGS $OPTFLAGS $MPIFLAGS -Wall $MACFLAG"
-
- AC_PROG_CC([$COMP_LIST])
-
diff --git a/sci-biology/gibbs/gibbs-3.1.ebuild b/sci-biology/gibbs/gibbs-3.1.ebuild
deleted file mode 100644
index a06d0880ee4d..000000000000
--- a/sci-biology/gibbs/gibbs-3.1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools
-
-DESCRIPTION="Identify motifs, conserved regions, in DNA or protein sequences"
-HOMEPAGE="http://bayesweb.wadsworth.org/gibbs/gibbs.html"
-SRC_URI="mirror://gentoo/gibbs-${PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE="mpi"
-
-DEPEND="
- mpi? (
- virtual/mpi
- sys-cluster/mpe2
- )"
-RDEPEND="${DEPEND}"
-
-PATCHES=( "${FILESDIR}"/${PN}-3.1-fix-CFLAGS.patch )
-
-src_prepare() {
- default
- mv configure.{in,ac} || die
- eautoreconf
-}
-
-src_configure() {
- use mpi && export CC=mpicc
- econf $(use_enable mpi)
-}
-
-src_install() {
- default
-
- exeinto /usr/$(get_libdir)/${PN}
- doexe *.pl
-}
-
-pkg_postinst() {
- einfo "Supplementary Perl scripts for Gibbs have been installed into ${EROOT}/usr/$(get_libdir)/${PN}."
- einfo "These scripts require installation of sci-biology/bioperl."
-}
diff --git a/sci-biology/gibbs/metadata.xml b/sci-biology/gibbs/metadata.xml
deleted file mode 100644
index a0cd7b42b3ab..000000000000
--- a/sci-biology/gibbs/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <longdescription>
- The Gibbs motif sampler stochastically examines candidate alignments
- in an effort to find the best alignment as measured by the maximum
- a posteriori (MAP) log-likelihood ratio.
- </longdescription>
-</pkgmetadata>