* [gentoo-commits] repo/gentoo:master commit in: sci-biology/tophat/
@ 2015-10-19 20:48 Sergey Popov
0 siblings, 0 replies; 5+ messages in thread
From: Sergey Popov @ 2015-10-19 20:48 UTC (permalink / raw
To: gentoo-commits
commit: 2dfd0d1135bd7e78005d7c72ef253ada96f985ce
Author: Sergey Popov <pinkbyte <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 19 20:45:48 2015 +0000
Commit: Sergey Popov <pinkbyte <AT> gentoo <DOT> org>
CommitDate: Mon Oct 19 20:45:48 2015 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2dfd0d11
sci-biology/tophat: correct dependency on sci-biology/seqan
Gentoo-Bug: 546816
Package-Manager: portage-2.2.20
sci-biology/tophat/tophat-2.0.8.ebuild | 2 +-
sci-biology/tophat/tophat-2.0.9.ebuild | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/tophat/tophat-2.0.8.ebuild b/sci-biology/tophat/tophat-2.0.8.ebuild
index c20007c..4a99dfd 100644
--- a/sci-biology/tophat/tophat-2.0.8.ebuild
+++ b/sci-biology/tophat/tophat-2.0.8.ebuild
@@ -20,7 +20,7 @@ IUSE="debug"
DEPEND="
dev-libs/boost
sci-biology/samtools
- sci-biology/seqan"
+ ~sci-biology/seqan-1.3.1"
RDEPEND="${DEPEND}
sci-biology/bowtie"
diff --git a/sci-biology/tophat/tophat-2.0.9.ebuild b/sci-biology/tophat/tophat-2.0.9.ebuild
index 91cc2d4..d362ebe 100644
--- a/sci-biology/tophat/tophat-2.0.9.ebuild
+++ b/sci-biology/tophat/tophat-2.0.9.ebuild
@@ -21,7 +21,7 @@ IUSE="debug"
DEPEND="
dev-libs/boost
sci-biology/samtools
- sci-biology/seqan"
+ ~sci-biology/seqan-1.3.1"
RDEPEND="${DEPEND}
sci-biology/bowtie"
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/tophat/
@ 2016-09-03 8:37 David Seifert
0 siblings, 0 replies; 5+ messages in thread
From: David Seifert @ 2016-09-03 8:37 UTC (permalink / raw
To: gentoo-commits
commit: 1fef751f90def6048c9066f9c5cc35bcc6681a33
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 3 08:37:31 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep 3 08:37:51 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1fef751f
sci-biology/tophat: Various QA fixes, handle python properly
* Add subslot operator := for dev-libs/boost
* DEPEND on virtual/pkgconfig
* Add missing ${PYTHON_REQUIRED_USE} and ${PYTHON_DEPS}
* Install python scripts and modules properly using
'python_doscript' and 'python_domodule'
Package-Manager: portage-2.3.0
.../{tophat-2.1.1.ebuild => tophat-2.1.1-r1.ebuild} | 18 ++++++++++++++----
1 file changed, 14 insertions(+), 4 deletions(-)
diff --git a/sci-biology/tophat/tophat-2.1.1.ebuild b/sci-biology/tophat/tophat-2.1.1-r1.ebuild
similarity index 76%
rename from sci-biology/tophat/tophat-2.1.1.ebuild
rename to sci-biology/tophat/tophat-2.1.1-r1.ebuild
index fc80ea8..a850175 100644
--- a/sci-biology/tophat/tophat-2.1.1.ebuild
+++ b/sci-biology/tophat/tophat-2.1.1-r1.ebuild
@@ -6,7 +6,7 @@ EAPI=6
PYTHON_COMPAT=( python2_7 )
-inherit autotools eutils flag-o-matic python-single-r1
+inherit autotools eutils flag-o-matic python-single-r1 toolchain-funcs
DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie2"
HOMEPAGE="https://ccb.jhu.edu/software/tophat/"
@@ -16,11 +16,14 @@ LICENSE="Artistic"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="debug"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-RDEPEND="dev-libs/boost
+RDEPEND="${PYTHON_DEPS}
+ dev-libs/boost:=
sci-biology/samtools:0.1-legacy
sci-biology/bowtie:2"
DEPEND="${RDEPEND}
+ virtual/pkgconfig
sci-biology/seqan:1.4"
PATCHES=(
@@ -46,7 +49,7 @@ src_prepare() {
# innocuous non-security flags, prevent log pollution
append-cflags -Wno-unused-but-set-variable -Wno-unused-variable
- append-cppflags "$(pkg-config --cflags seqan-1.4)"
+ append-cppflags "$($(tc-getPKG_CONFIG) --cflags seqan-1.4)"
eautoreconf
}
@@ -59,8 +62,15 @@ src_install() {
default
local i
+ # install scripts properly
for i in bed_to_juncs contig_to_chr_coords sra_to_solid tophat tophat-fusion-post; do
- python_fix_shebang "${ED}"/usr/bin/${i}
+ python_doscript "${ED%/}/usr/bin/${i}"
+ done
+
+ # install python modules properly
+ for i in intervaltree sortedcontainers; do
+ python_domodule "${ED%/}/usr/bin/${i}"
+ rm -rf "${ED%/}/usr/bin/${i}" || die
done
}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/tophat/
@ 2016-09-27 16:52 David Seifert
0 siblings, 0 replies; 5+ messages in thread
From: David Seifert @ 2016-09-27 16:52 UTC (permalink / raw
To: gentoo-commits
commit: 982e9dfdf15d8bc9da0c795d93278de2bae027d2
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 27 16:51:12 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Tue Sep 27 16:51:12 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=982e9dfd
sci-biology/tophat: Remove old and ancient 1.0 ebuilds
Package-Manager: portage-2.3.1
sci-biology/tophat/Manifest | 1 -
sci-biology/tophat/tophat-1.0.12.ebuild | 38 ---------------------------------
2 files changed, 39 deletions(-)
diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest
index 2bf8121..a0a9b79 100644
--- a/sci-biology/tophat/Manifest
+++ b/sci-biology/tophat/Manifest
@@ -1,2 +1 @@
-DIST tophat-1.0.12.tar.gz 468781 SHA256 f67b3f89aa79c7e14b40bcdba87f5aba6d322f869ca4260503e64ffcd2b621b2 SHA512 275e14cb6fb5f7a0874adcf843aabfda6c6868f835faa2d03e6561646ca1fc80804fe1887c51a375125f2f5ed6242e304f97ff12774a7d676b4964614d4a5bf1 WHIRLPOOL ea62ce14aae28dc0cc2b18fde870a0d3c021d9fb0c2ffb728b02b008b5f5bd416f29176fe81ed2ad8b1a41014f8a7114e2b8032426e2767effe9cc6933417cee
DIST tophat-2.1.1.tar.gz 2259554 SHA256 37840b96f3219630082b15642c47f5ef95d14f6ee99c06a369b08b3d05684da5 SHA512 e2e0943a6f3d34b83922e6e403b65a3bee480a2b2bb4bf2de0cae7e0ef5bb166b66fec923316c2b643e8550e43c842f0f1bcc2ca7249d20fbcf5a4733fbdeabc WHIRLPOOL 1e0d2bc4031eaa56a3b77ca5966c2ed439a85c9b05f028f69f4477d517e51371156bbe73d499536148eb42d60641af7f294641ee79bc855fcc4df74d70dae26c
diff --git a/sci-biology/tophat/tophat-1.0.12.ebuild b/sci-biology/tophat/tophat-1.0.12.ebuild
deleted file mode 100644
index 88870c9..00000000
--- a/sci-biology/tophat/tophat-1.0.12.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="2"
-
-inherit autotools
-
-DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
-HOMEPAGE="http://tophat.cbcb.umd.edu/"
-SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 x86"
-
-DEPEND=""
-RDEPEND="sci-biology/bowtie"
-
-src_prepare() {
- # fix missing includes
- sed -i '/#include <string>/ a #include <stdio.h>' "${S}/src/gff_juncs.cpp" || die
- sed -i \
- -e '/#include <stdio.h>/ a #include <unistd.h>' \
- "${S}/src/prep_reads.cpp" \
- "${S}/src/extract_reads.cpp" || die
- # fix parallel make race
- sed -i -e 's/\$(top_builddir)\/src\///g' src/Makefile.am || die
- # remove broken arch-dependent CFLAGS setting
- perl -i -ne 'print unless /case "\${host_cpu}-\${host_os}" in/../^esac/' configure.ac || die
- eautoreconf
-}
-
-src_install() {
- einstall || die
- dodoc AUTHORS NEWS THANKS
-}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/tophat/
@ 2016-10-03 20:21 David Seifert
0 siblings, 0 replies; 5+ messages in thread
From: David Seifert @ 2016-10-03 20:21 UTC (permalink / raw
To: gentoo-commits
commit: 43ec20457f931039230784be90893ef70f4a2f3c
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Oct 3 20:16:56 2016 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Oct 3 20:21:26 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=43ec2045
sci-biology/tophat: Do not wrap scripts
Package-Manager: portage-2.3.1
sci-biology/tophat/{tophat-2.1.1-r2.ebuild => tophat-2.1.1-r3.ebuild} | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/tophat/tophat-2.1.1-r2.ebuild b/sci-biology/tophat/tophat-2.1.1-r3.ebuild
similarity index 95%
rename from sci-biology/tophat/tophat-2.1.1-r2.ebuild
rename to sci-biology/tophat/tophat-2.1.1-r3.ebuild
index 52a75a6..4d784fa 100644
--- a/sci-biology/tophat/tophat-2.1.1-r2.ebuild
+++ b/sci-biology/tophat/tophat-2.1.1-r3.ebuild
@@ -6,7 +6,7 @@ EAPI=6
PYTHON_COMPAT=( python2_7 )
-inherit autotools eutils flag-o-matic python-single-r1 toolchain-funcs
+inherit autotools flag-o-matic python-single-r1 toolchain-funcs
DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie2"
HOMEPAGE="https://ccb.jhu.edu/software/tophat/"
@@ -70,7 +70,7 @@ src_install() {
local i
# install scripts properly
for i in bed_to_juncs contig_to_chr_coords sra_to_solid tophat tophat-fusion-post; do
- python_doscript "${ED%/}/usr/bin/${i}"
+ python_fix_shebang "${ED%/}/usr/bin/${i}"
done
# install python modules properly
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/tophat/
@ 2020-02-16 20:24 David Seifert
0 siblings, 0 replies; 5+ messages in thread
From: David Seifert @ 2020-02-16 20:24 UTC (permalink / raw
To: gentoo-commits
commit: 872be18108da9051ff8a79c563d2141a992f55fd
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 16 20:24:11 2020 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Feb 16 20:24:11 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=872be181
sci-biology/tophat: [QA] inherit eutils.eclass directly
Package-Manager: Portage-2.3.89, Repoman-2.3.20
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/tophat/tophat-2.1.1-r5.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/tophat/tophat-2.1.1-r5.ebuild b/sci-biology/tophat/tophat-2.1.1-r5.ebuild
index 84f3d82b39d..75318877138 100644
--- a/sci-biology/tophat/tophat-2.1.1-r5.ebuild
+++ b/sci-biology/tophat/tophat-2.1.1-r5.ebuild
@@ -5,7 +5,7 @@ EAPI=6
PYTHON_COMPAT=( python2_7 )
-inherit autotools flag-o-matic python-single-r1 toolchain-funcs
+inherit autotools eutils flag-o-matic python-single-r1 toolchain-funcs
DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie2"
HOMEPAGE="https://ccb.jhu.edu/software/tophat/"
^ permalink raw reply related [flat|nested] 5+ messages in thread
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