* [gentoo-commits] proj/sci:master commit in: sci-biology/transdecoder/
@ 2015-01-08 22:35 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2015-01-08 22:35 UTC (permalink / raw
To: gentoo-commits
commit: 7d88d8fde0145c729b2cf3f147370866db7ed14c
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jan 8 22:31:12 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jan 8 22:31:12 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7d88d8fd
sci-biology/transdecoder: new package
Package-Manager: portage-2.2.7
---
sci-biology/transdecoder/ChangeLog | 9 +++++
sci-biology/transdecoder/metadata.xml | 9 +++++
.../transdecoder/transdecoder-20140704.ebuild | 44 ++++++++++++++++++++++
3 files changed, 62 insertions(+)
diff --git a/sci-biology/transdecoder/ChangeLog b/sci-biology/transdecoder/ChangeLog
new file mode 100644
index 0000000..252ef53
--- /dev/null
+++ b/sci-biology/transdecoder/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/transdecoder
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*transdecoder-20140704 (08 Jan 2015)
+
+ 08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
+ +transdecoder-20140704.ebuild:
+ sci-biology/transdecoder: new package
diff --git a/sci-biology/transdecoder/metadata.xml b/sci-biology/transdecoder/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/transdecoder/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>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/transdecoder/transdecoder-20140704.ebuild b/sci-biology/transdecoder/transdecoder-20140704.ebuild
new file mode 100644
index 0000000..c539231
--- /dev/null
+++ b/sci-biology/transdecoder/transdecoder-20140704.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit perl-module
+
+DESCRIPTION="Extract ORF/CDS regions from FASTA sequences"
+HOMEPAGE="http://sourceforge.net/projects/transdecoder/"
+SRC_URI="http://downloads.sourceforge.net/project/transdecoder/TransDecoder_r20140704.tar.gz"
+
+LICENSE="BSD-BroadInstitute"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="sys-cluster/openmpi
+ sci-biology/hmmer
+ sci-biology/cd-hit
+ sci-biology/parafly
+ sci-biology/ffindex"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/TransDecoder_r20140704
+
+src_prepare(){
+ rm -rf 3rd_party
+ mv Makefile Makefile.old
+}
+
+# avoid fetching 1.5TB "${S}"/pfam/Pfam-AB.hmm.bin, see
+# "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704" thread in archives
+#
+# you cna get it from http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin
+
+src_install(){
+ dobin TransDecoder *.pl util/*.pl util/*.sh
+ eval `perl '-V:installvendorlib'`
+ vendor_lib_install_dir="${installvendorlib}"
+ dodir ${vendor_lib_install_dir}
+ insinto ${vendor_lib_install_dir}
+ doins PerlLib/*.pm
+}
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/transdecoder/
@ 2015-01-10 1:18 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2015-01-10 1:18 UTC (permalink / raw
To: gentoo-commits
commit: bd7c62b252cc5351963dafbe3473571d8d1fe1c0
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jan 10 01:17:40 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Jan 10 01:17:40 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bd7c62b2
install *.pm into PERL5LIB/TransDecoder and pass that via env.d
Package-Manager: portage-2.2.7
---
sci-biology/transdecoder/ChangeLog | 4 ++++
sci-biology/transdecoder/transdecoder-20140704.ebuild | 6 ++++--
2 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/sci-biology/transdecoder/ChangeLog b/sci-biology/transdecoder/ChangeLog
index c564760..123bd82 100644
--- a/sci-biology/transdecoder/ChangeLog
+++ b/sci-biology/transdecoder/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 10 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ transdecoder-20140704.ebuild:
+ install *.pm into PERL5LIB/TransDecoder and pass that via env.d
+
09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+files/TransDecoder.patch, +files/pfam_runner.pl.patch,
transdecoder-20140704.ebuild:
diff --git a/sci-biology/transdecoder/transdecoder-20140704.ebuild b/sci-biology/transdecoder/transdecoder-20140704.ebuild
index af5bb4f..c6398f8 100644
--- a/sci-biology/transdecoder/transdecoder-20140704.ebuild
+++ b/sci-biology/transdecoder/transdecoder-20140704.ebuild
@@ -39,9 +39,11 @@ src_install(){
dobin TransDecoder *.pl util/*.pl util/*.sh
eval `perl '-V:installvendorlib'`
vendor_lib_install_dir="${installvendorlib}"
- dodir ${vendor_lib_install_dir}
- insinto ${vendor_lib_install_dir}
+ dodir ${vendor_lib_install_dir}/TransDecoder
+ insinto ${vendor_lib_install_dir}/TransDecoder
doins PerlLib/*.pm
+ echo "PERL5LIB="${vendor_lib_install_dir}"/TransDecoder" > ${S}"/99TransDecoder"
+ doenvd ${S}"/99TransDecoder" || die
einfo "Fetch on your own:"
einfo "wget --mirror -nH -nd http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin"
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/transdecoder/
@ 2015-02-15 16:57 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2015-02-15 16:57 UTC (permalink / raw
To: gentoo-commits
commit: 4a7fd2dfaa719149b004affe5349bf245e30cc59
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Feb 15 16:55:12 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Feb 15 16:55:12 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4a7fd2df
drop hmmer-3 dependency, it is an optional dependency only
Package-Manager: portage-2.2.15
---
sci-biology/transdecoder/ChangeLog | 4 ++++
sci-biology/transdecoder/transdecoder-20140704.ebuild | 2 +-
2 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/sci-biology/transdecoder/ChangeLog b/sci-biology/transdecoder/ChangeLog
index 123bd82..87a58f9 100644
--- a/sci-biology/transdecoder/ChangeLog
+++ b/sci-biology/transdecoder/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 15 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ transdecoder-20140704.ebuild:
+ drop hmmer-3 dependency, it is an optional dependency only
+
10 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
transdecoder-20140704.ebuild:
install *.pm into PERL5LIB/TransDecoder and pass that via env.d
diff --git a/sci-biology/transdecoder/transdecoder-20140704.ebuild b/sci-biology/transdecoder/transdecoder-20140704.ebuild
index c6398f8..c8af896 100644
--- a/sci-biology/transdecoder/transdecoder-20140704.ebuild
+++ b/sci-biology/transdecoder/transdecoder-20140704.ebuild
@@ -15,7 +15,7 @@ SLOT="0"
KEYWORDS="~amd64"
IUSE=""
-DEPEND=">=sci-biology/hmmer-3.0
+DEPEND="sci-biology/hmmer
sci-biology/cd-hit
sci-biology/parafly
sci-biology/ffindex"
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/transdecoder/
@ 2015-03-19 10:37 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2015-03-19 10:37 UTC (permalink / raw
To: gentoo-commits
commit: a4cb204b1513efc3901a92bebacf0cb45f134a5b
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 19 10:33:12 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 19 10:33:12 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a4cb204b
removing KEYWORDS until the perl files are installed to some other place. At the moment I get: 'perl-module.eclass: Suspicious environment values found. PERL5LIB="/usr/lib64/perl5/vendor_perl/5.18.2/TransDecoder"'
Package-Manager: portage-2.2.15
sci-biology/transdecoder/ChangeLog | 8 ++++++++
...ecoder-20140704.ebuild => transdecoder-2.0.1.ebuild} | 17 ++++++++---------
sci-biology/transdecoder/transdecoder-20140704.ebuild | 2 +-
3 files changed, 17 insertions(+), 10 deletions(-)
diff --git a/sci-biology/transdecoder/ChangeLog b/sci-biology/transdecoder/ChangeLog
index 87a58f9..2b30ad0 100644
--- a/sci-biology/transdecoder/ChangeLog
+++ b/sci-biology/transdecoder/ChangeLog
@@ -2,6 +2,14 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*transdecoder-2.0.1 (19 Mar 2015)
+
+ 19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +transdecoder-2.0.1.ebuild, transdecoder-20140704.ebuild:
+ removing KEYWORDS until the perl files are installed to some other place. At
+ the moment I get: 'perl-module.eclass: Suspicious environment values found.
+ PERL5LIB="/usr/lib64/perl5/vendor_perl/5.18.2/TransDecoder"'
+
15 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
transdecoder-20140704.ebuild:
drop hmmer-3 dependency, it is an optional dependency only
diff --git a/sci-biology/transdecoder/transdecoder-20140704.ebuild b/sci-biology/transdecoder/transdecoder-2.0.1.ebuild
similarity index 80%
copy from sci-biology/transdecoder/transdecoder-20140704.ebuild
copy to sci-biology/transdecoder/transdecoder-2.0.1.ebuild
index c8af896..eaa6e69 100644
--- a/sci-biology/transdecoder/transdecoder-20140704.ebuild
+++ b/sci-biology/transdecoder/transdecoder-2.0.1.ebuild
@@ -8,11 +8,11 @@ inherit perl-module
DESCRIPTION="Extract ORF/CDS regions from FASTA sequences"
HOMEPAGE="http://sourceforge.net/projects/transdecoder/"
-SRC_URI="http://downloads.sourceforge.net/project/transdecoder/TransDecoder_r20140704.tar.gz"
+SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/"${PV}".tar.gz -> ${P}.tar.gz"
LICENSE="BSD-BroadInstitute"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS=""
IUSE=""
DEPEND="sci-biology/hmmer
@@ -21,14 +21,13 @@ DEPEND="sci-biology/hmmer
sci-biology/ffindex"
RDEPEND="${DEPEND}"
-S="${WORKDIR}"/TransDecoder_r20140704
+S="${WORKDIR}"/TransDecoder-2.0.1
-src_prepare(){
- rm -rf 3rd_party
- mv Makefile Makefile.old
- epatch "${FILESDIR}"/TransDecoder.patch
- epatch "${FILESDIR}"/pfam_runner.pl.patch
-}
+##src_prepare(){
+# #mv Makefile Makefile.old
+# #epatch "${FILESDIR}"/TransDecoder.patch
+# #epatch "${FILESDIR}"/pfam_runner.pl.patch
+#}
# avoid fetching 1.5TB "${S}"/pfam/Pfam-AB.hmm.bin, see
# "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704" thread in archives
diff --git a/sci-biology/transdecoder/transdecoder-20140704.ebuild b/sci-biology/transdecoder/transdecoder-20140704.ebuild
index c8af896..ed060b3 100644
--- a/sci-biology/transdecoder/transdecoder-20140704.ebuild
+++ b/sci-biology/transdecoder/transdecoder-20140704.ebuild
@@ -12,7 +12,7 @@ SRC_URI="http://downloads.sourceforge.net/project/transdecoder/TransDecoder_r201
LICENSE="BSD-BroadInstitute"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS=""
IUSE=""
DEPEND="sci-biology/hmmer
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/transdecoder/
@ 2015-03-19 10:47 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2015-03-19 10:47 UTC (permalink / raw
To: gentoo-commits
commit: 2d947262e46f78e5769b5ee8c3d1e5a8dc6fe462
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 19 10:46:20 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 19 10:46:20 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2d947262
dropped hmmer dependency altogether, added pkg_postinst() with usage/dependency info
Package-Manager: portage-2.2.15
sci-biology/transdecoder/ChangeLog | 5 +++++
sci-biology/transdecoder/transdecoder-2.0.1.ebuild | 9 ++++++++-
2 files changed, 13 insertions(+), 1 deletion(-)
diff --git a/sci-biology/transdecoder/ChangeLog b/sci-biology/transdecoder/ChangeLog
index 2b30ad0..7e276d1 100644
--- a/sci-biology/transdecoder/ChangeLog
+++ b/sci-biology/transdecoder/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ transdecoder-2.0.1.ebuild:
+ dropped hmmer dependency altogether, added pkg_postinst() with
+ usage/dependency info
+
*transdecoder-2.0.1 (19 Mar 2015)
19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/transdecoder/transdecoder-2.0.1.ebuild b/sci-biology/transdecoder/transdecoder-2.0.1.ebuild
index eaa6e69..43edbbb 100644
--- a/sci-biology/transdecoder/transdecoder-2.0.1.ebuild
+++ b/sci-biology/transdecoder/transdecoder-2.0.1.ebuild
@@ -15,7 +15,7 @@ SLOT="0"
KEYWORDS=""
IUSE=""
-DEPEND="sci-biology/hmmer
+DEPEND="
sci-biology/cd-hit
sci-biology/parafly
sci-biology/ffindex"
@@ -48,3 +48,10 @@ src_install(){
einfo "wget --mirror -nH -nd http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin"
einfo "hmmpress Pfam-AB.hmm.bin"
}
+
+pkg_postinst(){
+ einfo "It is recommended to use TransDecoder with hmmer-3 or at least NCBI blast"
+ einfo "from either sci-biology/ncbi-blast+ (released more often) or"
+ einfo "from sci-biology/ncbi-toolkit++ (huge bundle with releases and less frequent bugfixes)"
+ einfo "Author says the minimum requirement is sci-biology/cd-hit"
+}
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/transdecoder/
@ 2015-04-17 22:21 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2015-04-17 22:21 UTC (permalink / raw
To: gentoo-commits
commit: 27400967c2a16c819a1a57f687b4fbb3bdb18b7d
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 17 22:20:44 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 17 22:20:44 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=27400967
sci-biology/transdecoder: fixed installation of perl-related files
Package-Manager: portage-2.2.18
sci-biology/transdecoder/ChangeLog | 4 ++++
sci-biology/transdecoder/transdecoder-2.0.1.ebuild | 14 +++++---------
.../transdecoder/transdecoder-20140704.ebuild | 21 ++++++++++++---------
3 files changed, 21 insertions(+), 18 deletions(-)
diff --git a/sci-biology/transdecoder/ChangeLog b/sci-biology/transdecoder/ChangeLog
index 7e276d1..f69ae4d 100644
--- a/sci-biology/transdecoder/ChangeLog
+++ b/sci-biology/transdecoder/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ transdecoder-2.0.1.ebuild, transdecoder-20140704.ebuild:
+ sci-biology/transdecoder: fixed installation of perl-related files
+
19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
transdecoder-2.0.1.ebuild:
dropped hmmer dependency altogether, added pkg_postinst() with
diff --git a/sci-biology/transdecoder/transdecoder-2.0.1.ebuild b/sci-biology/transdecoder/transdecoder-2.0.1.ebuild
index 43edbbb..b4476f7 100644
--- a/sci-biology/transdecoder/transdecoder-2.0.1.ebuild
+++ b/sci-biology/transdecoder/transdecoder-2.0.1.ebuild
@@ -4,7 +4,8 @@
EAPI=5
-inherit perl-module
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit perl-module eutils toolchain-funcs
DESCRIPTION="Extract ORF/CDS regions from FASTA sequences"
HOMEPAGE="http://sourceforge.net/projects/transdecoder/"
@@ -36,14 +37,9 @@ S="${WORKDIR}"/TransDecoder-2.0.1
src_install(){
dobin TransDecoder *.pl util/*.pl util/*.sh
- eval `perl '-V:installvendorlib'`
- vendor_lib_install_dir="${installvendorlib}"
- dodir ${vendor_lib_install_dir}/TransDecoder
- insinto ${vendor_lib_install_dir}/TransDecoder
- doins PerlLib/*.pm
- echo "PERL5LIB="${vendor_lib_install_dir}"/TransDecoder" > ${S}"/99TransDecoder"
- doenvd ${S}"/99TransDecoder" || die
-
+ perl_set_version
+ insinto ${VENDOR_LIB}/TransDecoder
+ dobin PerlLib/*.pm
einfo "Fetch on your own:"
einfo "wget --mirror -nH -nd http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin"
einfo "hmmpress Pfam-AB.hmm.bin"
diff --git a/sci-biology/transdecoder/transdecoder-20140704.ebuild b/sci-biology/transdecoder/transdecoder-20140704.ebuild
index ed060b3..db7c9a8 100644
--- a/sci-biology/transdecoder/transdecoder-20140704.ebuild
+++ b/sci-biology/transdecoder/transdecoder-20140704.ebuild
@@ -4,7 +4,8 @@
EAPI=5
-inherit perl-module
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit perl-module eutils toolchain-funcs
DESCRIPTION="Extract ORF/CDS regions from FASTA sequences"
HOMEPAGE="http://sourceforge.net/projects/transdecoder/"
@@ -37,15 +38,17 @@ src_prepare(){
src_install(){
dobin TransDecoder *.pl util/*.pl util/*.sh
- eval `perl '-V:installvendorlib'`
- vendor_lib_install_dir="${installvendorlib}"
- dodir ${vendor_lib_install_dir}/TransDecoder
- insinto ${vendor_lib_install_dir}/TransDecoder
- doins PerlLib/*.pm
- echo "PERL5LIB="${vendor_lib_install_dir}"/TransDecoder" > ${S}"/99TransDecoder"
- doenvd ${S}"/99TransDecoder" || die
-
+ perl_set_version
+ insinto ${VENDOR_LIB}/TransDecoder
+ dobin PerlLib/*.pm
einfo "Fetch on your own:"
einfo "wget --mirror -nH -nd http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin"
einfo "hmmpress Pfam-AB.hmm.bin"
}
+
+pkg_postinst(){
+ einfo "It is recommended to use TransDecoder with hmmer-3 or at least NCBI blast"
+ einfo "from either sci-biology/ncbi-blast+ (released more often) or"
+ einfo "from sci-biology/ncbi-toolkit++ (huge bundle with releases and less frequent bugfixes)"
+ einfo "Author says the minimum requirement is sci-biology/cd-hit"
+}
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/transdecoder/
@ 2015-04-27 12:48 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2015-04-27 12:48 UTC (permalink / raw
To: gentoo-commits
commit: 5f4adb868d4fb9b93c3db90ad3aa8354d3d132b9
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Apr 27 12:48:28 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Apr 27 12:48:28 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5f4adb86
sci-biology/transdecoder: drop old
Package-Manager: portage-2.2.18
sci-biology/transdecoder/ChangeLog | 4 ++
sci-biology/transdecoder/transdecoder-2.0.1.ebuild | 5 +-
.../transdecoder/transdecoder-20140704.ebuild | 54 ----------------------
3 files changed, 7 insertions(+), 56 deletions(-)
diff --git a/sci-biology/transdecoder/ChangeLog b/sci-biology/transdecoder/ChangeLog
index f69ae4d..8e5aa08 100644
--- a/sci-biology/transdecoder/ChangeLog
+++ b/sci-biology/transdecoder/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ -transdecoder-20140704.ebuild, transdecoder-2.0.1.ebuild:
+ sci-biology/transdecoder: drop old
+
17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
transdecoder-2.0.1.ebuild, transdecoder-20140704.ebuild:
sci-biology/transdecoder: fixed installation of perl-related files
diff --git a/sci-biology/transdecoder/transdecoder-2.0.1.ebuild b/sci-biology/transdecoder/transdecoder-2.0.1.ebuild
index b4476f7..1774caf 100644
--- a/sci-biology/transdecoder/transdecoder-2.0.1.ebuild
+++ b/sci-biology/transdecoder/transdecoder-2.0.1.ebuild
@@ -16,11 +16,12 @@ SLOT="0"
KEYWORDS=""
IUSE=""
-DEPEND="
+DEPEND=""
+RDEPEND="${DEPEND}
+ sci-biology/hmmer
sci-biology/cd-hit
sci-biology/parafly
sci-biology/ffindex"
-RDEPEND="${DEPEND}"
S="${WORKDIR}"/TransDecoder-2.0.1
diff --git a/sci-biology/transdecoder/transdecoder-20140704.ebuild b/sci-biology/transdecoder/transdecoder-20140704.ebuild
deleted file mode 100644
index db7c9a8..0000000
--- a/sci-biology/transdecoder/transdecoder-20140704.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
-
-DESCRIPTION="Extract ORF/CDS regions from FASTA sequences"
-HOMEPAGE="http://sourceforge.net/projects/transdecoder/"
-SRC_URI="http://downloads.sourceforge.net/project/transdecoder/TransDecoder_r20140704.tar.gz"
-
-LICENSE="BSD-BroadInstitute"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="sci-biology/hmmer
- sci-biology/cd-hit
- sci-biology/parafly
- sci-biology/ffindex"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/TransDecoder_r20140704
-
-src_prepare(){
- rm -rf 3rd_party
- mv Makefile Makefile.old
- epatch "${FILESDIR}"/TransDecoder.patch
- epatch "${FILESDIR}"/pfam_runner.pl.patch
-}
-
-# avoid fetching 1.5TB "${S}"/pfam/Pfam-AB.hmm.bin, see
-# "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704" thread in archives
-#
-# you cna get it from http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin
-
-src_install(){
- dobin TransDecoder *.pl util/*.pl util/*.sh
- perl_set_version
- insinto ${VENDOR_LIB}/TransDecoder
- dobin PerlLib/*.pm
- einfo "Fetch on your own:"
- einfo "wget --mirror -nH -nd http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin"
- einfo "hmmpress Pfam-AB.hmm.bin"
-}
-
-pkg_postinst(){
- einfo "It is recommended to use TransDecoder with hmmer-3 or at least NCBI blast"
- einfo "from either sci-biology/ncbi-blast+ (released more often) or"
- einfo "from sci-biology/ncbi-toolkit++ (huge bundle with releases and less frequent bugfixes)"
- einfo "Author says the minimum requirement is sci-biology/cd-hit"
-}
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/transdecoder/
@ 2015-04-27 12:49 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2015-04-27 12:49 UTC (permalink / raw
To: gentoo-commits
commit: c1d3d8e25843747ebe141b9305c24b5e481e1d07
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Apr 27 12:49:30 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Apr 27 12:49:30 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c1d3d8e2
sci-biology/transdecoder: ebuild cleanup
Package-Manager: portage-2.2.18
sci-biology/transdecoder/ChangeLog | 4 ++++
sci-biology/transdecoder/transdecoder-2.0.1.ebuild | 2 +-
2 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/sci-biology/transdecoder/ChangeLog b/sci-biology/transdecoder/ChangeLog
index 8e5aa08..fbadc5c 100644
--- a/sci-biology/transdecoder/ChangeLog
+++ b/sci-biology/transdecoder/ChangeLog
@@ -3,6 +3,10 @@
# $Header: $
27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ transdecoder-2.0.1.ebuild:
+ sci-biology/transdecoder: ebuild cleanup
+
+ 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
-transdecoder-20140704.ebuild, transdecoder-2.0.1.ebuild:
sci-biology/transdecoder: drop old
diff --git a/sci-biology/transdecoder/transdecoder-2.0.1.ebuild b/sci-biology/transdecoder/transdecoder-2.0.1.ebuild
index 1774caf..11a7413 100644
--- a/sci-biology/transdecoder/transdecoder-2.0.1.ebuild
+++ b/sci-biology/transdecoder/transdecoder-2.0.1.ebuild
@@ -13,7 +13,7 @@ SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/"${PV}".tar.gz ->
LICENSE="BSD-BroadInstitute"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
IUSE=""
DEPEND=""
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/transdecoder/
@ 2015-04-27 13:04 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2015-04-27 13:04 UTC (permalink / raw
To: gentoo-commits
commit: 39736ebd797835df74a7c9dfee1d39bdcf4e7baf
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Apr 27 13:03:43 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Apr 27 13:03:43 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=39736ebd
sci-biology/transdecoder: more ebuild cleanup
Package-Manager: portage-2.2.18
sci-biology/transdecoder/ChangeLog | 4 ++++
sci-biology/transdecoder/transdecoder-2.0.1.ebuild | 23 ++++++++++++++++++----
2 files changed, 23 insertions(+), 4 deletions(-)
diff --git a/sci-biology/transdecoder/ChangeLog b/sci-biology/transdecoder/ChangeLog
index fbadc5c..6fd8f5c 100644
--- a/sci-biology/transdecoder/ChangeLog
+++ b/sci-biology/transdecoder/ChangeLog
@@ -4,6 +4,10 @@
27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
transdecoder-2.0.1.ebuild:
+ sci-biology/transdecoder: more ebuild cleanup
+
+ 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ transdecoder-2.0.1.ebuild:
sci-biology/transdecoder: ebuild cleanup
27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/transdecoder/transdecoder-2.0.1.ebuild b/sci-biology/transdecoder/transdecoder-2.0.1.ebuild
index 11a7413..e8f5134 100644
--- a/sci-biology/transdecoder/transdecoder-2.0.1.ebuild
+++ b/sci-biology/transdecoder/transdecoder-2.0.1.ebuild
@@ -18,10 +18,11 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
- sci-biology/hmmer
sci-biology/cd-hit
+ sci-biology/hmmer
sci-biology/parafly
sci-biology/ffindex"
+# cdhit-4.6.1 is a real dependency, at least hmmer is optional (also ncbi-tools++ is now used for ORF searches)
S="${WORKDIR}"/TransDecoder-2.0.1
@@ -37,10 +38,24 @@ S="${WORKDIR}"/TransDecoder-2.0.1
# you cna get it from http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin
src_install(){
- dobin TransDecoder *.pl util/*.pl util/*.sh
+ dobin TransDecoder.Predict TransDecoder.LongOrfs
+ insinto /usr/share/${PN}/util
+ dobin util/*.pl
+ # zap the bundled cdhit binaries copied from transdecoder_plugins/cdhit/ to util/bin
+ rm -rf util/bin
+ #
+ # * sci-biology/trinityrnaseq-20140413:0::science
+ # * /usr/bin/Fasta_reader.pm
+ # * /usr/bin/GFF3_utils.pm
+ # * /usr/bin/Gene_obj.pm
+ # * /usr/bin/Gene_obj_indexer.pm
+ # * /usr/bin/Longest_orf.pm
+ # * /usr/bin/Nuc_translator.pm
+ # * /usr/bin/TiedHash.pm
+ #
perl_set_version
- insinto ${VENDOR_LIB}/TransDecoder
- dobin PerlLib/*.pm
+ insinto ${VENDOR_LIB}/${PN}
+ dobin PerlLib/*.pm # BUG: install into /usr/bin but wanted to have it readable and executable in ${VENDOR_LIB}/${PN} instead
einfo "Fetch on your own:"
einfo "wget --mirror -nH -nd http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin"
einfo "hmmpress Pfam-AB.hmm.bin"
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/TransDecoder/
@ 2015-06-06 10:23 Justin Lecher
0 siblings, 0 replies; 15+ messages in thread
From: Justin Lecher @ 2015-06-06 10:23 UTC (permalink / raw
To: gentoo-commits
commit: c5e6229967c5663d3c2b514cbe17409806e8a577
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 6 10:13:00 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun 6 10:13:00 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c5e62299
sci-biology/TransDecoder: Add github to remote-id in metadata.xml
Package-Manager: portage-2.2.20
sci-biology/TransDecoder/ChangeLog | 5 ++++-
sci-biology/TransDecoder/metadata.xml | 3 +++
2 files changed, 7 insertions(+), 1 deletion(-)
diff --git a/sci-biology/TransDecoder/ChangeLog b/sci-biology/TransDecoder/ChangeLog
index 6fd8f5c..4e2164c 100644
--- a/sci-biology/TransDecoder/ChangeLog
+++ b/sci-biology/TransDecoder/ChangeLog
@@ -1,7 +1,10 @@
-# ChangeLog for sci-biology/transdecoder
+# ChangeLog for sci-biology/TransDecoder
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
+ sci-biology/TransDecoder: Add github to remote-id in metadata.xml
+
27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
transdecoder-2.0.1.ebuild:
sci-biology/transdecoder: more ebuild cleanup
diff --git a/sci-biology/TransDecoder/metadata.xml b/sci-biology/TransDecoder/metadata.xml
index 2bc8930..33de46b 100644
--- a/sci-biology/TransDecoder/metadata.xml
+++ b/sci-biology/TransDecoder/metadata.xml
@@ -6,4 +6,7 @@
<email>mmokrejs@fold.natur.cuni.cz</email>
<name>Martin Mokrejs</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">TransDecoder/TransDecoder</remote-id>
+ </upstream>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/TransDecoder/
@ 2015-11-19 20:35 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2015-11-19 20:35 UTC (permalink / raw
To: gentoo-commits
commit: 49c3b13f199c94e36b9d9d03642a22aa81191628
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Nov 19 20:34:35 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Nov 19 20:34:35 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=49c3b13f
sci-biology/TransDecoder: update homepage
Package-Manager: portage-2.2.18
sci-biology/TransDecoder/ChangeLog | 4 ++++
sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild | 2 +-
2 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/sci-biology/TransDecoder/ChangeLog b/sci-biology/TransDecoder/ChangeLog
index 67b410e..2445e83 100644
--- a/sci-biology/TransDecoder/ChangeLog
+++ b/sci-biology/TransDecoder/ChangeLog
@@ -3,6 +3,10 @@
# $Id$
19 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ TransDecoder-2.0.1.ebuild:
+ sci-biology/TransDecoder: update homepage
+
+ 19 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+files/TransDecoder-2.0.1__fix_paths.patch, -files/TransDecoder.patch,
TransDecoder-2.0.1.ebuild, files/pfam_runner.pl.patch:
sci-biology/TransDecoder: install properly perl modules; fix PERL5INC paths by
diff --git a/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild b/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild
index 5894f2a..bac0a96 100644
--- a/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild
+++ b/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild
@@ -10,7 +10,7 @@ PERL_EXPORT_PHASE_FUNCTIONS=no
inherit perl-module eutils toolchain-funcs
DESCRIPTION="Extract ORF/CDS regions from FASTA sequences"
-HOMEPAGE="http://sourceforge.net/projects/transdecoder/"
+HOMEPAGE="http://transdecoder.github.io"
if [ "$PV" == "9999" ]; then
EGIT_REPO_URI="https://github.com/TransDecoder/TransDecoder.git"
KEYWORDS=""
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/TransDecoder/
@ 2015-11-19 20:56 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2015-11-19 20:56 UTC (permalink / raw
To: gentoo-commits
commit: 8bb47dd4462917d5054c9e4e43b063e1f0db5c95
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Nov 19 20:55:08 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Nov 19 20:55:08 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8bb47dd4
sci-biology/TransDecoder: note that Pfam-AB was discontinued
Package-Manager: portage-2.2.18
sci-biology/TransDecoder/ChangeLog | 4 ++++
sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild | 6 +++---
2 files changed, 7 insertions(+), 3 deletions(-)
diff --git a/sci-biology/TransDecoder/ChangeLog b/sci-biology/TransDecoder/ChangeLog
index 2445e83..ee19193 100644
--- a/sci-biology/TransDecoder/ChangeLog
+++ b/sci-biology/TransDecoder/ChangeLog
@@ -4,6 +4,10 @@
19 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
TransDecoder-2.0.1.ebuild:
+ sci-biology/TransDecoder: note that Pfam-AB was discontinued
+
+ 19 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ TransDecoder-2.0.1.ebuild:
sci-biology/TransDecoder: update homepage
19 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild b/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild
index bac0a96..113c915 100644
--- a/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild
+++ b/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild
@@ -70,9 +70,9 @@ src_install(){
insinto ${VENDOR_LIB}/${PN}
doins PerlLib/*.pm
dodoc Release.Notes
- einfo "Fetch on your own:"
- einfo "wget --mirror -nH -nd http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin"
- einfo "hmmpress Pfam-AB.hmm.bin"
+ einfo "Fetch on your own Pfam-A.hmm (Pfam-AB.hmm is discontinued since 05/2015):"
+ einfo "wget --mirror -nH -nd ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz"
+ einfo "hmmpress Pfam-A.hmm.bin"
}
pkg_postinst(){
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/TransDecoder/
@ 2015-12-25 21:00 Marius Brehler
0 siblings, 0 replies; 15+ messages in thread
From: Marius Brehler @ 2015-12-25 21:00 UTC (permalink / raw
To: gentoo-commits
commit: f08c7474c8fed99cd2614babe0ea5462f31752ae
Author: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Fri Dec 25 20:47:28 2015 +0000
Commit: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Fri Dec 25 20:47:28 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f08c7474
sci-biology/TransDecoder: Fix minorsyn, add missing die
Package-Manager: portage-2.2.24
sci-biology/TransDecoder/ChangeLog | 4 ++++
sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild | 4 ++--
2 files changed, 6 insertions(+), 2 deletions(-)
diff --git a/sci-biology/TransDecoder/ChangeLog b/sci-biology/TransDecoder/ChangeLog
index ee19193..e9110b4 100644
--- a/sci-biology/TransDecoder/ChangeLog
+++ b/sci-biology/TransDecoder/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+ 25 Dec 2015; Marius Brehler <marbre@linux.sungazer.de>
+ TransDecoder-2.0.1.ebuild:
+ sci-biology/TransDecoder: Fix minorsyn, add missing die
+
19 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
TransDecoder-2.0.1.ebuild:
sci-biology/TransDecoder: note that Pfam-AB was discontinued
diff --git a/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild b/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild
index 113c915..dfe3fbb 100644
--- a/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild
+++ b/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild
@@ -15,7 +15,7 @@ if [ "$PV" == "9999" ]; then
EGIT_REPO_URI="https://github.com/TransDecoder/TransDecoder.git"
KEYWORDS=""
else
- SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/"${PV}".tar.gz -> ${P}.tar.gz"
+ SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/"${PV}".tar.gz -> ${P}.tar.gz"
KEYWORDS="~amd64"
S="${WORKDIR}"/TransDecoder-"${PV}"
fi
@@ -34,7 +34,7 @@ src_prepare(){
rm -rf transdecoder_plugins/cd-hit
for f in PerlLib/*.pm; do
p=`basename $f .pm`;
- sed -e "s#use $p;#use TransDecoder::$p;#" -i PerlLib/*.pm util/*.pl TransDecoder.LongOrfs TransDecoder.Predict;
+ sed -e "s#use $p;#use TransDecoder::$p;#" -i PerlLib/*.pm util/*.pl TransDecoder.LongOrfs TransDecoder.Predict || die;
done
epatch "${FILESDIR}"/"${P}"__fix_paths.patch
epatch "${FILESDIR}"/pfam_runner.pl.patch
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/TransDecoder/
@ 2016-07-11 9:11 Martin Mokrejs
0 siblings, 0 replies; 15+ messages in thread
From: Martin Mokrejs @ 2016-07-11 9:11 UTC (permalink / raw
To: gentoo-commits
commit: 918d50a836b2cd7639dfaea61628b94c87a5c186
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jul 11 09:10:57 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jul 11 09:10:57 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=918d50a8
sci-biology/TransDecoder: respect EPREFIX, add missing die
Package-Manager: portage-2.2.28
sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild | 2 +-
sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild | 6 +++++-
2 files changed, 6 insertions(+), 2 deletions(-)
diff --git a/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild b/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild
index dfe3fbb..9ca6b2b 100644
--- a/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild
+++ b/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild
@@ -53,7 +53,7 @@ src_install(){
dobin TransDecoder.Predict TransDecoder.LongOrfs
insinto /usr/share/${PN}/util
doins util/*.pl
- chmod -R a+rx "${D}"/usr/share/${PN}/util
+ chmod -R a+rx "${D}"/"${EPREFIX}"/usr/share/${PN}/util || die
# zap the bundled cdhit binaries copied from transdecoder_plugins/cdhit/ to util/bin
rm -rf util/bin
#
diff --git a/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild b/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild
index 9fbcea5..2a65c0c 100644
--- a/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild
+++ b/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild
@@ -53,7 +53,7 @@ src_install(){
dobin TransDecoder.Predict TransDecoder.LongOrfs
insinto /usr/share/${PN}/util
doins util/*.pl
- chmod -R a+rx "${D}"/usr/share/${PN}/util
+ chmod -R a+rx "${D}"/"${EPREFIX}"/usr/share/${PN}/util || die
# zap the bundled cdhit binaries copied from transdecoder_plugins/cdhit/ to util/bin
rm -rf util/bin
#
@@ -67,6 +67,10 @@ src_install(){
# * /usr/bin/TiedHash.pm
#
perl_set_version
+ # this is broken and installs into
+ # /scratch/mmokrejs/gentoo/var/tmp/portage/sci-biology/TransDecoder-2.1.0/image/scratch/mmokrejs/gentoo/scratch/mmokrejs/gentoo/usr/lib/perl5/vendor_perl/
+ # instead of
+ # /scratch/mmokrejs/gentoo/var/tmp/portage/sci-biology/TransDecoder-2.1.0/image/scratch/mmokrejs/gentoo/usr/lib/perl5/vendor_perl/
insinto ${VENDOR_LIB}/${PN}
doins PerlLib/*.pm
# dodoc Release.Notes
^ permalink raw reply related [flat|nested] 15+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/TransDecoder/
@ 2021-01-19 16:26 Andrew Ammerlaan
0 siblings, 0 replies; 15+ messages in thread
From: Andrew Ammerlaan @ 2021-01-19 16:26 UTC (permalink / raw
To: gentoo-commits
commit: 60791ac1314964a122e24e480fbba07c64939ef1
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 16:12:28 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 16:12:28 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=60791ac1
sci-biology/TransDecoder: remove unnecessary slash strip
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/TransDecoder/TransDecoder-5.5.0.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/TransDecoder/TransDecoder-5.5.0.ebuild b/sci-biology/TransDecoder/TransDecoder-5.5.0.ebuild
index c485d4b86..ed37d3a05 100644
--- a/sci-biology/TransDecoder/TransDecoder-5.5.0.ebuild
+++ b/sci-biology/TransDecoder/TransDecoder-5.5.0.ebuild
@@ -57,7 +57,7 @@ src_install() {
insinto /usr/share/${PN}/util
doins util/*.pl
- chmod -R a+rx "${ED%/}"/usr/share/${PN}/util || die
+ chmod -R a+rx "${ED}"/usr/share/${PN}/util || die
# zap the bundled cdhit binaries copied from transdecoder_plugins/cdhit/ to util/bin
rm -rf util/bin || die
^ permalink raw reply related [flat|nested] 15+ messages in thread
end of thread, other threads:[~2021-01-19 16:26 UTC | newest]
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2016-07-11 9:11 Martin Mokrejs
2015-12-25 21:00 Marius Brehler
2015-11-19 20:56 Martin Mokrejs
2015-11-19 20:35 Martin Mokrejs
2015-04-27 13:04 [gentoo-commits] proj/sci:master commit in: sci-biology/transdecoder/ Martin Mokrejs
2015-04-27 12:49 Martin Mokrejs
2015-04-27 12:48 Martin Mokrejs
2015-04-17 22:21 Martin Mokrejs
2015-03-19 10:47 Martin Mokrejs
2015-03-19 10:37 Martin Mokrejs
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