* [gentoo-commits] proj/sci:master commit in: sci-biology/Trinotate/
@ 2015-04-30 22:48 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2015-04-30 22:48 UTC (permalink / raw
To: gentoo-commits
commit: 61dd48b0c1dc243678bc613f51ab3aedd6e13ba7
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 30 22:46:51 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 30 22:46:51 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=61dd48b0
sci-biology/Trinotate: new package
Package-Manager: portage-2.2.18
sci-biology/Trinotate/ChangeLog | 9 ++++++
sci-biology/Trinotate/Trinotate-2.0.1.ebuild | 45 ++++++++++++++++++++++++++++
sci-biology/Trinotate/metadata.xml | 9 ++++++
3 files changed, 63 insertions(+)
diff --git a/sci-biology/Trinotate/ChangeLog b/sci-biology/Trinotate/ChangeLog
new file mode 100644
index 0000000..4ef519a
--- /dev/null
+++ b/sci-biology/Trinotate/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/Trinotate
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*Trinotate-2.0.1 (30 Apr 2015)
+
+ 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +Trinotate-2.0.1.ebuild, +metadata.xml:
+ sci-biology/Trinotate: new package
diff --git a/sci-biology/Trinotate/Trinotate-2.0.1.ebuild b/sci-biology/Trinotate/Trinotate-2.0.1.ebuild
new file mode 100644
index 0000000..8665fb4
--- /dev/null
+++ b/sci-biology/Trinotate/Trinotate-2.0.1.ebuild
@@ -0,0 +1,45 @@
+# 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="Annotation and analysis pipeline for de novo assembled transcriptomes"
+HOMEPAGE="http://trinotate.github.io"
+SRC_URI="https://github.com/Trinotate/Trinotate/archive/v${PV}.tar.gz"
+
+LICENSE="BSD-BroadInstitute"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ sci-biology/ncbi-tools++
+ sci-biology/trinityrnaseq
+ sci-biology/TransDecoder"
+
+# http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer
+# >=sci-biology/rnammer-2.3.2
+#
+# http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp
+# >=sci-biology/signalp-4
+#
+# http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm
+
+# We suggest you rename this version of hmmsearch from hmmer-2 package to 'hmmsearch2'.
+# In the 'rnammer' software configuration, edit the rnammer script to point
+# $HMMSEARCH_BINARY = "/path/to/hmmsearch2";
+
+src_install(){
+ perl_set_version
+ dobin Trinotate
+ insinto /usr/share/"${PN}"
+ doins -r admin java sample_data util TrinotateWeb
+ insinto ${VENDOR_LIB}/${PN}
+ doins -r PerlLib/*
+ dodoc Release.Notes
+}
diff --git a/sci-biology/Trinotate/metadata.xml b/sci-biology/Trinotate/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/Trinotate/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>
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Trinotate/
@ 2015-06-06 10:23 Justin Lecher
0 siblings, 0 replies; 9+ messages in thread
From: Justin Lecher @ 2015-06-06 10:23 UTC (permalink / raw
To: gentoo-commits
commit: 0b143bbbb191539e37ab9979c5b25d65a4872e34
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 6 10:13:32 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun 6 10:13:32 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0b143bbb
sci-biology/Trinotate: Add github to remote-id in metadata.xml
Package-Manager: portage-2.2.20
sci-biology/Trinotate/ChangeLog | 3 +++
sci-biology/Trinotate/metadata.xml | 3 +++
2 files changed, 6 insertions(+)
diff --git a/sci-biology/Trinotate/ChangeLog b/sci-biology/Trinotate/ChangeLog
index 4ef519a..f83c1be 100644
--- a/sci-biology/Trinotate/ChangeLog
+++ b/sci-biology/Trinotate/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
+ sci-biology/Trinotate: Add github to remote-id in metadata.xml
+
*Trinotate-2.0.1 (30 Apr 2015)
30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/Trinotate/metadata.xml b/sci-biology/Trinotate/metadata.xml
index 2bc8930..2fa34fe 100644
--- a/sci-biology/Trinotate/metadata.xml
+++ b/sci-biology/Trinotate/metadata.xml
@@ -6,4 +6,7 @@
<email>mmokrejs@fold.natur.cuni.cz</email>
<name>Martin Mokrejs</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">Trinotate/Trinotate</remote-id>
+ </upstream>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Trinotate/
@ 2015-06-06 10:23 Justin Lecher
0 siblings, 0 replies; 9+ messages in thread
From: Justin Lecher @ 2015-06-06 10:23 UTC (permalink / raw
To: gentoo-commits
commit: f020b85eb2a1e678aa5a9c9ba4dec662cfe06c0c
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 6 10:14:17 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun 6 10:14:17 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f020b85e
sci-biology/Trinotate: Fix whitespaces
Package-Manager: portage-2.2.20
sci-biology/Trinotate/ChangeLog | 3 +++
sci-biology/Trinotate/Trinotate-2.0.1.ebuild | 4 ++--
2 files changed, 5 insertions(+), 2 deletions(-)
diff --git a/sci-biology/Trinotate/ChangeLog b/sci-biology/Trinotate/ChangeLog
index f83c1be..86519b9 100644
--- a/sci-biology/Trinotate/ChangeLog
+++ b/sci-biology/Trinotate/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 06 Jun 2015; Justin Lecher <jlec@gentoo.org> Trinotate-2.0.1.ebuild:
+ sci-biology/Trinotate: Fix whitespaces
+
06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
sci-biology/Trinotate: Add github to remote-id in metadata.xml
diff --git a/sci-biology/Trinotate/Trinotate-2.0.1.ebuild b/sci-biology/Trinotate/Trinotate-2.0.1.ebuild
index 8665fb4..0cf1116 100644
--- a/sci-biology/Trinotate/Trinotate-2.0.1.ebuild
+++ b/sci-biology/Trinotate/Trinotate-2.0.1.ebuild
@@ -35,8 +35,8 @@ RDEPEND="${DEPEND}
# $HMMSEARCH_BINARY = "/path/to/hmmsearch2";
src_install(){
- perl_set_version
- dobin Trinotate
+ perl_set_version
+ dobin Trinotate
insinto /usr/share/"${PN}"
doins -r admin java sample_data util TrinotateWeb
insinto ${VENDOR_LIB}/${PN}
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Trinotate/
@ 2016-01-06 8:49 Justin Lecher
0 siblings, 0 replies; 9+ messages in thread
From: Justin Lecher @ 2016-01-06 8:49 UTC (permalink / raw
To: gentoo-commits
commit: 9c210103b141e8157442501198f89850a0f02f4d
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jan 6 08:41:37 2016 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Jan 6 08:41:37 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9c210103
sci-biology/Trinotate: Drop all KEYWORDS because of missing revdeps
Package-Manager: portage-2.2.26
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/Trinotate/Trinotate-2.0.1.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/Trinotate/Trinotate-2.0.1.ebuild b/sci-biology/Trinotate/Trinotate-2.0.1.ebuild
index 100dec7..0b73a75 100644
--- a/sci-biology/Trinotate/Trinotate-2.0.1.ebuild
+++ b/sci-biology/Trinotate/Trinotate-2.0.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -13,7 +13,7 @@ SRC_URI="https://github.com/Trinotate/Trinotate/archive/v${PV}.tar.gz"
LICENSE="BSD-BroadInstitute"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS=""
IUSE=""
DEPEND=""
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Trinotate/
@ 2021-01-19 16:26 Andrew Ammerlaan
0 siblings, 0 replies; 9+ messages in thread
From: Andrew Ammerlaan @ 2021-01-19 16:26 UTC (permalink / raw
To: gentoo-commits
commit: 3a049f99bc0cdc27afb7febc95897b36e5ed65fb
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 16:13:13 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 16:13:13 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3a049f99
sci-biology/Trinotate: properly name tarball
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/Trinotate/Trinotate-2.0.1.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/Trinotate/Trinotate-2.0.1.ebuild b/sci-biology/Trinotate/Trinotate-2.0.1.ebuild
index 61d7e233e..13dd775aa 100644
--- a/sci-biology/Trinotate/Trinotate-2.0.1.ebuild
+++ b/sci-biology/Trinotate/Trinotate-2.0.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -8,7 +8,7 @@ inherit perl-module eutils toolchain-funcs
DESCRIPTION="Annotation and analysis pipeline for de novo assembled transcriptomes"
HOMEPAGE="http://trinotate.github.io"
-SRC_URI="https://github.com/Trinotate/Trinotate/archive/v${PV}.tar.gz"
+SRC_URI="https://github.com/Trinotate/Trinotate/archive/v${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="BSD-BroadInstitute"
SLOT="0"
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Trinotate/
@ 2021-02-01 9:14 Andrew Ammerlaan
0 siblings, 0 replies; 9+ messages in thread
From: Andrew Ammerlaan @ 2021-02-01 9:14 UTC (permalink / raw
To: gentoo-commits
commit: 28a4553de32754b0a5bba92424537bb31bd72e1f
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Feb 1 09:14:09 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Feb 1 09:14:09 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=28a4553d
sci-biology/Trinotate: version bump 3.2.1
no keywords, because dep trinityrnaseq is missing them
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
...{Trinotate-2.0.1.ebuild => Trinotate-3.2.1.ebuild} | 19 ++++++++++---------
1 file changed, 10 insertions(+), 9 deletions(-)
diff --git a/sci-biology/Trinotate/Trinotate-2.0.1.ebuild b/sci-biology/Trinotate/Trinotate-3.2.1.ebuild
similarity index 71%
rename from sci-biology/Trinotate/Trinotate-2.0.1.ebuild
rename to sci-biology/Trinotate/Trinotate-3.2.1.ebuild
index 13dd775aa..85807d4a0 100644
--- a/sci-biology/Trinotate/Trinotate-2.0.1.ebuild
+++ b/sci-biology/Trinotate/Trinotate-3.2.1.ebuild
@@ -1,25 +1,24 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
+inherit perl-module toolchain-funcs
DESCRIPTION="Annotation and analysis pipeline for de novo assembled transcriptomes"
-HOMEPAGE="http://trinotate.github.io"
-SRC_URI="https://github.com/Trinotate/Trinotate/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki"
+SRC_URI="https://github.com/Trinotate/Trinotate/archive/${PN}-v${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="BSD-BroadInstitute"
SLOT="0"
KEYWORDS=""
-IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
sci-biology/ncbi-tools++
sci-biology/trinityrnaseq
- sci-biology/TransDecoder"
+ sci-biology/TransDecoder
+"
# http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer
# >=sci-biology/rnammer-2.3.2
@@ -33,12 +32,14 @@ RDEPEND="${DEPEND}
# In the 'rnammer' software configuration, edit the rnammer script to point
# $HMMSEARCH_BINARY = "/path/to/hmmsearch2";
+S="${WORKDIR}/${PN}-${PN}-v${PV}"
+
src_install(){
perl_set_version
dobin Trinotate
insinto /usr/share/"${PN}"
- doins -r admin java sample_data util TrinotateWeb
+ doins -r admin sample_data util TrinotateWeb
insinto ${VENDOR_LIB}/${PN}
doins -r PerlLib/*
- dodoc Release.Notes
+ dodoc notes README.md README.txt Changelog.txt
}
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Trinotate/
@ 2021-03-18 18:54 Andrew Ammerlaan
0 siblings, 0 replies; 9+ messages in thread
From: Andrew Ammerlaan @ 2021-03-18 18:54 UTC (permalink / raw
To: gentoo-commits
commit: 9b1833de52a142c55ed9669ad73760e41417e1be
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Mar 18 18:45:22 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Mar 18 18:45:22 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9b1833de
sci-biology/Trinotate: use perl_domodule
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/Trinotate/Trinotate-3.2.1.ebuild | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/sci-biology/Trinotate/Trinotate-3.2.1.ebuild b/sci-biology/Trinotate/Trinotate-3.2.1.ebuild
index 85807d4a0..1af77dccd 100644
--- a/sci-biology/Trinotate/Trinotate-3.2.1.ebuild
+++ b/sci-biology/Trinotate/Trinotate-3.2.1.ebuild
@@ -39,7 +39,6 @@ src_install(){
dobin Trinotate
insinto /usr/share/"${PN}"
doins -r admin sample_data util TrinotateWeb
- insinto ${VENDOR_LIB}/${PN}
- doins -r PerlLib/*
+ perl_domodule -r PerlLib/*
dodoc notes README.md README.txt Changelog.txt
}
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Trinotate/
@ 2022-01-25 14:24 Andrew Ammerlaan
0 siblings, 0 replies; 9+ messages in thread
From: Andrew Ammerlaan @ 2022-01-25 14:24 UTC (permalink / raw
To: gentoo-commits
commit: bf80472ee8ddd7d21ecf1b519d588a080b794c1b
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 14:03:28 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 14:03:28 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=bf80472e
sci-biology/Trinotate: add keywords
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
.../Trinotate/{Trinotate-3.2.1.ebuild => Trinotate-3.2.2.ebuild} | 9 ++++-----
1 file changed, 4 insertions(+), 5 deletions(-)
diff --git a/sci-biology/Trinotate/Trinotate-3.2.1.ebuild b/sci-biology/Trinotate/Trinotate-3.2.2.ebuild
similarity index 94%
rename from sci-biology/Trinotate/Trinotate-3.2.1.ebuild
rename to sci-biology/Trinotate/Trinotate-3.2.2.ebuild
index ca61abdf4..794de03ae 100644
--- a/sci-biology/Trinotate/Trinotate-3.2.1.ebuild
+++ b/sci-biology/Trinotate/Trinotate-3.2.2.ebuild
@@ -1,17 +1,18 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit perl-module
DESCRIPTION="Annotation and analysis pipeline for de novo assembled transcriptomes"
HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki"
SRC_URI="https://github.com/Trinotate/Trinotate/archive/${PN}-v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-${PN}-v${PV}"
LICENSE="BSD-BroadInstitute"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
DEPEND=""
RDEPEND="${DEPEND}
@@ -32,8 +33,6 @@ RDEPEND="${DEPEND}
# In the 'rnammer' software configuration, edit the rnammer script to point
# $HMMSEARCH_BINARY = "/path/to/hmmsearch2";
-S="${WORKDIR}/${PN}-${PN}-v${PV}"
-
src_install(){
perl_set_version
dobin Trinotate
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Trinotate/
@ 2023-05-02 12:27 Andrew Ammerlaan
0 siblings, 0 replies; 9+ messages in thread
From: Andrew Ammerlaan @ 2023-05-02 12:27 UTC (permalink / raw
To: gentoo-commits
commit: 57c33d4c76231f270c8d5c5cabe32acfa59e6455
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May 2 12:26:38 2023 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May 2 12:26:38 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=57c33d4c
sci-biology/Trinotate: treeclean
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/Trinotate/Trinotate-3.2.2.ebuild | 43 ----------------------------
sci-biology/Trinotate/metadata.xml | 15 ----------
2 files changed, 58 deletions(-)
diff --git a/sci-biology/Trinotate/Trinotate-3.2.2.ebuild b/sci-biology/Trinotate/Trinotate-3.2.2.ebuild
deleted file mode 100644
index 794de03ae..000000000
--- a/sci-biology/Trinotate/Trinotate-3.2.2.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit perl-module
-
-DESCRIPTION="Annotation and analysis pipeline for de novo assembled transcriptomes"
-HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki"
-SRC_URI="https://github.com/Trinotate/Trinotate/archive/${PN}-v${PV}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/${PN}-${PN}-v${PV}"
-
-LICENSE="BSD-BroadInstitute"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND=""
-RDEPEND="${DEPEND}
- sci-biology/ncbi-tools++
- sci-biology/trinityrnaseq
- sci-biology/TransDecoder
-"
-
-# http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer
-# >=sci-biology/rnammer-2.3.2
-#
-# http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp
-# >=sci-biology/signalp-4
-#
-# http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm
-
-# We suggest you rename this version of hmmsearch from hmmer-2 package to 'hmmsearch2'.
-# In the 'rnammer' software configuration, edit the rnammer script to point
-# $HMMSEARCH_BINARY = "/path/to/hmmsearch2";
-
-src_install(){
- perl_set_version
- dobin Trinotate
- insinto /usr/share/"${PN}"
- doins -r admin sample_data util TrinotateWeb
- perl_domodule -r PerlLib/*
- dodoc notes README.md README.txt Changelog.txt
-}
diff --git a/sci-biology/Trinotate/metadata.xml b/sci-biology/Trinotate/metadata.xml
deleted file mode 100644
index eaf731f09..000000000
--- a/sci-biology/Trinotate/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">Trinotate/Trinotate</remote-id>
- </upstream>
-</pkgmetadata>
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