* [gentoo-commits] proj/sci:master commit in: sci-biology/prot4EST/
@ 2014-06-24 10:48 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2014-06-24 10:48 UTC (permalink / raw
To: gentoo-commits
commit: 1cb6ae89c8b2c693dad53a44dc28c069464a1362
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jun 24 10:47:58 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jun 24 10:47:58 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1cb6ae89
sci-biology/prot4EST: new package, missing LICENSE, missing dev-perl/ deps
---
sci-biology/prot4EST/prot4EST-3.1b.ebuild | 37 +++++++++++++++++++++++++++++++
1 file changed, 37 insertions(+)
diff --git a/sci-biology/prot4EST/prot4EST-3.1b.ebuild b/sci-biology/prot4EST/prot4EST-3.1b.ebuild
new file mode 100644
index 0000000..b7b4642
--- /dev/null
+++ b/sci-biology/prot4EST/prot4EST-3.1b.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit perl-module
+
+DESCRIPTION="Predict proteins from EST sequences overcoming errors in ORFs"
+HOMEPAGE="http://www.compsysbio.org/lab/?q=prot4EST"
+SRC_URI="http://www.compsysbio.org/lab/james/prot4EST_rl3.1b.tgz"
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="sci-biology/emboss
+ sci-biology/estscan
+ sci-biology/bioperl
+ dev-perl/Algorithm-Loops
+ perl-core/File-Path
+ dev-perl/File-Copy
+ perl-core/Getopt-Long
+ dev-perl/Statistics-Descriptive
+ dev-perl/Tie-IxHash"
+
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/"p4e3.1b"
+
+src_install(){
+ mydoc="README"
+ perl-module_src_install
+ dobin bin/*.pl
+ dodoc doc/*
+}
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/prot4EST/
@ 2014-06-24 10:49 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2014-06-24 10:49 UTC (permalink / raw
To: gentoo-commits
commit: b6cc46c3c63decdb095aa02234d8aefd8cff81d5
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jun 24 10:48:45 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jun 24 10:48:45 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b6cc46c3
sci-biology/prot4EST: new package, missing LICENSE, missing dev-perl/ deps
---
sci-biology/prot4EST/ChangeLog | 7 +++++++
sci-biology/prot4EST/metadata.xml | 9 +++++++++
2 files changed, 16 insertions(+)
diff --git a/sci-biology/prot4EST/ChangeLog b/sci-biology/prot4EST/ChangeLog
new file mode 100644
index 0000000..2469055
--- /dev/null
+++ b/sci-biology/prot4EST/ChangeLog
@@ -0,0 +1,7 @@
+# ChangeLog for sci-biology/prot4EST
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 24 Jun 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml:
+ sci-biology/prot4EST: new package, missing LICENSE, missing dev-perl/ deps
+
diff --git a/sci-biology/prot4EST/metadata.xml b/sci-biology/prot4EST/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/prot4EST/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/prot4EST/
@ 2014-06-27 7:52 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2014-06-27 7:52 UTC (permalink / raw
To: gentoo-commits
commit: 4af735ef8a1ff95fa9b32415b383c55721d93b90
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jun 27 07:52:06 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jun 27 07:52:06 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4af735ef
sci-biology/prot4EST: remove version numbers from the installed binary filename
---
sci-biology/prot4EST/prot4EST-3.1b.ebuild | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-biology/prot4EST/prot4EST-3.1b.ebuild b/sci-biology/prot4EST/prot4EST-3.1b.ebuild
index b7b4642..6b4ecf1 100644
--- a/sci-biology/prot4EST/prot4EST-3.1b.ebuild
+++ b/sci-biology/prot4EST/prot4EST-3.1b.ebuild
@@ -32,6 +32,7 @@ S="${WORKDIR}"/"p4e3.1b"
src_install(){
mydoc="README"
perl-module_src_install
+ mv bin/prot4EST*.pl bin/prot4EST.pl
dobin bin/*.pl
dodoc doc/*
}
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/prot4EST/
@ 2014-09-16 4:07 Christoph Junghans
0 siblings, 0 replies; 9+ messages in thread
From: Christoph Junghans @ 2014-09-16 4:07 UTC (permalink / raw
To: gentoo-commits
commit: 34c5d10d6dd86ca8fe2b72948af77c76ea1332f9
Author: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 16 03:07:38 2014 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Sep 16 03:07:38 2014 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=34c5d10d
added license
Package-Manager: portage-2.2.8-r1
---
sci-biology/prot4EST/ChangeLog | 4 +++-
sci-biology/prot4EST/prot4EST-3.1b.ebuild | 7 ++++---
2 files changed, 7 insertions(+), 4 deletions(-)
diff --git a/sci-biology/prot4EST/ChangeLog b/sci-biology/prot4EST/ChangeLog
index 2469055..07d8873 100644
--- a/sci-biology/prot4EST/ChangeLog
+++ b/sci-biology/prot4EST/ChangeLog
@@ -2,6 +2,8 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> prot4EST-3.1b.ebuild:
+ added license
+
24 Jun 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml:
sci-biology/prot4EST: new package, missing LICENSE, missing dev-perl/ deps
-
diff --git a/sci-biology/prot4EST/prot4EST-3.1b.ebuild b/sci-biology/prot4EST/prot4EST-3.1b.ebuild
index 6b4ecf1..fb83884 100644
--- a/sci-biology/prot4EST/prot4EST-3.1b.ebuild
+++ b/sci-biology/prot4EST/prot4EST-3.1b.ebuild
@@ -10,7 +10,8 @@ DESCRIPTION="Predict proteins from EST sequences overcoming errors in ORFs"
HOMEPAGE="http://www.compsysbio.org/lab/?q=prot4EST"
SRC_URI="http://www.compsysbio.org/lab/james/prot4EST_rl3.1b.tgz"
-LICENSE=""
+#http://www.biomedcentral.com/1471-2105/5/187
+LICENSE="GPL-1"
SLOT="0"
KEYWORDS=""
IUSE=""
@@ -18,12 +19,12 @@ IUSE=""
DEPEND="sci-biology/emboss
sci-biology/estscan
sci-biology/bioperl
- dev-perl/Algorithm-Loops
perl-core/File-Path
- dev-perl/File-Copy
perl-core/Getopt-Long
dev-perl/Statistics-Descriptive
dev-perl/Tie-IxHash"
+ #dev-perl/Algorithm-Loops
+ #dev-perl/File-Copy
RDEPEND="${DEPEND}"
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/prot4EST/
@ 2014-11-13 13:00 Justin Lecher
0 siblings, 0 replies; 9+ messages in thread
From: Justin Lecher @ 2014-11-13 13:00 UTC (permalink / raw
To: gentoo-commits
commit: a847bf961a96037696d98e6344692a3526c8d1a4
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Nov 13 13:00:36 2014 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Nov 13 13:00:36 2014 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a847bf96
sci-biology/prot4EST: Use perl virtuals instead of core
Package-Manager: portage-2.2.14
---
sci-biology/prot4EST/ChangeLog | 3 +++
sci-biology/prot4EST/prot4EST-3.1b.ebuild | 4 ++--
2 files changed, 5 insertions(+), 2 deletions(-)
diff --git a/sci-biology/prot4EST/ChangeLog b/sci-biology/prot4EST/ChangeLog
index 07d8873..16dc650 100644
--- a/sci-biology/prot4EST/ChangeLog
+++ b/sci-biology/prot4EST/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 13 Nov 2014; Justin Lecher <jlec@gentoo.org> prot4EST-3.1b.ebuild:
+ Use perl virtuals instead of core
+
16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> prot4EST-3.1b.ebuild:
added license
diff --git a/sci-biology/prot4EST/prot4EST-3.1b.ebuild b/sci-biology/prot4EST/prot4EST-3.1b.ebuild
index fb83884..3533a14 100644
--- a/sci-biology/prot4EST/prot4EST-3.1b.ebuild
+++ b/sci-biology/prot4EST/prot4EST-3.1b.ebuild
@@ -19,8 +19,8 @@ IUSE=""
DEPEND="sci-biology/emboss
sci-biology/estscan
sci-biology/bioperl
- perl-core/File-Path
- perl-core/Getopt-Long
+ virtual/perl-File-Path
+ virtual/perl-Getopt-Long
dev-perl/Statistics-Descriptive
dev-perl/Tie-IxHash"
#dev-perl/Algorithm-Loops
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/prot4EST/
@ 2016-05-03 16:29 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2016-05-03 16:29 UTC (permalink / raw
To: gentoo-commits
commit: ab81c954929bf42695635e178814e48bdf053ba9
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue May 3 16:29:07 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue May 3 16:29:07 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ab81c954
sci-biology/prot4EST: add more DEPS, cleanup
Package-Manager: portage-2.2.28
sci-biology/prot4EST/prot4EST-3.1b.ebuild | 17 ++++++++---------
1 file changed, 8 insertions(+), 9 deletions(-)
diff --git a/sci-biology/prot4EST/prot4EST-3.1b.ebuild b/sci-biology/prot4EST/prot4EST-3.1b.ebuild
index d4528a6..ea30cf4 100644
--- a/sci-biology/prot4EST/prot4EST-3.1b.ebuild
+++ b/sci-biology/prot4EST/prot4EST-3.1b.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -6,11 +6,11 @@ EAPI=5
inherit perl-module
-DESCRIPTION="Predict proteins from EST sequences overcoming errors in ORFs"
-HOMEPAGE="http://www.compsysbio.org/lab/?q=prot4EST"
+DESCRIPTION="Predict proteins from EST sequences overcoming frameshifts"
+HOMEPAGE="http://www.compsysbio.org/lab/?q=prot4EST
+ http://www.biomedcentral.com/1471-2105/5/187"
SRC_URI="http://www.compsysbio.org/lab/james/prot4EST_rl3.1b.tgz"
-#http://www.biomedcentral.com/1471-2105/5/187
LICENSE="GPL-1"
SLOT="0"
KEYWORDS=""
@@ -19,19 +19,18 @@ IUSE=""
DEPEND="sci-biology/emboss
sci-biology/estscan
sci-biology/bioperl
+ sci-biology/ncbi-tools
virtual/perl-File-Path
virtual/perl-Getopt-Long
dev-perl/Statistics-Descriptive
- dev-perl/Tie-IxHash"
- #dev-perl/Algorithm-Loops
- #dev-perl/File-Copy
-
+ dev-perl/Tie-IxHash
+ dev-perl/Algorithm-Loops"
RDEPEND="${DEPEND}"
S="${WORKDIR}"/"p4e3.1b"
src_install(){
- mydoc="README"
+ mydoc="README INSTALL"
perl-module_src_install
mv bin/prot4EST*.pl bin/prot4EST.pl
dobin bin/*.pl
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/prot4EST/
@ 2016-07-12 16:18 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2016-07-12 16:18 UTC (permalink / raw
To: gentoo-commits
commit: c94394ee9f5030b5b2610b5b1f3319d5bb3080bf
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jul 12 16:15:01 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jul 12 16:15:01 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c94394ee
sci-biology/prot4EST: document another DEPENDency
Package-Manager: portage-2.2.28
sci-biology/prot4EST/prot4EST-3.1b.ebuild | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-biology/prot4EST/prot4EST-3.1b.ebuild b/sci-biology/prot4EST/prot4EST-3.1b.ebuild
index ea30cf4..0f5d7c4 100644
--- a/sci-biology/prot4EST/prot4EST-3.1b.ebuild
+++ b/sci-biology/prot4EST/prot4EST-3.1b.ebuild
@@ -25,6 +25,7 @@ DEPEND="sci-biology/emboss
dev-perl/Statistics-Descriptive
dev-perl/Tie-IxHash
dev-perl/Algorithm-Loops"
+ # sci-biology/DECODER
RDEPEND="${DEPEND}"
S="${WORKDIR}"/"p4e3.1b"
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/prot4EST/
@ 2021-02-03 7:00 Andrew Ammerlaan
0 siblings, 0 replies; 9+ messages in thread
From: Andrew Ammerlaan @ 2021-02-03 7:00 UTC (permalink / raw
To: gentoo-commits
commit: c7f4932ad11efd2d6b3f26f4c32f1bdd33890170
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Feb 3 07:00:13 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Feb 3 07:00:13 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c7f4932a
sci-biology/prot4EST: EAPI bump
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/prot4EST/prot4EST-3.1b.ebuild | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/sci-biology/prot4EST/prot4EST-3.1b.ebuild b/sci-biology/prot4EST/prot4EST-3.1b.ebuild
index 344a0b383..fc4058de5 100644
--- a/sci-biology/prot4EST/prot4EST-3.1b.ebuild
+++ b/sci-biology/prot4EST/prot4EST-3.1b.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
inherit perl-module
@@ -12,10 +12,10 @@ SRC_URI="http://www.compsysbio.org/lab/james/prot4EST_rl3.1b.tgz"
LICENSE="GPL-1"
SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
-DEPEND="sci-biology/emboss
+DEPEND="
+ sci-biology/emboss
sci-biology/estscan
sci-biology/bioperl
sci-biology/ncbi-tools
@@ -27,7 +27,7 @@ DEPEND="sci-biology/emboss
# sci-biology/DECODER
RDEPEND="${DEPEND}"
-S="${WORKDIR}"/"p4e3.1b"
+S="${WORKDIR}/p4e3.1b"
src_install(){
mydoc="README INSTALL"
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/prot4EST/
@ 2021-02-25 14:54 Andrew Ammerlaan
0 siblings, 0 replies; 9+ messages in thread
From: Andrew Ammerlaan @ 2021-02-25 14:54 UTC (permalink / raw
To: gentoo-commits
commit: 6430dec6397f25750791c08480b47237d6c9fe60
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Feb 25 14:45:45 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Feb 25 14:45:45 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6430dec6
sci-biology/prot4EST: update homepage: 500
Package-Manager: Portage-3.0.15, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/prot4EST/prot4EST-3.1b.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/prot4EST/prot4EST-3.1b.ebuild b/sci-biology/prot4EST/prot4EST-3.1b.ebuild
index fc4058de5..9f8fb4302 100644
--- a/sci-biology/prot4EST/prot4EST-3.1b.ebuild
+++ b/sci-biology/prot4EST/prot4EST-3.1b.ebuild
@@ -6,7 +6,7 @@ EAPI=7
inherit perl-module
DESCRIPTION="Predict proteins from EST sequences overcoming frameshifts"
-HOMEPAGE="http://www.compsysbio.org/lab/?q=prot4EST
+HOMEPAGE="http://www.compsysbio.org/
http://www.biomedcentral.com/1471-2105/5/187"
SRC_URI="http://www.compsysbio.org/lab/james/prot4EST_rl3.1b.tgz"
^ permalink raw reply related [flat|nested] 9+ messages in thread
end of thread, other threads:[~2021-02-25 14:54 UTC | newest]
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2021-02-25 14:54 Andrew Ammerlaan
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2016-07-12 16:18 Martin Mokrejs
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