* [gentoo-commits] proj/sci:master commit in: sci-biology/fsa/
@ 2014-03-23 19:19 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2014-03-23 19:19 UTC (permalink / raw
To: gentoo-commits
commit: 3c3a34aa80b0005596c8d817848f47531712d9f6
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 19:17:50 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 19:17:50 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3c3a34aa
sci-biology/fsa: new package, enforces its own CXXFLAGS, compiles also some java stuff, source code does not compile
Package-Manager: portage-2.2.7
---
sci-biology/fsa/ChangeLog | 10 ++++++++++
sci-biology/fsa/fsa-1.15.7.ebuild | 19 +++++++++++++++++++
sci-biology/fsa/metadata.xml | 9 +++++++++
3 files changed, 38 insertions(+)
diff --git a/sci-biology/fsa/ChangeLog b/sci-biology/fsa/ChangeLog
new file mode 100644
index 0000000..04f0887
--- /dev/null
+++ b/sci-biology/fsa/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/fsa
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*fsa-1.15.7 (23 Mar 2014)
+
+ 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +fsa-1.15.7.ebuild,
+ +metadata.xml:
+ sci-biology/fsa: new package, enforces its own CXXFLAGS, compiles also some
+ java stuff, source code does not compile
diff --git a/sci-biology/fsa/fsa-1.15.7.ebuild b/sci-biology/fsa/fsa-1.15.7.ebuild
new file mode 100644
index 0000000..e527ee6
--- /dev/null
+++ b/sci-biology/fsa/fsa-1.15.7.ebuild
@@ -0,0 +1,19 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="Distance-based probabilistic multiple sequence alignment algorithm for DNA/RNA/protein"
+HOMEPAGE="http://fsa.sourceforge.net"
+SRC_URI="http://downloads.sourceforge.net/project/fsa/fsa-1.15.7.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/fsa/metadata.xml b/sci-biology/fsa/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/fsa/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] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsa/
@ 2016-07-01 12:23 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2016-07-01 12:23 UTC (permalink / raw
To: gentoo-commits
commit: 6eaf96697abf7c0bc7662a2f25ae5762c2d17cfc
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 1 12:23:15 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 1 12:23:15 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6eaf9669
sci-biology/fsa: version bump
Package-Manager: portage-2.2.28
sci-biology/fsa/{fsa-1.15.7.ebuild => fsa-1.15.9.ebuild} | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/fsa/fsa-1.15.7.ebuild b/sci-biology/fsa/fsa-1.15.9.ebuild
similarity index 64%
rename from sci-biology/fsa/fsa-1.15.7.ebuild
rename to sci-biology/fsa/fsa-1.15.9.ebuild
index 89f90a8..879a1c0 100644
--- a/sci-biology/fsa/fsa-1.15.7.ebuild
+++ b/sci-biology/fsa/fsa-1.15.9.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
# $Id$
@@ -6,9 +6,9 @@ EAPI=5
inherit eutils
-DESCRIPTION="Distance-based probabilistic multiple sequence alignment algorithm for DNA/RNA/protein"
+DESCRIPTION="Distance-based probabilistic multiple sequence alignment algo for DNA/RNA/prot"
HOMEPAGE="http://fsa.sourceforge.net"
-SRC_URI="http://downloads.sourceforge.net/project/fsa/fsa-1.15.7.tar.gz"
+SRC_URI="http://downloads.sourceforge.net/project/fsa/"${P}".tar.gz"
LICENSE="GPL-2"
SLOT="0"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsa/
@ 2016-07-01 12:33 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2016-07-01 12:33 UTC (permalink / raw
To: gentoo-commits
commit: 65cbf3d51c23c49ac206a0b38f0f94b0a2546d56
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 1 12:32:51 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 1 12:32:51 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=65cbf3d5
sci-biology/fsa: fix license, document optional packages, add DEPEND on java-config
Package-Manager: portage-2.2.28
sci-biology/fsa/fsa-1.15.9.ebuild | 18 ++++++++++++++++--
1 file changed, 16 insertions(+), 2 deletions(-)
diff --git a/sci-biology/fsa/fsa-1.15.9.ebuild b/sci-biology/fsa/fsa-1.15.9.ebuild
index 879a1c0..d37d56b 100644
--- a/sci-biology/fsa/fsa-1.15.9.ebuild
+++ b/sci-biology/fsa/fsa-1.15.9.ebuild
@@ -10,10 +10,24 @@ DESCRIPTION="Distance-based probabilistic multiple sequence alignment algo for D
HOMEPAGE="http://fsa.sourceforge.net"
SRC_URI="http://downloads.sourceforge.net/project/fsa/"${P}".tar.gz"
-LICENSE="GPL-2"
+LICENSE="GPL-3+"
SLOT="0"
KEYWORDS=""
IUSE=""
-DEPEND=""
+DEPEND="dev-java/java-config"
RDEPEND="${DEPEND}"
+
+# needs java for fsa-1.15.9/display/ processing:
+# jar cmf mad/manifest.mf mad.jar \
+# -C . mad \
+# -C . JMF-2.1.1e/lib/jmf.jar \
+# -C . jai-1_1_3/lib/jai_core.jar \
+# -C . jai-1_1_3/lib/jai_codec.jar
+# * Home for VM '' does not exist:
+# * Invalid System VM:
+
+pkg_postinst(){
+ einfo "Optionally you may want to install sci-biology/mummer and"
+ einfo "sci-biology/exonerate"
+}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsa/
@ 2016-07-01 12:45 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2016-07-01 12:45 UTC (permalink / raw
To: gentoo-commits
commit: 4c11d0f2c46ccb8d43bff240df36a43c69bde1a0
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 1 12:45:37 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 1 12:45:37 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4c11d0f2
sci-biology/fsa: prevent file collision
Package-Manager: portage-2.2.28
sci-biology/fsa/fsa-1.15.9.ebuild | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/sci-biology/fsa/fsa-1.15.9.ebuild b/sci-biology/fsa/fsa-1.15.9.ebuild
index d37d56b..71fccc8 100644
--- a/sci-biology/fsa/fsa-1.15.9.ebuild
+++ b/sci-biology/fsa/fsa-1.15.9.ebuild
@@ -27,6 +27,12 @@ RDEPEND="${DEPEND}"
# * Home for VM '' does not exist:
# * Invalid System VM:
+src_install(){
+ default
+ # avoid file collision with sci-biology/ESTate-0.5
+ mv "${D}"/"${EPREFIX}"/usr/bin/translate "${D}"/"${EPREFIX}"/usr/bin/fsa_translate || die
+}
+
pkg_postinst(){
einfo "Optionally you may want to install sci-biology/mummer and"
einfo "sci-biology/exonerate"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsa/
@ 2023-03-21 23:07 Horea Christian
0 siblings, 0 replies; 6+ messages in thread
From: Horea Christian @ 2023-03-21 23:07 UTC (permalink / raw
To: gentoo-commits
commit: fe06018d03259cfc2f1bf507e618f3f858fa74bb
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Tue Mar 21 23:07:15 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue Mar 21 23:07:24 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=fe06018d
sci-biology/fsa: update EAPI 7 -> 8, HTTPS update
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/fsa/fsa-1.15.9.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/fsa/fsa-1.15.9.ebuild b/sci-biology/fsa/fsa-1.15.9.ebuild
index 44e1d5cff..f77ae61aa 100644
--- a/sci-biology/fsa/fsa-1.15.9.ebuild
+++ b/sci-biology/fsa/fsa-1.15.9.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
DESCRIPTION="Distance-based probabilistic multiple sequence alignment algo for DNA/RNA/prot"
-HOMEPAGE="http://fsa.sourceforge.net"
+HOMEPAGE="https://fsa.sourceforge.net"
SRC_URI="https://downloads.sourceforge.net/project/fsa/${P}.tar.gz"
LICENSE="GPL-3+"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fsa/
@ 2023-03-22 19:58 Horea Christian
0 siblings, 0 replies; 6+ messages in thread
From: Horea Christian @ 2023-03-22 19:58 UTC (permalink / raw
To: gentoo-commits
commit: fdbc6363cdf1bef7a3092916deb662690d78fdfa
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Wed Mar 22 19:58:27 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Wed Mar 22 19:58:27 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=fdbc6363
sci-biology/fsa: update upstream metadata
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/fsa/metadata.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/fsa/metadata.xml b/sci-biology/fsa/metadata.xml
index 0f267b755..e8c9d160f 100644
--- a/sci-biology/fsa/metadata.xml
+++ b/sci-biology/fsa/metadata.xml
@@ -10,6 +10,6 @@
<name>Gentoo Biology Project</name>
</maintainer>
<upstream>
- <remote-id type="sourceforge">downloads</remote-id>
+ <remote-id type="sourceforge">fsa</remote-id>
</upstream>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 6+ messages in thread
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