* [gentoo-commits] proj/sci:master commit in: sci-chemistry/panav/
@ 2013-07-31 16:45 Nicolas Bock
0 siblings, 0 replies; 6+ messages in thread
From: Nicolas Bock @ 2013-07-31 16:45 UTC (permalink / raw
To: gentoo-commits
commit: e778add7c5e5b9a163df522b00ac5fe85bef0d77
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jul 30 10:02:25 2013 +0000
Commit: Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Tue Jul 30 10:02:25 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e778add7
sci-chemistry/panav: New addition written by me
Package-Manager: portage-2.2.0_alpha190
---
sci-chemistry/panav/ChangeLog | 10 +++++++++
sci-chemistry/panav/metadata.xml | 30 +++++++++++++++++++++++++
sci-chemistry/panav/panav-0.20130730.ebuild | 34 +++++++++++++++++++++++++++++
3 files changed, 74 insertions(+)
diff --git a/sci-chemistry/panav/ChangeLog b/sci-chemistry/panav/ChangeLog
new file mode 100644
index 0000000..f6add7e
--- /dev/null
+++ b/sci-chemistry/panav/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-chemistry/panav
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*panav-0.20130730 (30 Jul 2013)
+
+ 30 Jul 2013; Justin Lecher <jlec@gentoo.org> +panav-0.20130730.ebuild,
+ +metadata.xml:
+ New addition written by me
+
diff --git a/sci-chemistry/panav/metadata.xml b/sci-chemistry/panav/metadata.xml
new file mode 100644
index 0000000..3eacfae
--- /dev/null
+++ b/sci-chemistry/panav/metadata.xml
@@ -0,0 +1,30 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-chemistry</herd>
+ <maintainer>
+ <email>jlec@gentoo.org</email>
+ </maintainer>
+ <longdescription>
+It has been estimated that more than 20% of the proteins in the BMRB are
+improperly referenced and that about 1% of all chemical shift assignments are
+mis-assigned. These statistics also reflect the likelihood that any newly
+assigned protein will have shift assignment or shift referencing errors. The
+relatively high frequency of these errors continues to be a concern for the
+biomolecular NMR community. While several programs do exist to detect and/or
+correct chemical shift mis-referencing or chemical shift mis-assignments, most
+can only do one, or the other. The one program (SHIFTCOR) that is capable of
+handling both chemical shift mis-referencing and mis-assignments, requires the
+3D structure coordinates of the target protein. Given that chemical shift
+mis-assignments and chemical shift re-referencing issues should ideally be
+addressed prior to 3D structure determination, there is a clear need to develop
+a structure-independent approach. Here, we present a new structure-independent
+protocol, which is based on using residue-specific and secondary
+structure-specific chemical shift distributions calculated over
+small (3–6 residue) fragments to identify mis-assigned resonances. The method
+is also able to identify and re-reference mis-referenced chemical shift
+ assignments. Comparisons against existing re-referencing or mis-assignment
+ detection programs show that the method is as good or superior to existing
+ approaches.
+</longdescription>
+</pkgmetadata>
diff --git a/sci-chemistry/panav/panav-0.20130730.ebuild b/sci-chemistry/panav/panav-0.20130730.ebuild
new file mode 100644
index 0000000..bc3d32c
--- /dev/null
+++ b/sci-chemistry/panav/panav-0.20130730.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit java-pkg-2
+
+MY_PN="PANAV"
+
+DESCRIPTION="Probabilistic approach for validating protein NMR chemical shift assignments"
+HOMEPAGE="http://link.springer.com/article/10.1007%2Fs10858-010-9407-y/fulltext.html"
+SRC_URI="http://www.wishartlab.com/download/${MY_PN}.zip -> ${P}.zip"
+
+SLOT="0"
+LICENSE="all-rights-reserved"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+ dev-java/cos
+ >=virtual/jre-1.6"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"/${MY_PN}
+
+src_compile() { :; }
+
+src_install() {
+ java-pkg_newjar ${MY_PN}.jar ${PN}.jar
+ java-pkg_dolauncher
+ java-pkg_regjar "${EPREFIX}"/usr/share/cos/lib/cos.jar
+ dodoc README
+}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/panav/
@ 2015-09-21 17:44 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2015-09-21 17:44 UTC (permalink / raw
To: gentoo-commits
commit: d43a04b7d94cfb686e0c9ec11cdd1b46a24340ea
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 21 17:27:09 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 21 17:27:09 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d43a04b7
sci-chemistry/panav: Add subslot operators
Package-Manager: portage-2.2.20.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-chemistry/panav/panav-0.20130730.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-chemistry/panav/panav-0.20130730.ebuild b/sci-chemistry/panav/panav-0.20130730.ebuild
index e091cb8..660b935 100644
--- a/sci-chemistry/panav/panav-0.20130730.ebuild
+++ b/sci-chemistry/panav/panav-0.20130730.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -19,7 +19,7 @@ IUSE=""
RDEPEND="
dev-java/cos
- >=virtual/jre-1.6"
+ >=virtual/jre-1.6:*"
DEPEND="${RDEPEND}"
S="${WORKDIR}"/${MY_PN}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/panav/
@ 2015-10-06 21:11 Marius Brehler
0 siblings, 0 replies; 6+ messages in thread
From: Marius Brehler @ 2015-10-06 21:11 UTC (permalink / raw
To: gentoo-commits
commit: 4a8ff1169b59651d2cbd21122cc03155c9d2472c
Author: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Tue Oct 6 21:09:16 2015 +0000
Commit: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Tue Oct 6 21:09:16 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4a8ff116
sci-chemistry/panav: Drop keywords
Dependency dev-java/cos is masked and marked for removal.
See bug #562370.
Package-Manager: portage-2.2.20.1
sci-chemistry/panav/ChangeLog | 8 ++++++--
sci-chemistry/panav/panav-0.20130730.ebuild | 2 +-
2 files changed, 7 insertions(+), 3 deletions(-)
diff --git a/sci-chemistry/panav/ChangeLog b/sci-chemistry/panav/ChangeLog
index b2bd8f8..ec45999 100644
--- a/sci-chemistry/panav/ChangeLog
+++ b/sci-chemistry/panav/ChangeLog
@@ -1,10 +1,14 @@
# ChangeLog for sci-chemistry/panav
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+ 06 Oct 2015; Marius Brehler <marbre@linux.sungazer.de>
+ panav-0.20130730.ebuild:
+ sci-chemistry/panav: Drop keywords Dependency dev-java/cos is masked and
+ marked for removal. See bug #562370.
+
*panav-0.20130730 (30 Jul 2013)
30 Jul 2013; Justin Lecher <jlec@gentoo.org> +panav-0.20130730.ebuild,
+metadata.xml:
New addition written by me
-
diff --git a/sci-chemistry/panav/panav-0.20130730.ebuild b/sci-chemistry/panav/panav-0.20130730.ebuild
index 660b935..82d8080 100644
--- a/sci-chemistry/panav/panav-0.20130730.ebuild
+++ b/sci-chemistry/panav/panav-0.20130730.ebuild
@@ -14,7 +14,7 @@ SRC_URI="http://www.wishartlab.com/download/${MY_PN}.zip -> ${P}.zip"
SLOT="0"
LICENSE="all-rights-reserved"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS=""
IUSE=""
RDEPEND="
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/panav/
@ 2021-01-10 18:37 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-01-10 18:37 UTC (permalink / raw
To: gentoo-commits
commit: dd52e248bee00d06a7e560bd51e791babcc4502d
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 10 18:37:16 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Jan 10 18:37:16 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=dd52e248
sci-chemistry/panav: EAPI bump, drop dep on dev-java/cos
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-chemistry/panav/panav-0.20130730.ebuild | 18 ++++++++----------
1 file changed, 8 insertions(+), 10 deletions(-)
diff --git a/sci-chemistry/panav/panav-0.20130730.ebuild b/sci-chemistry/panav/panav-0.20130730.ebuild
index ad98f0187..2ee95c8f7 100644
--- a/sci-chemistry/panav/panav-0.20130730.ebuild
+++ b/sci-chemistry/panav/panav-0.20130730.ebuild
@@ -1,33 +1,31 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
inherit java-pkg-2
MY_PN="PANAV"
DESCRIPTION="Probabilistic approach for validating protein NMR chemical shift assignments"
-HOMEPAGE="http://link.springer.com/article/10.1007%2Fs10858-010-9407-y/fulltext.html"
-SRC_URI="http://www.wishartlab.com/download/${MY_PN}.zip -> ${P}.zip"
+HOMEPAGE="https://link.springer.com/article/10.1007%2Fs10858-010-9407-y/fulltext.html"
+SRC_URI="https://www.wishartlab.com/download/${MY_PN}.zip -> ${P}.zip"
SLOT="0"
LICENSE="all-rights-reserved"
KEYWORDS=""
-IUSE=""
-RDEPEND="
- dev-java/cos
- >=virtual/jre-1.6:*"
+RDEPEND=">=virtual/jre-1.7:*"
DEPEND="${RDEPEND}"
S="${WORKDIR}"/${MY_PN}
-src_compile() { :; }
+src_compile() {
+ return
+}
src_install() {
java-pkg_newjar ${MY_PN}.jar ${PN}.jar
java-pkg_dolauncher
- java-pkg_regjar "${EPREFIX}"/usr/share/cos/lib/cos.jar
dodoc README
}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/panav/
@ 2021-01-19 16:56 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-01-19 16:56 UTC (permalink / raw
To: gentoo-commits
commit: 8a3317266fcc539de5f50f6aad6ddbddac3a67b2
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 16:40:33 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 16:40:33 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8a331726
sci-chemistry/panav: bdepend on unzip
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-chemistry/panav/panav-0.20130730.ebuild | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-chemistry/panav/panav-0.20130730.ebuild b/sci-chemistry/panav/panav-0.20130730.ebuild
index 2ee95c8f7..3bf392e9a 100644
--- a/sci-chemistry/panav/panav-0.20130730.ebuild
+++ b/sci-chemistry/panav/panav-0.20130730.ebuild
@@ -17,6 +17,7 @@ KEYWORDS=""
RDEPEND=">=virtual/jre-1.7:*"
DEPEND="${RDEPEND}"
+BDEPEND="app-arch/unzip"
S="${WORKDIR}"/${MY_PN}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-chemistry/panav/
@ 2021-02-04 8:05 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-02-04 8:05 UTC (permalink / raw
To: gentoo-commits
commit: a1b18019c56c8960dc087de16eed666c7cf5cf7b
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Feb 4 08:05:01 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Feb 4 08:05:01 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a1b18019
sci-chemistry/panav: add keyword
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-chemistry/panav/panav-0.20130730.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-chemistry/panav/panav-0.20130730.ebuild b/sci-chemistry/panav/panav-0.20130730.ebuild
index 3bf392e9a..cd315c348 100644
--- a/sci-chemistry/panav/panav-0.20130730.ebuild
+++ b/sci-chemistry/panav/panav-0.20130730.ebuild
@@ -13,7 +13,7 @@ SRC_URI="https://www.wishartlab.com/download/${MY_PN}.zip -> ${P}.zip"
SLOT="0"
LICENSE="all-rights-reserved"
-KEYWORDS=""
+KEYWORDS="~amd64"
RDEPEND=">=virtual/jre-1.7:*"
DEPEND="${RDEPEND}"
^ permalink raw reply related [flat|nested] 6+ messages in thread
end of thread, other threads:[~2021-02-04 8:05 UTC | newest]
Thread overview: 6+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2021-02-04 8:05 [gentoo-commits] proj/sci:master commit in: sci-chemistry/panav/ Andrew Ammerlaan
-- strict thread matches above, loose matches on Subject: below --
2021-01-19 16:56 Andrew Ammerlaan
2021-01-10 18:37 Andrew Ammerlaan
2015-10-06 21:11 Marius Brehler
2015-09-21 17:44 Justin Lecher
2013-07-31 16:45 Nicolas Bock
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox