* [gentoo-commits] proj/sci:master commit in: sci-biology/Sibelia/
@ 2018-01-19 22:53 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2018-01-19 22:53 UTC (permalink / raw
To: gentoo-commits
commit: f01d815ad584ba9fba254dadefb663bce8eeb010
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jan 19 22:53:13 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jan 19 22:53:13 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f01d815a
sci-biology/Sibelia: new package
It installs despite the fact it contains bundled
3rd-party stuff. I will contact upstream and see
whether they will manage to unbundle the many libs
and apps.
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/Sibelia/Sibelia-9999.ebuild | 31 +++++++++++++++++++++++++++++++
sci-biology/Sibelia/metadata.xml | 12 ++++++++++++
2 files changed, 43 insertions(+)
diff --git a/sci-biology/Sibelia/Sibelia-9999.ebuild b/sci-biology/Sibelia/Sibelia-9999.ebuild
new file mode 100644
index 000000000..cfaae8765
--- /dev/null
+++ b/sci-biology/Sibelia/Sibelia-9999.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit cmake-utils git-r3
+
+DESCRIPTION="Draw synteny plots using circos"
+HOMEPAGE="http://bioinf.spbau.ru/en/sibelia"
+EGIT_REPO_URI="https://github.com/bioinf/Sibelia.git"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="
+ dev-libs/boost:0
+ dev-cpp/tclap
+ >=dev-libs/libdivsufsort-2.0.1
+ sci-biology/seqan:*
+ sci-biology/lagan
+ sci-biology/SnpEff"
+# it contains bundled copies of all the above
+# we would need to create also a Gentoo package for D3.js
+# (BSD License) http://d3js.org
+# it links using bundled libdivsufsort-2.0.1/lib/libdivsufsort.a
+# it install stuff into /usr/lib/Sibelia/{lagan,snpEff}/
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/"${P}"/src
diff --git a/sci-biology/Sibelia/metadata.xml b/sci-biology/Sibelia/metadata.xml
new file mode 100644
index 000000000..138cb7705
--- /dev/null
+++ b/sci-biology/Sibelia/metadata.xml
@@ -0,0 +1,12 @@
+<?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>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Sibelia/
@ 2018-01-19 22:58 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2018-01-19 22:58 UTC (permalink / raw
To: gentoo-commits
commit: 68fa1c9491bfe1e8c819ef1eae076b5ded96b198
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jan 19 22:58:33 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jan 19 22:58:33 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=68fa1c94
sci-biology/Sibelia: add runtime dependencies
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/Sibelia/Sibelia-9999.ebuild | 3 +++
1 file changed, 3 insertions(+)
diff --git a/sci-biology/Sibelia/Sibelia-9999.ebuild b/sci-biology/Sibelia/Sibelia-9999.ebuild
index cfaae8765..1713316d3 100644
--- a/sci-biology/Sibelia/Sibelia-9999.ebuild
+++ b/sci-biology/Sibelia/Sibelia-9999.ebuild
@@ -3,6 +3,8 @@
EAPI=6
+PYTHON_COMPAT=( python2_7 )
+
inherit cmake-utils git-r3
DESCRIPTION="Draw synteny plots using circos"
@@ -15,6 +17,7 @@ KEYWORDS=""
IUSE=""
DEPEND="
+ dev-lang/perl
dev-libs/boost:0
dev-cpp/tclap
>=dev-libs/libdivsufsort-2.0.1
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Sibelia/
@ 2018-01-19 23:15 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2018-01-19 23:15 UTC (permalink / raw
To: gentoo-commits
commit: 41f2686167fb345b1ebe95aa0db9437ddf31d2bd
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jan 19 23:15:03 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jan 19 23:15:03 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=41f26861
sci-biology/Sibelia: have opened github issue #181
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/Sibelia/Sibelia-9999.ebuild | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-biology/Sibelia/Sibelia-9999.ebuild b/sci-biology/Sibelia/Sibelia-9999.ebuild
index 1713316d3..c579abe59 100644
--- a/sci-biology/Sibelia/Sibelia-9999.ebuild
+++ b/sci-biology/Sibelia/Sibelia-9999.ebuild
@@ -24,6 +24,7 @@ DEPEND="
sci-biology/seqan:*
sci-biology/lagan
sci-biology/SnpEff"
+# https://github.com/bioinf/Sibelia/issues/181
# it contains bundled copies of all the above
# we would need to create also a Gentoo package for D3.js
# (BSD License) http://d3js.org
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Sibelia/
@ 2018-01-19 23:21 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2018-01-19 23:21 UTC (permalink / raw
To: gentoo-commits
commit: 8fda0c7e86d23431f9802384e81bc87106d0a660
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jan 19 23:21:12 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jan 19 23:21:12 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8fda0c7e
sci-biology/Sibelia: add version of budled snpEff
https://github.com/bioinf/Sibelia/issues/181
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/Sibelia/Sibelia-9999.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/Sibelia/Sibelia-9999.ebuild b/sci-biology/Sibelia/Sibelia-9999.ebuild
index c579abe59..b173755c4 100644
--- a/sci-biology/Sibelia/Sibelia-9999.ebuild
+++ b/sci-biology/Sibelia/Sibelia-9999.ebuild
@@ -23,7 +23,7 @@ DEPEND="
>=dev-libs/libdivsufsort-2.0.1
sci-biology/seqan:*
sci-biology/lagan
- sci-biology/SnpEff"
+ >=sci-biology/SnpEff-3.3"
# https://github.com/bioinf/Sibelia/issues/181
# it contains bundled copies of all the above
# we would need to create also a Gentoo package for D3.js
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Sibelia/
@ 2021-01-24 13:54 Andrew Ammerlaan
0 siblings, 0 replies; 5+ messages in thread
From: Andrew Ammerlaan @ 2021-01-24 13:54 UTC (permalink / raw
To: gentoo-commits
commit: da86f4336db39ba5430c386b296791fc0f5c86ae
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 24 13:53:51 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Jan 24 13:54:11 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=da86f433
sci-biology/Sibelia: cmake-utils --> cmake
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/Sibelia/Sibelia-9999.ebuild | 9 ++++-----
1 file changed, 4 insertions(+), 5 deletions(-)
diff --git a/sci-biology/Sibelia/Sibelia-9999.ebuild b/sci-biology/Sibelia/Sibelia-9999.ebuild
index b173755c4..9235b5abb 100644
--- a/sci-biology/Sibelia/Sibelia-9999.ebuild
+++ b/sci-biology/Sibelia/Sibelia-9999.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
PYTHON_COMPAT=( python2_7 )
-inherit cmake-utils git-r3
+inherit cmake git-r3
DESCRIPTION="Draw synteny plots using circos"
HOMEPAGE="http://bioinf.spbau.ru/en/sibelia"
@@ -14,7 +14,6 @@ EGIT_REPO_URI="https://github.com/bioinf/Sibelia.git"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS=""
-IUSE=""
DEPEND="
dev-lang/perl
@@ -32,4 +31,4 @@ DEPEND="
# it install stuff into /usr/lib/Sibelia/{lagan,snpEff}/
RDEPEND="${DEPEND}"
-S="${WORKDIR}"/"${P}"/src
+S="${WORKDIR}/${P}/src"
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