[gentoo-commits] proj/sci:master commit in: sci-biology/mip-scaffolder/

[gentoo-commits] proj/sci:master commit in: sci-biology/mip-scaffolder/

[Martin Mokrejs]

commit:     aeab720fe4e2a73d39d79fa4570cd71219f256f6
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Feb 14 16:14:42 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Feb 14 16:14:42 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=aeab720f

new package

Package-Manager: portage-2.2.15

---
 sci-biology/mip-scaffolder/ChangeLog               |  9 ++++++
 sci-biology/mip-scaffolder/metadata.xml            |  9 ++++++
 .../mip-scaffolder/mip-scaffolder-0.6.ebuild       | 32 ++++++++++++++++++++++
 3 files changed, 50 insertions(+)

diff --git a/sci-biology/mip-scaffolder/ChangeLog b/sci-biology/mip-scaffolder/ChangeLog
new file mode 100644
index 0000000..0cba1df
--- /dev/null
+++ b/sci-biology/mip-scaffolder/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/mip-scaffolder
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*mip-scaffolder-0.6 (14 Feb 2015)
+
+  14 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
+  +mip-scaffolder-0.6.ebuild:
+  new package

diff --git a/sci-biology/mip-scaffolder/metadata.xml b/sci-biology/mip-scaffolder/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/mip-scaffolder/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>

diff --git a/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild b/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild
new file mode 100644
index 0000000..525ecbe
--- /dev/null
+++ b/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit toolchain-funcs
+
+DESCRIPTION="Scaffold contigs using ABI Solid or Illumina mate pair info"
+HOMEPAGE="http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder"
+SRC_URI="http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder/"${P}".tar.gz"
+
+LICENSE="mip-scaffolder"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="sci-libs/lemon
+	sci-mathematics/lpsolve
+	dev-lang/perl"
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	sed -e 's:/home/user/lp-solve/:/usr/include/lpsolve/:; s:/home/user/lemon/:/usr/include/lemon:; s:/home/user/mip-scaffolder-0.6/:/usr/bin:' -i Makefile
+	find . -name Makefile | while read f; do sed -e "s:CC=g++:CC=$(tc-getCXX):; s:CFLAGS=-Wall -g -O9:CFLAGS=${CFLAGS}:" -i $f; done
+	sed -e 's:$(LPSOLVEROOT)/liblpsolve55.a:-llpsolve55:' -i split-scaffold/Makefile
+}
+
+src_install(){
+	dobin combine-scaffold/combine-scaffold filter-mappings/filter-mappings split-scaffold/split-scaffold write-scaffold/write-scaffold scripts/*.pl scripts/*.sh
+	dodoc README
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/mip-scaffolder/

[Christoph Junghans]

commit:     f30685a15c7b75978d8dffd572f05d45a0ee4b2c
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Feb 17 01:50:02 2015 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Feb 17 01:50:02 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f30685a1

fixed LICENSE

Package-Manager: portage-2.2.14

---
 sci-biology/mip-scaffolder/ChangeLog                 | 3 +++
 sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-biology/mip-scaffolder/ChangeLog b/sci-biology/mip-scaffolder/ChangeLog
index 0cba1df..b9261e6 100644
--- a/sci-biology/mip-scaffolder/ChangeLog
+++ b/sci-biology/mip-scaffolder/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  17 Feb 2015; Christoph Junghans <ottxor@gentoo.org> mip-scaffolder-0.6.ebuild:
+  fixed LICENSE
+
 *mip-scaffolder-0.6 (14 Feb 2015)
 
   14 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,

diff --git a/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild b/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild
index 525ecbe..0bcf6d7 100644
--- a/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild
+++ b/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild
@@ -10,7 +10,7 @@ DESCRIPTION="Scaffold contigs using ABI Solid or Illumina mate pair info"
 HOMEPAGE="http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder"
 SRC_URI="http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder/"${P}".tar.gz"
 
-LICENSE="mip-scaffolder"
+LICENSE="BSD-2"
 SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""

[gentoo-commits] proj/sci:master commit in: sci-biology/mip-scaffolder/

[Martin Mokrejs]

commit:     4e1e8b5b8a489f899ff9149e6e9b908052a055c7
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 17 23:50:03 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 17 23:50:03 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4e1e8b5b

sci-biology/mip-scaffolder: respect CXXFLAGS although the Makefile speaks about CFLAGS

Package-Manager: portage-2.2.18

 sci-biology/mip-scaffolder/ChangeLog                 | 5 +++++
 sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/sci-biology/mip-scaffolder/ChangeLog b/sci-biology/mip-scaffolder/ChangeLog
index b9261e6..1574e92 100644
--- a/sci-biology/mip-scaffolder/ChangeLog
+++ b/sci-biology/mip-scaffolder/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  mip-scaffolder-0.6.ebuild:
+  sci-biology/mip-scaffolder: respect CXXFLAGS although the Makefile speaks
+  about CFLAGS
+
   17 Feb 2015; Christoph Junghans <ottxor@gentoo.org> mip-scaffolder-0.6.ebuild:
   fixed LICENSE
 

diff --git a/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild b/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild
index 0bcf6d7..967ecc6 100644
--- a/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild
+++ b/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild
@@ -22,7 +22,7 @@ RDEPEND="${DEPEND}"
 
 src_prepare(){
 	sed -e 's:/home/user/lp-solve/:/usr/include/lpsolve/:; s:/home/user/lemon/:/usr/include/lemon:; s:/home/user/mip-scaffolder-0.6/:/usr/bin:' -i Makefile
-	find . -name Makefile | while read f; do sed -e "s:CC=g++:CC=$(tc-getCXX):; s:CFLAGS=-Wall -g -O9:CFLAGS=${CFLAGS}:" -i $f; done
+	find . -name Makefile | while read f; do sed -e "s:CC=g++:CC=$(tc-getCXX):; s:CFLAGS=-Wall -g -O9:CFLAGS=${CXXFLAGS}:" -i $f; done
 	sed -e 's:$(LPSOLVEROOT)/liblpsolve55.a:-llpsolve55:' -i split-scaffold/Makefile
 }
 

[gentoo-commits] proj/sci:master commit in: sci-biology/mip-scaffolder/

[Andrew Ammerlaan]

commit:     6929b1a09d3e66fd239b9ea5983306aeaf9ec249
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 12:33:26 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 12:33:26 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6929b1a0

sci-biology/mip-scaffolder: EAPI bump

Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild b/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild
index cb1da348f..aa2c6b3e7 100644
--- a/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild
+++ b/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild
@@ -1,18 +1,17 @@
-# 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 toolchain-funcs
 
 DESCRIPTION="Scaffold contigs using ABI Solid or Illumina mate pair info"
 HOMEPAGE="http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder"
-SRC_URI="http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder/"${P}".tar.gz"
+SRC_URI="http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder/${P}.tar.gz"
 
 LICENSE="BSD-2"
 SLOT="0"
 KEYWORDS="~amd64"
-IUSE=""
 
 DEPEND="sci-libs/lemon
 	sci-mathematics/lpsolve
@@ -20,6 +19,7 @@ DEPEND="sci-libs/lemon
 RDEPEND="${DEPEND}"
 
 src_prepare(){
+	default
 	sed -e 's:/home/user/lp-solve/:/usr/include/lpsolve/:; s:/home/user/lemon/:/usr/include/lemon:; s:/home/user/mip-scaffolder-0.6/:/usr/bin:' -i Makefile
 	find . -name Makefile | while read f; do sed -e "s:CC=g++:CC=$(tc-getCXX):; s:CFLAGS=-Wall -g -O9:CFLAGS=${CXXFLAGS}:" -i $f; done
 	sed -e 's:$(LPSOLVEROOT)/liblpsolve55.a:-llpsolve55:' -i split-scaffold/Makefile