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

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

[Martin Mokrejs]

commit:     f16a3ab142fe2668ba1985cdc09c3c0a6f8840c7
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan  7 22:29:27 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan  7 22:29:27 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f16a3ab1

Initial ebuild

---
 sci-biology/BRANCH/BRANCH-9999.ebuild | 37 +++++++++++++++++++++++++++++++++++
 sci-biology/BRANCH/ChangeLog          | 10 ++++++++++
 sci-biology/BRANCH/metadata.xml       |  9 +++++++++
 3 files changed, 56 insertions(+)

diff --git a/sci-biology/BRANCH/BRANCH-9999.ebuild b/sci-biology/BRANCH/BRANCH-9999.ebuild
new file mode 100644
index 0000000..74be1b1
--- /dev/null
+++ b/sci-biology/BRANCH/BRANCH-9999.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+[ "$PV" == "9999" ] && inherit git-2
+
+inherit eutils
+
+DESCRIPTION="Extend partial transcripts with sequence from other reads or genomic contigs"
+HOMEPAGE=""
+if [ "$PV" == "9999" ]; then
+	EGIT_REPO_URI="https://github.com/baoe/BRANCH"
+	KEYWORDS=""
+else
+	SRC_URI=""
+	KEYWORDS=""
+fi
+
+
+LICENSE="Artistic-2"
+SLOT="0"
+IUSE=""
+
+DEPEND="sci-biology/blat
+	sci-libs/lemon"
+RDEPEND="${DEPEND}"
+
+src_compile(){
+	cd BRANCH || die
+	g++ -o BRANCH BRANCH.cpp -lemon -lpthread || die
+}
+
+src_install(){
+	dobin BRANCH/BRANCH
+}

diff --git a/sci-biology/BRANCH/ChangeLog b/sci-biology/BRANCH/ChangeLog
new file mode 100644
index 0000000..8954ba6
--- /dev/null
+++ b/sci-biology/BRANCH/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/BRANCH
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*BRANCH-9999 (07 Jan 2015)
+
+  07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +BRANCH-9999.ebuild, +metadata.xml:
+  initial ebuild
+

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

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

[Justin Lecher]

commit:     e9a2b3ddeae5c85652ba3c6758a00a7f22d9203c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 10 13:29:21 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 13:29:21 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e9a2b3dd

sci-biology/BRANCH: Move from git-2 to git-r3 eclass; add HOMEPAGE; be verbose during compilation; install docs

Package-Manager: portage-2.2.15

---
 sci-biology/BRANCH/BRANCH-9999.ebuild | 15 ++++++++-------
 sci-biology/BRANCH/ChangeLog          |  4 ++++
 2 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/sci-biology/BRANCH/BRANCH-9999.ebuild b/sci-biology/BRANCH/BRANCH-9999.ebuild
index 74be1b1..923f5b4 100644
--- a/sci-biology/BRANCH/BRANCH-9999.ebuild
+++ b/sci-biology/BRANCH/BRANCH-9999.ebuild
@@ -4,12 +4,12 @@
 
 EAPI=5
 
-[ "$PV" == "9999" ] && inherit git-2
+[ "$PV" == "9999" ] && inherit git-r3
 
-inherit eutils
+inherit eutils toolchain-funcs
 
 DESCRIPTION="Extend partial transcripts with sequence from other reads or genomic contigs"
-HOMEPAGE=""
+HOMEPAGE="https://github.com/baoe/BRANCH"
 if [ "$PV" == "9999" ]; then
 	EGIT_REPO_URI="https://github.com/baoe/BRANCH"
 	KEYWORDS=""
@@ -18,20 +18,21 @@ else
 	KEYWORDS=""
 fi
 
-
 LICENSE="Artistic-2"
 SLOT="0"
 IUSE=""
 
-DEPEND="sci-biology/blat
+DEPEND="
+	sci-biology/blat
 	sci-libs/lemon"
 RDEPEND="${DEPEND}"
 
 src_compile(){
-	cd BRANCH || die
-	g++ -o BRANCH BRANCH.cpp -lemon -lpthread || die
+	einfo "$(tc-getCXX) ${CXXFLAGS} ${LDFLAGS} -o BRANCH BRANCH.cpp -lemon -lpthread"
+	$(tc-getCXX) ${CXXFLAGS} ${LDFLAGS} -o BRANCH/BRANCH BRANCH/BRANCH.cpp -lemon -lpthread || die
 }
 
 src_install(){
 	dobin BRANCH/BRANCH
+	dodoc README.md
 }

diff --git a/sci-biology/BRANCH/ChangeLog b/sci-biology/BRANCH/ChangeLog
index 8954ba6..03ab1fc 100644
--- a/sci-biology/BRANCH/ChangeLog
+++ b/sci-biology/BRANCH/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  10 Jan 2015; Justin Lecher <jlec@gentoo.org> BRANCH-9999.ebuild:
+  Move from git-2 to git-r3 eclass; add HOMEPAGE; be verbose during
+  compilation; install docs
+
 *BRANCH-9999 (07 Jan 2015)
 
   07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

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

[Andrew Ammerlaan]

commit:     90959a3e7df6b477d838b8aedfff9f11fda8828b
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Fri Mar  5 15:28:58 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Fri Mar  5 15:29:12 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=90959a3e

sci-biology/BRANCH: EAPI bump

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

 sci-biology/BRANCH/BRANCH-9999.ebuild | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/sci-biology/BRANCH/BRANCH-9999.ebuild b/sci-biology/BRANCH/BRANCH-9999.ebuild
index 1700c4a09..ef3d12e24 100644
--- a/sci-biology/BRANCH/BRANCH-9999.ebuild
+++ b/sci-biology/BRANCH/BRANCH-9999.ebuild
@@ -1,15 +1,14 @@
-# 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
 
-[ "$PV" == "9999" ] && inherit git-r3
-
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
 
 DESCRIPTION="Extend partial transcripts with sequence from other reads or genomic contigs"
 HOMEPAGE="https://github.com/baoe/BRANCH"
 if [ "$PV" == "9999" ]; then
+	inherit git-r3
 	EGIT_REPO_URI="https://github.com/baoe/BRANCH"
 	KEYWORDS=""
 else
@@ -19,11 +18,11 @@ fi
 
 LICENSE="Artistic-2"
 SLOT="0"
-IUSE=""
 
 DEPEND="
 	sci-biology/blat
-	sci-libs/lemon"
+	sci-libs/lemon
+"
 RDEPEND="${DEPEND}"
 
 src_compile(){

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

[Andrew Ammerlaan]

commit:     8c712aa70c57b7fd04db7814440dbfb6ab20af7f
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar 20 11:19:57 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar 20 11:19:57 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8c712aa7

sci-biology/BRANCH: fix MultipleKeywordsLines

Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/BRANCH/BRANCH-9999.ebuild | 1 -
 1 file changed, 1 deletion(-)

diff --git a/sci-biology/BRANCH/BRANCH-9999.ebuild b/sci-biology/BRANCH/BRANCH-9999.ebuild
index ef3d12e24..409cc3b12 100644
--- a/sci-biology/BRANCH/BRANCH-9999.ebuild
+++ b/sci-biology/BRANCH/BRANCH-9999.ebuild
@@ -10,7 +10,6 @@ HOMEPAGE="https://github.com/baoe/BRANCH"
 if [ "$PV" == "9999" ]; then
 	inherit git-r3
 	EGIT_REPO_URI="https://github.com/baoe/BRANCH"
-	KEYWORDS=""
 else
 	SRC_URI=""
 	KEYWORDS=""