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

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

[Martin Mokrejs]

commit:     64dcae2a7b0f8bdbf5a737b2a440c95376e99ba6
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 24 13:50:09 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 24 13:50:09 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=64dcae2a

sci-biology/stringtie: new package

Package-Manager: portage-2.2.28

 sci-biology/stringtie/metadata.xml           | 12 ++++++++++++
 sci-biology/stringtie/stringtie-1.2.2.ebuild | 28 ++++++++++++++++++++++++++++
 2 files changed, 40 insertions(+)

diff --git a/sci-biology/stringtie/metadata.xml b/sci-biology/stringtie/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/stringtie/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>

diff --git a/sci-biology/stringtie/stringtie-1.2.2.ebuild b/sci-biology/stringtie/stringtie-1.2.2.ebuild
new file mode 100644
index 0000000..f948342
--- /dev/null
+++ b/sci-biology/stringtie/stringtie-1.2.2.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+DESCRIPTION="Transcriptome assembler and RNA-Seq analysis using BAM files (like cufflinks)"
+HOMEPAGE="https://ccb.jhu.edu/software/stringtie
+	https://github.com/gpertea/stringtie"
+SRC_URI="http://ccb.jhu.edu/software/stringtie/dl/${P}.tar.gz"
+
+LICENSE="Artistic-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+# contains bundled gclib
+DEPEND="sci-biology/samtools:0.1-legacy" # bundled samtools-0.1.18
+RDEPEND="${DEPEND}"
+
+src_compile(){
+	emake release
+}
+
+src_install(){
+	dobin stringtie
+	dodoc README
+}

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

[Martin Mokrejs]

commit:     e035d84de52892630a985838e23f7afcfd8b386a
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 24 14:08:40 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 24 14:08:40 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e035d84d

sci-biology/stringtie: shorten DESCRIPTION line

Package-Manager: portage-2.2.28

 sci-biology/stringtie/stringtie-1.2.2.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/stringtie/stringtie-1.2.2.ebuild b/sci-biology/stringtie/stringtie-1.2.2.ebuild
index f948342..135ddec 100644
--- a/sci-biology/stringtie/stringtie-1.2.2.ebuild
+++ b/sci-biology/stringtie/stringtie-1.2.2.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=6
 
-DESCRIPTION="Transcriptome assembler and RNA-Seq analysis using BAM files (like cufflinks)"
+DESCRIPTION="Transcriptome assembler and RNA-Seq analysis on BAM files aka cufflinks"
 HOMEPAGE="https://ccb.jhu.edu/software/stringtie
 	https://github.com/gpertea/stringtie"
 SRC_URI="http://ccb.jhu.edu/software/stringtie/dl/${P}.tar.gz"

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

[Martin Mokrejs]

commit:     b28a9f9525962c8e86f6773132e15222e7f0980c
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jun 25 22:19:50 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jun 25 22:19:50 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b28a9f95

sci-biology/stringtie: document bundled sci-biology/gclib copy

Package-Manager: Portage-2.3.40, Repoman-2.3.9

 sci-biology/stringtie/stringtie-1.2.2.ebuild | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/sci-biology/stringtie/stringtie-1.2.2.ebuild b/sci-biology/stringtie/stringtie-1.2.2.ebuild
index 1f38bf7cd..37c0f26cf 100644
--- a/sci-biology/stringtie/stringtie-1.2.2.ebuild
+++ b/sci-biology/stringtie/stringtie-1.2.2.ebuild
@@ -13,8 +13,10 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-# contains bundled gclib
-DEPEND="sci-biology/samtools:0.1-legacy" # bundled samtools-0.1.18
+# contains bundled gclib (0.9.8?), well they are just headers
+DEPEND="
+	sci-biology/gclib
+	sci-biology/samtools:0.1-legacy" # bundled samtools-0.1.18
 RDEPEND="${DEPEND}"
 
 PATCHES=( "${FILESDIR}"/Makefile.patch )
@@ -22,6 +24,7 @@ PATCHES=( "${FILESDIR}"/Makefile.patch )
 src_prepare(){
 	default
 	rm -r samtools-0.1.18 || die
+	# TODO: `rm -rf ./gclib' and fix Makefile
 }
 
 src_compile(){

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

[Martin Mokrejs]

commit:     52f6543d76a8f92aa522c384dac27dc2bd213994
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jun 26 08:30:42 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jun 26 08:30:42 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=52f6543d

sci-biology/stringtie: drop KEYWORDS as it does not compile

Package-Manager: Portage-2.3.40, Repoman-2.3.9

 sci-biology/stringtie/stringtie-1.2.2.ebuild | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sci-biology/stringtie/stringtie-1.2.2.ebuild b/sci-biology/stringtie/stringtie-1.2.2.ebuild
index 953999e87..cb26b6961 100644
--- a/sci-biology/stringtie/stringtie-1.2.2.ebuild
+++ b/sci-biology/stringtie/stringtie-1.2.2.ebuild
@@ -10,7 +10,8 @@ SRC_URI="http://ccb.jhu.edu/software/stringtie/dl/${P}.tar.gz"
 
 LICENSE="Artistic-2 MIT" # MIT from bundled samtools-0.1.18
 SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="" # gclib/GThreads.h:804:19: error: conflicting declaration 
+#                                             'typedef long long int __intmax_t'
 IUSE=""
 
 # contains bundled and modified samtools-0.1.18

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

[Andrew Ammerlaan]

commit:     da853fc6e6037207166108a7e7b76c74cda34360
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 14:54:52 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 14:54:52 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=da853fc6

sci-biology/stringtie: EAPI bump, version bump

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

 sci-biology/stringtie/stringtie-2.1.5.ebuild | 29 ++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/sci-biology/stringtie/stringtie-2.1.5.ebuild b/sci-biology/stringtie/stringtie-2.1.5.ebuild
new file mode 100644
index 000000000..9b1e205da
--- /dev/null
+++ b/sci-biology/stringtie/stringtie-2.1.5.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Transcriptome assembler and RNA-Seq analysis on BAM files aka cufflinks"
+HOMEPAGE="https://ccb.jhu.edu/software/stringtie
+	https://github.com/gpertea/stringtie"
+SRC_URI="https://github.com/gpertea/stringtie/releases/download/v${PV}/${P}.tar.gz"
+
+LICENSE="Artistic-2 MIT" # MIT from bundled samtools-0.1.18
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# requires network
+RESTRICT="test"
+
+# contains bundled and modified samtools-0.1.18
+# https://github.com/gpertea/stringtie/issues/185#issuecomment-400128090
+#
+# contains bundled gclib (0.9.8?), a modified version?
+# https://github.com/gpertea/stringtie/issues/186#issuecomment-400131844
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_install(){
+	dobin stringtie
+	einstalldocs
+}