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

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

[Martin Mokrejs]

commit:     b953ee4a8586fae91d8457b31b8baea000160533
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 12 07:27:37 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 12 07:27:37 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b953ee4a

sci-biology/genometools: bump 1.5.7 to 1.5.9

https://github.com/genometools/genometools/blob/master/CHANGELOG

changes in version 1.5.9 (2016-07-21)

- bugfixes and cleanups
- update MD5 module to upstream version 1.2
- set verbatim dates in documentation files
- add support for GCC 6
- gtlua: complete GtRegionMapping bindings
- extend wording options for speck matchers
- add tabular output format for speck
- make unit tests compatible with Python 2.6
- improvements on `gt seed_extend'
- improve compatibility with Ruby <1.9.2
- several changes to build system (verbosity etc.)
- allow to sort sequences by header (`gt seqorder')

changes in version 1.5.8 (2016-01-06)

- bugfixes and cleanups
- change number of spaces in GFF3 header
- improve documentation of 'gt gff3 -checkids'
- change GenBank and EMBL parsers to name sequences after LOCUS/ID fields
- add Python 3 support for Python bindings
- make build reproducible
- allow speck templates to be given as files
- updated genetic code table to most recent NCBI revision

Package-Manager: Portage-2.3.27, Repoman-2.3.9

 .../{genometools-1.5.7.ebuild => genometools-1.5.9.ebuild}          | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-biology/genometools/genometools-1.5.7.ebuild b/sci-biology/genometools/genometools-1.5.9.ebuild
similarity index 71%
rename from sci-biology/genometools/genometools-1.5.7.ebuild
rename to sci-biology/genometools/genometools-1.5.9.ebuild
index 70682d2ee..23fe474e2 100644
--- a/sci-biology/genometools/genometools-1.5.7.ebuild
+++ b/sci-biology/genometools/genometools-1.5.9.ebuild
@@ -1,15 +1,15 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
-DESCRIPTION="Tools for bioinformatics (notably Tallymer, Readjoiner, gff3validator)"
+DESCRIPTION="Tools for bioinformatics (Tallymer, Readjoiner, gff3validator, ...)"
 HOMEPAGE="http://genometools.org"
 SRC_URI="http://genometools.org/pub/${P}.tar.gz"
 
 LICENSE="ICS"
 SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS="~amd64 ~x86"
 IUSE=""
 
 DEPEND="

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

[Martin Mokrejs]

commit:     0730dfd94091a11a2778f58b026aea8b7c378f41
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Oct 12 11:22:57 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Oct 12 11:22:57 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0730dfd9

sci-biology/genometools: move pango dependency under USE=cairo

Package-Manager: Portage-2.3.50, Repoman-2.3.10

 sci-biology/genometools/genometools-1.5.10.ebuild | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/sci-biology/genometools/genometools-1.5.10.ebuild b/sci-biology/genometools/genometools-1.5.10.ebuild
index 809bd4d38..9e69302c6 100644
--- a/sci-biology/genometools/genometools-1.5.10.ebuild
+++ b/sci-biology/genometools/genometools-1.5.10.ebuild
@@ -14,8 +14,7 @@ IUSE="cairo"
 
 DEPEND="
 	dev-libs/glib
-	x11-libs/pango
-	cairo? ( x11-libs/cairo )
+	cairo? ( x11-libs/cairo x11-libs/pango )
 	sci-biology/samtools:0.1-legacy
 	dev-db/sqlite:3
 	>=dev-lang/lua-5.1:=

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

[Martin Mokrejs]

commit:     d209b24ac3b9de78f7048fb76467c42bad604263
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Sep 11 15:03:38 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Sep 11 15:03:38 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d209b24a

sci-biology/genometools: remove comment

Package-Manager: Portage-2.3.48, Repoman-2.3.10

 sci-biology/genometools/genometools-1.5.10.ebuild | 1 -
 1 file changed, 1 deletion(-)

diff --git a/sci-biology/genometools/genometools-1.5.10.ebuild b/sci-biology/genometools/genometools-1.5.10.ebuild
index 7bb048305..809bd4d38 100644
--- a/sci-biology/genometools/genometools-1.5.10.ebuild
+++ b/sci-biology/genometools/genometools-1.5.10.ebuild
@@ -24,7 +24,6 @@ DEPEND="
 	dev-lua/lua-md5
 	dev-lang/luajit
 	dev-libs/tre"
-# http://keplerproject.org/cgilua
 RDEPEND="${DEPEND}"
 
 src_prepare(){

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

[Martin Mokrejs]

commit:     5b1a011238d2671169928c5145b572ecf2768855
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Sep 11 14:44:00 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Sep 11 14:45:21 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5b1a0112

sci-biology/genometools: add missing dependency on dev-lua/lua-md5

Package-Manager: Portage-2.3.48, Repoman-2.3.10

 sci-biology/genometools/genometools-1.5.10.ebuild | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sci-biology/genometools/genometools-1.5.10.ebuild b/sci-biology/genometools/genometools-1.5.10.ebuild
index 682688d52..7bb048305 100644
--- a/sci-biology/genometools/genometools-1.5.10.ebuild
+++ b/sci-biology/genometools/genometools-1.5.10.ebuild
@@ -21,8 +21,9 @@ DEPEND="
 	>=dev-lang/lua-5.1:=
 	dev-lua/lpeg
 	dev-lua/luafilesystem
+	dev-lua/lua-md5
+	dev-lang/luajit
 	dev-libs/tre"
-# http://keplerproject.github.io/md5/
 # http://keplerproject.org/cgilua
 RDEPEND="${DEPEND}"
 

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

[Martin Mokrejs]

commit:     95513c7a3bc7c3ce3588f60b8730259f3cd26360
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 12 09:09:37 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 12 09:09:37 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=95513c7a

sci-biology/genometools: be more explicit with lua version

Package-Manager: Portage-2.3.27, Repoman-2.3.9

 sci-biology/genometools/genometools-1.5.10.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/genometools/genometools-1.5.10.ebuild b/sci-biology/genometools/genometools-1.5.10.ebuild
index 9fe27a4a7..682688d52 100644
--- a/sci-biology/genometools/genometools-1.5.10.ebuild
+++ b/sci-biology/genometools/genometools-1.5.10.ebuild
@@ -18,7 +18,7 @@ DEPEND="
 	cairo? ( x11-libs/cairo )
 	sci-biology/samtools:0.1-legacy
 	dev-db/sqlite:3
-	dev-lang/lua:*
+	>=dev-lang/lua-5.1:=
 	dev-lua/lpeg
 	dev-lua/luafilesystem
 	dev-libs/tre"

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

[Martin Mokrejs]

commit:     009bcce4827e81fd1c7f90d87bd327e34baf8804
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 12 08:50:57 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 12 08:50:57 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=009bcce4

sci-biology/genometools: add missing SLOT for lua

Package-Manager: Portage-2.3.27, Repoman-2.3.9

 sci-biology/genometools/genometools-1.5.10.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/genometools/genometools-1.5.10.ebuild b/sci-biology/genometools/genometools-1.5.10.ebuild
index 026eabc48..9fe27a4a7 100644
--- a/sci-biology/genometools/genometools-1.5.10.ebuild
+++ b/sci-biology/genometools/genometools-1.5.10.ebuild
@@ -18,7 +18,7 @@ DEPEND="
 	cairo? ( x11-libs/cairo )
 	sci-biology/samtools:0.1-legacy
 	dev-db/sqlite:3
-	dev-lang/lua
+	dev-lang/lua:*
 	dev-lua/lpeg
 	dev-lua/luafilesystem
 	dev-libs/tre"

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

[Martin Mokrejs]

commit:     3a1f44b97d5e3f2579efe5b83c93cf3114835c84
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 12 08:49:25 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 12 08:49:25 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3a1f44b9

sci-biology/genometools: disable building using bundled libs

The build packaging system is suboptimal. Hand-edit the Makefile
to force use of shared libs from system-wide. This brings us
to a non-functional package because two lua-based packages are
not yet in the tree.

https://github.com/genometools/genometools/issues/742
https://github.com/genometools/genometools/pull/748

Package-Manager: Portage-2.3.27, Repoman-2.3.9

 sci-biology/genometools/genometools-1.5.10.ebuild | 26 +++++++++++++++++++----
 1 file changed, 22 insertions(+), 4 deletions(-)

diff --git a/sci-biology/genometools/genometools-1.5.10.ebuild b/sci-biology/genometools/genometools-1.5.10.ebuild
index 23fe474e2..026eabc48 100644
--- a/sci-biology/genometools/genometools-1.5.10.ebuild
+++ b/sci-biology/genometools/genometools-1.5.10.ebuild
@@ -9,16 +9,34 @@ SRC_URI="http://genometools.org/pub/${P}.tar.gz"
 
 LICENSE="ICS"
 SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
+KEYWORDS=""
+IUSE="cairo"
 
 DEPEND="
 	dev-libs/glib
 	x11-libs/pango
-	x11-libs/cairo"
+	cairo? ( x11-libs/cairo )
+	sci-biology/samtools:0.1-legacy
+	dev-db/sqlite:3
+	dev-lang/lua
+	dev-lua/lpeg
+	dev-lua/luafilesystem
+	dev-libs/tre"
+# http://keplerproject.github.io/md5/
+# http://keplerproject.org/cgilua
 RDEPEND="${DEPEND}"
 
 src_prepare(){
-	sed -e "s#/usr/local#"${EPREFIX}"/usr#" -i Makefile || die
+	sed -e "s#/usr/local#"${EPREFIX}"/usr#g" -i Makefile || die
+	sed -e "s#/usr/include/bam#${EPREFIX}/usr/include/bam-0.1-legacy#" -i Makefile || die
+	sed -e "s#-lbam#-lbam-0.1-legacy#" -i Makefile || die
 	eapply_user
 }
+
+src_compile(){
+	local myemakeargs=( useshared=yes )
+	! use cairo && myemakeargs+=( cairo=no )
+	use x86 && myemakeargs+=( 32bit=yes )
+	use amd64 && myemakeargs+=( 64bit=yes )
+	emake ${myemakeargs}
+}

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

[Martin Mokrejs]

commit:     b9e06f46a3f5f869f54182fd19a01dffa34f4309
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 12 07:29:17 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 12 07:29:17 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b9e06f46

sci-biology/genometools: bump to 1.5.10

https://github.com/genometools/genometools/blob/master/CHANGELOG

changes in version 1.5.10 (2017-08-04)

- bugfixes and cleanups
- add Readjoiner output in GFA format
- improve building on GCC 7
- add arbitrary N values for `gt seqstat`
- install gtdata into $PREFIX/share/genometools by default
- improve robustness of test suite
- add Travis tests for Mac OS X
- `gt seed_extend` now speaks GFA2
- improvements to `gt seed_extend` w.r.t. runtime and
  output format
- new implementation of functionality for computing
  E-values for local alignments according to the
Karlin-Altschul statistics

Package-Manager: Portage-2.3.27, Repoman-2.3.9

 .../genometools/{genometools-1.5.9.ebuild => genometools-1.5.10.ebuild}   | 0
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/sci-biology/genometools/genometools-1.5.9.ebuild b/sci-biology/genometools/genometools-1.5.10.ebuild
similarity index 100%
rename from sci-biology/genometools/genometools-1.5.9.ebuild
rename to sci-biology/genometools/genometools-1.5.10.ebuild

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

[Martin Mokrejs]

commit:     c312a1d8013da22fb314deb1ba49cb6314a21eb5
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Feb 18 20:44:33 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Feb 18 20:44:33 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c312a1d8

sci-biology/genometools: update DEPs, EAPI bump

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/genometools/genometools-1.5.7.ebuild | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/sci-biology/genometools/genometools-1.5.7.ebuild b/sci-biology/genometools/genometools-1.5.7.ebuild
index 248f13ba7..aaaea41ac 100644
--- a/sci-biology/genometools/genometools-1.5.7.ebuild
+++ b/sci-biology/genometools/genometools-1.5.7.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=5
+EAPI=6
 
 DESCRIPTION="Tools for bioinformatics (notably Tallymer, Readjoiner, gff3validator)"
 HOMEPAGE="http://genometools.org"
@@ -13,10 +13,13 @@ SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""
 
-DEPEND="x11-libs/pango
+DEPEND="
+	dev-libs/glib
+	x11-libs/pango
 	x11-libs/cairo"
 RDEPEND="${DEPEND}"
 
 src_prepare(){
 	sed -e "s#/usr/local#"${EPREFIX}"/usr#" -i Makefile || die
+	eapply_user
 }

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

[Martin Mokrejs]

commit:     ed6529107db37adbb199acfb0d1e9a9e6eddb105
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Feb 18 20:37:50 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Feb 18 20:37:50 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ed652910

sci-biology/genometools: respect EPREFIX

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/genometools/genometools-1.5.7.ebuild | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/sci-biology/genometools/genometools-1.5.7.ebuild b/sci-biology/genometools/genometools-1.5.7.ebuild
index 2a78a5ce9..248f13ba7 100644
--- a/sci-biology/genometools/genometools-1.5.7.ebuild
+++ b/sci-biology/genometools/genometools-1.5.7.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -16,3 +16,7 @@ IUSE=""
 DEPEND="x11-libs/pango
 	x11-libs/cairo"
 RDEPEND="${DEPEND}"
+
+src_prepare(){
+	sed -e "s#/usr/local#"${EPREFIX}"/usr#" -i Makefile || die
+}

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

[Martin Mokrejs]

commit:     db94883876b1a6bece4270fdca7208383888cfce
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jan  4 15:45:11 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jan  4 15:45:11 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=db948838

sci-biology/genometools: new package

Package-Manager: portage-2.2.26

 sci-biology/genometools/ChangeLog                |  9 +++++++++
 sci-biology/genometools/genometools-1.5.7.ebuild | 18 ++++++++++++++++++
 sci-biology/genometools/metadata.xml             |  9 +++++++++
 3 files changed, 36 insertions(+)

diff --git a/sci-biology/genometools/ChangeLog b/sci-biology/genometools/ChangeLog
new file mode 100644
index 0000000..6c12135
--- /dev/null
+++ b/sci-biology/genometools/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/genometools
+# Copyright 1999-2016 Gentoo Foundation; Distributed under the GPL v2
+# $Id$
+
+*genometools-1.5.7 (04 Jan 2016)
+
+  04 Jan 2016; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +genometools-1.5.7.ebuild, +metadata.xml:
+  sci-biology/genometools: new package

diff --git a/sci-biology/genometools/genometools-1.5.7.ebuild b/sci-biology/genometools/genometools-1.5.7.ebuild
new file mode 100644
index 0000000..124c9c6
--- /dev/null
+++ b/sci-biology/genometools/genometools-1.5.7.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="A collection of tools for bioinformatics (notably Tallymer, Readjoiner, gff3validator)"
+HOMEPAGE="http://genometools.org"
+SRC_URI="http://genometools.org/pub/${P}.tar.gz"
+
+LICENSE="ICS"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="x11-libs/pango
+	x11-libs/cairo"
+RDEPEND="${DEPEND}"

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