From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1Qn73y-0004iN-9l for garchives@archives.gentoo.org; Sat, 30 Jul 2011 10:46:38 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 040F421C22F; Sat, 30 Jul 2011 10:46:25 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id B0B3A21C22F for ; Sat, 30 Jul 2011 10:46:25 +0000 (UTC) Received: from pelican.gentoo.org (unknown [66.219.59.40]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 0757E67F82 for ; Sat, 30 Jul 2011 10:46:25 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id 5A4358003F for ; Sat, 30 Jul 2011 10:46:24 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <9f07546c0a41c51798aeca2c26010741db03535c.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/files/, sci-biology/gbrowse/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/gbrowse/ChangeLog sci-biology/gbrowse/files/GBrowseInstall.pm-2.38.patch sci-biology/gbrowse/files/GBrowseInstall.pm-2.39.patch sci-biology/gbrowse/gbrowse-2.38.ebuild sci-biology/gbrowse/gbrowse-2.39.ebuild X-VCS-Directories: sci-biology/gbrowse/files/ sci-biology/gbrowse/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 9f07546c0a41c51798aeca2c26010741db03535c Date: Sat, 30 Jul 2011 10:46:24 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: X-Archives-Hash: 4a43c6bd8c4ee2244916ed6ff17ed767 commit: 9f07546c0a41c51798aeca2c26010741db03535c Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Sat Jul 30 10:40:38 2011 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sat Jul 30 10:40:38 2011 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3D9f07546c version bump but still need to rewrite upstream's install procedure to pr= event 'mkdir /var/lib/gbrowse2' from happening (Portage version: 2.1.10.7/git/Linux i686, unsigned Manifest commit) --- sci-biology/gbrowse/ChangeLog | 14 ++++++++++++ ....pm-2.38.patch =3D> GBrowseInstall.pm-2.39.patch} | 0 .../{gbrowse-2.38.ebuild =3D> gbrowse-2.39.ebuild} | 22 ++++++++++--= -------- 3 files changed, 25 insertions(+), 11 deletions(-) diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLo= g index eaa41a4..b8780b1 100644 --- a/sci-biology/gbrowse/ChangeLog +++ b/sci-biology/gbrowse/ChangeLog @@ -2,6 +2,20 @@ # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/Ch= angeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $ =20 + 30 Jul 2011; Martin Mokrejs + -gbrowse-2.38.ebuild, -files/GBrowseInstall.pm-2.38.patch, + +gbrowse-2.39.ebuild, +files/GBrowseInstall.pm-2.39.patch: + version bump but still need to rewrite upstream's install procedure to + prevent 'mkdir /var/lib/gbrowse2' from happening + +*gbrowse-2.39 (30 Jul 2011) + + 30 Jul 2011; Martin Mokrejs + -gbrowse-2.38.ebuild, -files/GBrowseInstall.pm-2.38.patch, + +gbrowse-2.39.ebuild, +files/GBrowseInstall.pm-2.39.patch: + version bump but still need to rewrite upstream's install procedure to + prevent 'mkdir /var/lib/gbrowse2' from happening + 08 Jul 2011; Martin Mokrejs gbrowse-2.38.ebuild: Added dependency on >=3Dperl-gcpan/Text-ParseWords-3.27, documented re= quirement diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.38.patch b/sci= -biology/gbrowse/files/GBrowseInstall.pm-2.39.patch similarity index 100% rename from sci-biology/gbrowse/files/GBrowseInstall.pm-2.38.patch rename to sci-biology/gbrowse/files/GBrowseInstall.pm-2.39.patch diff --git a/sci-biology/gbrowse/gbrowse-2.38.ebuild b/sci-biology/gbrows= e/gbrowse-2.39.ebuild similarity index 92% rename from sci-biology/gbrowse/gbrowse-2.38.ebuild rename to sci-biology/gbrowse/gbrowse-2.39.ebuild index ea981ca..426ee4b 100644 --- a/sci-biology/gbrowse/gbrowse-2.38.ebuild +++ b/sci-biology/gbrowse/gbrowse-2.39.ebuild @@ -28,17 +28,17 @@ SRC_URI=3D" LICENSE=3D"Artistic" # webapp ebuilds do not set SLOT KEYWORDS=3D"~x86 ~amd64" -IUSE=3D"-minimal svg test" # lwp moby scf +IUSE=3D"cgi fastcgi minimal mysql postgres svg test" # lwp moby scf =20 S=3D"${WORKDIR}/${MY_P}" =20 # TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compat= ible w/perl-5.10) -# TODO: make sure www-servers/apache +cgi +# how about mod_fcgi and dev-libs/fcgi and mod_scgi? DEPEND=3D" >=3Dperl-core/Module-Build-0.380.0 >=3Ddev-lang/perl-5.8.8 dev-perl/Capture-Tiny - >=3Dsci-biology/bioperl-1.6 + >=3Dsci-biology/bioperl-1.6.901 >=3Ddev-perl/GD-2.07 dev-perl/IO-String virtual/perl-Digest-MD5 @@ -47,20 +47,17 @@ DEPEND=3D" >=3Ddev-perl/Bio-Graphics-1.97 >=3Ddev-perl/JSON-2.510.0 dev-perl/libwww-perl - svg? ( dev-perl/GD-SVG )" + svg? ( dev-perl/GD-SVG ) + mysql? ( dev-perl/DBD-mysql ) + postgres? ( dev-perl/DBD-Pg ) + sci-biology/ucsc-genome-browser" # that provides bigWig.h and jkweb.a, = aka Jim Kent's src =20 # TODO: based on the following message in apache/error_log the list of d= eps should be longer # GBROWSE NOTICE: To enable PDF generation, please enter the directory "= /home/httpd" and run the commands: "sudo mkdir .inkscape .gnome2" and "su= do chown apache .inkscape .gnome2". To turn off this message add "genera= te pdf =3D 0" to the [GENERAL] section of your GBrowse.conf configuration= file., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse_details/yeast?r= ef=3DchrII;start=3D90739;end=3D92028;name=3DYBL069W;class=3DSequence;feat= ure_id=3D881;db_id=3Dannotations%3Adatabase =20 -# TODO: implement ebuild checks for these version of packages -# ! Bio::Root::Version (1.006001) is installed, but we need version = >=3D 1.0069 -# * Bio::DB::BigFile is not installed -# * Bio::DB::Sam is not installed, install http://cpansearch.perl.or= g/src/LDS/Bio-SamTools-1.29 -# * DBD::Pg is not installed -# >=3Dperl-gcpan/Text-ParseWords-3.27 - RDEPEND=3D"${DEPEND} >=3Dwww-servers/apache-2.0.47 + fastcgi? ( dev-libs/fcgi ) www-apache/mod_fastcgi dev-perl/DBI || ( dev-perl/DBD-Pg dev-perl/DBD-mysql ) @@ -84,6 +81,9 @@ RDEPEND=3D"${DEPEND} dev-perl/XML-Parser dev-perl/Bio-Das dev-perl/Text-Shellwords + postgres? ( >=3Ddev-perl/Bio-DB-Das-Chado-0.32 ) + >=3Ddev-perl/Bio-SamTools-1.29 + >=3Ddev-perl/Bio-BigFile-1.06 )" =20 src_prepare() {