[gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/files/, sci-biology/gbrowse/

[Martin Mokrejs]

commit:     9f07546c0a41c51798aeca2c26010741db03535c
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jul 30 10:40:38 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Jul 30 10:40:38 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9f07546c

version bump but still need to rewrite upstream's install procedure to prevent '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 => GBrowseInstall.pm-2.39.patch} |    0
 .../{gbrowse-2.38.ebuild => gbrowse-2.39.ebuild}   |   22 ++++++++++----------
 3 files changed, 25 insertions(+), 11 deletions(-)

diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog
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/ChangeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $
 
+  30 Jul 2011; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
+  -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 <mmokrejs@×××××××××××××××.cz>
+  -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 <mmokrejs@×××××××××××××××.cz>
   gbrowse-2.38.ebuild:
   Added dependency on >=perl-gcpan/Text-ParseWords-3.27, documented requirement

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/gbrowse/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="
 LICENSE="Artistic"
 # webapp ebuilds do not set SLOT
 KEYWORDS="~x86 ~amd64"
-IUSE="-minimal svg test" # lwp moby scf
+IUSE="cgi fastcgi minimal mysql postgres svg test" # lwp moby scf
 
 S="${WORKDIR}/${MY_P}"
 
 # TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10)
-# TODO: make sure www-servers/apache +cgi
+# how about mod_fcgi and dev-libs/fcgi and mod_scgi?
 DEPEND="
 	>=perl-core/Module-Build-0.380.0
 	>=dev-lang/perl-5.8.8
 	dev-perl/Capture-Tiny
-	>=sci-biology/bioperl-1.6
+	>=sci-biology/bioperl-1.6.901
 	>=dev-perl/GD-2.07
 	dev-perl/IO-String
 	virtual/perl-Digest-MD5
@@ -47,20 +47,17 @@ DEPEND="
 	>=dev-perl/Bio-Graphics-1.97
 	>=dev-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
 
 # TODO: based on the following message in apache/error_log the list of deps should be longer
 # GBROWSE NOTICE: To enable PDF generation, please enter the directory "/home/httpd" and run the commands: "sudo mkdir .inkscape .gnome2" and "sudo chown apache .inkscape .gnome2".  To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse_details/yeast?ref=chrII;start=90739;end=92028;name=YBL069W;class=Sequence;feature_id=881;db_id=annotations%3Adatabase
 
-# TODO: implement ebuild checks for these version of packages
-#    !  Bio::Root::Version (1.006001) is installed, but we need version >= 1.0069
-#    *  Bio::DB::BigFile is not installed
-#    *  Bio::DB::Sam is not installed, install http://cpansearch.perl.org/src/LDS/Bio-SamTools-1.29
-#    *  DBD::Pg is not installed
-#    >=perl-gcpan/Text-ParseWords-3.27
-
 RDEPEND="${DEPEND}
 	>=www-servers/apache-2.0.47
+	fastcgi? ( dev-libs/fcgi )
 	www-apache/mod_fastcgi
 	dev-perl/DBI
 	|| ( dev-perl/DBD-Pg dev-perl/DBD-mysql )
@@ -84,6 +81,9 @@ RDEPEND="${DEPEND}
 		dev-perl/XML-Parser
 		dev-perl/Bio-Das
 		dev-perl/Text-Shellwords
+		postgres? ( >=dev-perl/Bio-DB-Das-Chado-0.32 )
+		>=dev-perl/Bio-SamTools-1.29
+		>=dev-perl/Bio-BigFile-1.06
 	)"
 
 src_prepare() {