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)

4 files changed, 29 insertions, 15 deletions

diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog
index eaa41a45d..b8780b15f 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@fold.natur.cuni.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@fold.natur.cuni.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@fold.natur.cuni.cz>
   gbrowse-2.38.ebuild:
   Added dependency on >=perl-gcpan/Text-ParseWords-3.27, documented requirement
diff --git a/sci-biology/gbrowse/Manifest b/sci-biology/gbrowse/Manifest
index b63129745..22f2fd5e1 100644
--- a/sci-biology/gbrowse/Manifest
+++ b/sci-biology/gbrowse/Manifest
@@ -1,8 +1,8 @@
-AUX GBrowseInstall.pm-2.38.patch 1278 RMD160 96c7f2c66537c6e01cf2619018f608607c0927dc SHA1 a3cb874018d2c7a5acf34381971cc09d83a13f73 SHA256 5a1018f582c2e0ffca034d04ce73f678dd879d90932e4e89ea664c7c113f4b7c
+AUX GBrowseInstall.pm-2.39.patch 1278 RMD160 96c7f2c66537c6e01cf2619018f608607c0927dc SHA1 a3cb874018d2c7a5acf34381971cc09d83a13f73 SHA256 5a1018f582c2e0ffca034d04ce73f678dd879d90932e4e89ea664c7c113f4b7c
 AUX gbrowse-slave.default 210 RMD160 77245190ab0d3a543f3103bb6f21864f73ea1cde SHA1 a19d60edd3fdc1f059ed8fa58f7e91fc47ec92dc SHA256 e4e6d68ade29681f442b2e1c7f8abbc7ff3255b3b8db3c59ed6368ba561d7d66
 AUX gbrowse-slave.init.d 2196 RMD160 8b565d1be23c89cbae0f9fd5cd2201f47a564b94 SHA1 738bc8f06486a0e6caa72642f79f9b7dbb356524 SHA256 de511a92757153ee648eb6cd39e3c69c1e30fa2c2ed406f24c08571c72609219
 AUX gbrowse.conf.vhosts.d 740 RMD160 e24f5132e37a84dd0bb9a39e2de99cd11d260844 SHA1 2c44fdcf04bef92eb6210d4e6667b994e5643a13 SHA256 8acd5a067ab3dd42cff0ab7cb0d783b2409ccb872590eba32ea55d4929f65f21
-DIST GBrowse-2.38.tar.gz 11966992 RMD160 dde50d49ee1b228103dffc9701e450ac9e3be3cd SHA1 4228a4938cbdbc409ddb23f81cd3186cdf15391d SHA256 acf7d3d0f32d0138640b2773ed580572ff63d646d4538f354dec8986607aa275
+DIST GBrowse-2.39.tar.gz 11969088 RMD160 47dd338a0b99632e77a532a3c27d0b9d9d514dca SHA1 2cc48cc1603aa3ae487c47259f9a896bec4eff8e SHA256 b4e76acfa1d8f64d5f227c3ba0258666928b4f357428549be85f05c944337d44
 DIST README-gff-files 5309 RMD160 8ba184fa8a6b921f925143cf53de06e3da353023 SHA1 ad2d2b3133c73a05ace4a0107ff1a3a4221bc8f8 SHA256 21f4f026b212698c5aac0e82045670f8397ab50fdfe74b938fcbc71a1d36c82a
 DIST Refseq_Genome_TBLASTX.tar.gz 56482234 RMD160 e188d9dfe12bed3fd299be4625f7e658f54bb8c4 SHA1 72ec3de9b9ca0e10c2dd8dcda24f9be74f98cf09 SHA256 7036bdd9aefbf44e384df83f4c1e973c1ab3eac8fe74b37499c4a3f1c55a18af
 DIST fly.fasta.gz 37349852 RMD160 4bedfcc5d0ea3d325f3d3e446713251a8ce34ca3 SHA1 8f2c7a2f24dbab0f27c73009fe51efb8f41d6769 SHA256 892ed03e17edd3469f1ed00cb9967fb905bbac57c1cb7858667381f34a6bfeea
@@ -13,6 +13,6 @@ DIST worm.fasta.gz 30593662 RMD160 674ef3d09cdfaa5d748f18c0e769f0a5ca3d48cf SHA1
 DIST worm.gff.gz 65789458 RMD160 ddced7c965963ce41a10bdecae949731ed305121 SHA1 ccfb0f287e27ff7849b099c81d811f468a7e617c SHA256 afd63c65c3fdb0ba8a1cf455bd4477a2d5d27d5b0e88c6a5a10d156d0567374f
 DIST yeast.fasta.gz 3801757 RMD160 5545054cf6ffa5381c7992141144107076fdf62e SHA1 c36fddc5fd2c79e01292f66644088654304bc438 SHA256 bf51cbced31aa6a30bca43cc72fdb53194fbb403407e2ebb9d70c901ab072e6d
 DIST yeast.gff.gz 249814 RMD160 64538d18de23d930915938bd00ae4a94a52f3960 SHA1 ec753b1ae409e1377f568531a53be8985a7bfa2e SHA256 20c93e6ba9457896a693d13e8fd8fa00d77acbb55aee9b19a31c2b29c4b7e9b1
-EBUILD gbrowse-2.38.ebuild 6381 RMD160 a8a14f370543197cde8816f4d0cc0797eba158b7 SHA1 6f67d008248a7fdef7848a55855788bc367c15d5 SHA256 1107ad4bd23e6c34d09d5e9bf026c64d302282d477fb6546936a0eee27b87de2
-MISC ChangeLog 2729 RMD160 de32f4faa78f55a913b316b8eea10e978e02a38b SHA1 7c533d5e014be35560270b678053679083160696 SHA256 a5190627f4800c65af6f0fb3cc8a97d3d54909ef83611bf0d346696a89e43583
+EBUILD gbrowse-2.39.ebuild 6353 RMD160 861a7ccc9131fa4c0cb90262b66f4bf2d812f348 SHA1 f15271be624fd4996e1a420620b188e72b0c69b5 SHA256 6f107f9adf9a3000ebd8a76f045c9775bfb52c1ddd8387ef1f69fd628edfe906
+MISC ChangeLog 3372 RMD160 d293a0f800aa84e937e7c8ce579c30df32d06c47 SHA1 c03cd02620dfbf30c435e8e2b20fbd042231f52d SHA256 5b3d0ab17974a42dba9c360c569de57bbf5621e3cf72fb756b6b64708419f998
 MISC metadata.xml 572 RMD160 bc941571413238acb3d77e61d49b959737ed4f5a SHA1 0c05303509c0e2dd21b37fc93c936809db49e530 SHA256 89b9964a9404a95dbb622a91735348da8e66d34d7dd7e7f144ed8c0159c43e31
diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.38.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.39.patch
index e91fe1634..e91fe1634 100644
--- a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.38.patch
+++ b/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
index ea981ca01..426ee4ba2 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() {