1 |
commit: 9f07546c0a41c51798aeca2c26010741db03535c |
2 |
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
3 |
AuthorDate: Sat Jul 30 10:40:38 2011 +0000 |
4 |
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
5 |
CommitDate: Sat Jul 30 10:40:38 2011 +0000 |
6 |
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9f07546c |
7 |
|
8 |
version bump but still need to rewrite upstream's install procedure to prevent 'mkdir /var/lib/gbrowse2' from happening |
9 |
|
10 |
(Portage version: 2.1.10.7/git/Linux i686, unsigned Manifest commit) |
11 |
|
12 |
--- |
13 |
sci-biology/gbrowse/ChangeLog | 14 ++++++++++++ |
14 |
....pm-2.38.patch => GBrowseInstall.pm-2.39.patch} | 0 |
15 |
.../{gbrowse-2.38.ebuild => gbrowse-2.39.ebuild} | 22 ++++++++++---------- |
16 |
3 files changed, 25 insertions(+), 11 deletions(-) |
17 |
|
18 |
diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLog |
19 |
index eaa41a4..b8780b1 100644 |
20 |
--- a/sci-biology/gbrowse/ChangeLog |
21 |
+++ b/sci-biology/gbrowse/ChangeLog |
22 |
@@ -2,6 +2,20 @@ |
23 |
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 |
24 |
# $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/ChangeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $ |
25 |
|
26 |
+ 30 Jul 2011; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
27 |
+ -gbrowse-2.38.ebuild, -files/GBrowseInstall.pm-2.38.patch, |
28 |
+ +gbrowse-2.39.ebuild, +files/GBrowseInstall.pm-2.39.patch: |
29 |
+ version bump but still need to rewrite upstream's install procedure to |
30 |
+ prevent 'mkdir /var/lib/gbrowse2' from happening |
31 |
+ |
32 |
+*gbrowse-2.39 (30 Jul 2011) |
33 |
+ |
34 |
+ 30 Jul 2011; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
35 |
+ -gbrowse-2.38.ebuild, -files/GBrowseInstall.pm-2.38.patch, |
36 |
+ +gbrowse-2.39.ebuild, +files/GBrowseInstall.pm-2.39.patch: |
37 |
+ version bump but still need to rewrite upstream's install procedure to |
38 |
+ prevent 'mkdir /var/lib/gbrowse2' from happening |
39 |
+ |
40 |
08 Jul 2011; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
41 |
gbrowse-2.38.ebuild: |
42 |
Added dependency on >=perl-gcpan/Text-ParseWords-3.27, documented requirement |
43 |
|
44 |
diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.38.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.39.patch |
45 |
similarity index 100% |
46 |
rename from sci-biology/gbrowse/files/GBrowseInstall.pm-2.38.patch |
47 |
rename to sci-biology/gbrowse/files/GBrowseInstall.pm-2.39.patch |
48 |
|
49 |
diff --git a/sci-biology/gbrowse/gbrowse-2.38.ebuild b/sci-biology/gbrowse/gbrowse-2.39.ebuild |
50 |
similarity index 92% |
51 |
rename from sci-biology/gbrowse/gbrowse-2.38.ebuild |
52 |
rename to sci-biology/gbrowse/gbrowse-2.39.ebuild |
53 |
index ea981ca..426ee4b 100644 |
54 |
--- a/sci-biology/gbrowse/gbrowse-2.38.ebuild |
55 |
+++ b/sci-biology/gbrowse/gbrowse-2.39.ebuild |
56 |
@@ -28,17 +28,17 @@ SRC_URI=" |
57 |
LICENSE="Artistic" |
58 |
# webapp ebuilds do not set SLOT |
59 |
KEYWORDS="~x86 ~amd64" |
60 |
-IUSE="-minimal svg test" # lwp moby scf |
61 |
+IUSE="cgi fastcgi minimal mysql postgres svg test" # lwp moby scf |
62 |
|
63 |
S="${WORKDIR}/${MY_P}" |
64 |
|
65 |
# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10) |
66 |
-# TODO: make sure www-servers/apache +cgi |
67 |
+# how about mod_fcgi and dev-libs/fcgi and mod_scgi? |
68 |
DEPEND=" |
69 |
>=perl-core/Module-Build-0.380.0 |
70 |
>=dev-lang/perl-5.8.8 |
71 |
dev-perl/Capture-Tiny |
72 |
- >=sci-biology/bioperl-1.6 |
73 |
+ >=sci-biology/bioperl-1.6.901 |
74 |
>=dev-perl/GD-2.07 |
75 |
dev-perl/IO-String |
76 |
virtual/perl-Digest-MD5 |
77 |
@@ -47,20 +47,17 @@ DEPEND=" |
78 |
>=dev-perl/Bio-Graphics-1.97 |
79 |
>=dev-perl/JSON-2.510.0 |
80 |
dev-perl/libwww-perl |
81 |
- svg? ( dev-perl/GD-SVG )" |
82 |
+ svg? ( dev-perl/GD-SVG ) |
83 |
+ mysql? ( dev-perl/DBD-mysql ) |
84 |
+ postgres? ( dev-perl/DBD-Pg ) |
85 |
+ sci-biology/ucsc-genome-browser" # that provides bigWig.h and jkweb.a, aka Jim Kent's src |
86 |
|
87 |
# TODO: based on the following message in apache/error_log the list of deps should be longer |
88 |
# 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 |
89 |
|
90 |
-# TODO: implement ebuild checks for these version of packages |
91 |
-# ! Bio::Root::Version (1.006001) is installed, but we need version >= 1.0069 |
92 |
-# * Bio::DB::BigFile is not installed |
93 |
-# * Bio::DB::Sam is not installed, install http://cpansearch.perl.org/src/LDS/Bio-SamTools-1.29 |
94 |
-# * DBD::Pg is not installed |
95 |
-# >=perl-gcpan/Text-ParseWords-3.27 |
96 |
- |
97 |
RDEPEND="${DEPEND} |
98 |
>=www-servers/apache-2.0.47 |
99 |
+ fastcgi? ( dev-libs/fcgi ) |
100 |
www-apache/mod_fastcgi |
101 |
dev-perl/DBI |
102 |
|| ( dev-perl/DBD-Pg dev-perl/DBD-mysql ) |
103 |
@@ -84,6 +81,9 @@ RDEPEND="${DEPEND} |
104 |
dev-perl/XML-Parser |
105 |
dev-perl/Bio-Das |
106 |
dev-perl/Text-Shellwords |
107 |
+ postgres? ( >=dev-perl/Bio-DB-Das-Chado-0.32 ) |
108 |
+ >=dev-perl/Bio-SamTools-1.29 |
109 |
+ >=dev-perl/Bio-BigFile-1.06 |
110 |
)" |
111 |
|
112 |
src_prepare() { |