sci-biology/gbrowse: version bump, more DEPS added, tiny webappconfig improvement

(Portage version: 2.1.9.28/git/Linux i686, unsigned Manifest commit)

3 files changed, 79 insertions, 6 deletions

diff --git a/sci-biology/gbrowse/Manifest b/sci-biology/gbrowse/Manifest
index 0af49e2a7..930f89d8b 100644
--- a/sci-biology/gbrowse/Manifest
+++ b/sci-biology/gbrowse/Manifest
@@ -1,9 +1,9 @@
-AUX GBrowseInstall.pm.patch 546 RMD160 a479d11e70b0c1340d50760e0f2aae5030b2aa26 SHA1 bac9d3692586c878b9a3f5a2df398e72bd73ede1 SHA256 0f4eaedce7f049628dc78ea2921bd1a5666981d77f54c6d240b1ae572f410c22
+AUX GBrowseInstall.pm.patch 2725 RMD160 233736db7a83e6c196c83aba928f3e935833afa6 SHA1 7e1916804d42ff5700bb1ccd0ba4b6d9b676da49 SHA256 64edd999fd5aa6ddcfaccea534aa2582462a8e95b184f227d6f120d42545100d
 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-2.00.tar.gz 3844690 RMD160 f3856ca620d8adc10172d8dfb644dfbbd25cbf88 SHA1 9d78393ca21d2569a975cfff7588cb7fe62d1082 SHA256 62c96ae1c6c1494ff67fbea1fde0d80d5051705c22167a55db317a0d33b1b8ea
-DIST GBrowse-2.03.tar.gz 11773792 RMD160 5f02c3f824ff6b0d2a32bbfb744be9bff71098a0 SHA1 92b6d4d43c663393f1a5a6b0283f0d740b2c0399 SHA256 279ec6546304888e506809bccefae9007e359e376a1abb643edfa30f7363574a
+DIST GBrowse-2.26.tar.gz 11937473 RMD160 c2c9d988e3183637b0a97f00e8de1387ad107eab SHA1 3153afc0ef7e6ea8ca6879343028673fdb062501 SHA256 4ac5c0fd87c5ab64b3c52ebb51f51433cb8c6062fd80a56d3de91f24594d3a3f
 DIST Generic-Genome-Browser-1.70.tar.gz 3331393 RMD160 056f72fc17bdbf803fce7e6bdde406566a80c204 SHA1 7a83abaedc4d2b061e1247972036025a713a845f SHA256 e08ef0d1ffff8186bffd30177808ad3dd7991a99abf3ea6350c8d487ba835486
 DIST README-gff-files 5309 RMD160 8ba184fa8a6b921f925143cf53de06e3da353023 SHA1 ad2d2b3133c73a05ace4a0107ff1a3a4221bc8f8 SHA256 21f4f026b212698c5aac0e82045670f8397ab50fdfe74b938fcbc71a1d36c82a
 DIST Refseq_Genome_TBLASTX.tar.gz 56482234 RMD160 e188d9dfe12bed3fd299be4625f7e658f54bb8c4 SHA1 72ec3de9b9ca0e10c2dd8dcda24f9be74f98cf09 SHA256 7036bdd9aefbf44e384df83f4c1e973c1ab3eac8fe74b37499c4a3f1c55a18af
@@ -17,6 +17,6 @@ DIST yeast.fasta.gz 3801757 RMD160 5545054cf6ffa5381c7992141144107076fdf62e SHA1
 DIST yeast.gff.gz 249814 RMD160 64538d18de23d930915938bd00ae4a94a52f3960 SHA1 ec753b1ae409e1377f568531a53be8985a7bfa2e SHA256 20c93e6ba9457896a693d13e8fd8fa00d77acbb55aee9b19a31c2b29c4b7e9b1
 EBUILD gbrowse-1.70.ebuild 1670 RMD160 e9bf6980abebabc6ff807ea3c682a3988d0a5f14 SHA1 0413b93216348184e79b3feea36cd68618bed688 SHA256 ecb0b9290e48b82a0d29520d8418593db7baa564bb3731ed7ed808f1b4b5ff3f
 EBUILD gbrowse-2.00.ebuild 1932 RMD160 5a0d15a10c2f6f9e4ac1f60ce048efcd2311cdb4 SHA1 186d5a91fbae9b6894091ac376addb84784d6a03 SHA256 21b035ef921900bc893a4de0fe123b6192860265e0594b73723c24b03dd5a23c
-EBUILD gbrowse-2.03.ebuild 5198 RMD160 b55f47213db96090869388c524b0505d709d9798 SHA1 0a050dc6a23998cd95ed65e8bd5c1d6fb91f2473 SHA256 49ab81d5ee5f33cd016618f3c17819731b91e75c759c877c3731a85d7c37424d
+EBUILD gbrowse-2.26.ebuild 5557 RMD160 bb48122780982dd945e025e614e143731f814206 SHA1 f44638ae42791b24f0ae88faec7908ed8234537a SHA256 cf2a7ef7d2e77fca60323d09a68e4ec36df6f4b6a63775794bdb8ad649534cd8
 MISC ChangeLog 1985 RMD160 9695d7522c6165b842087b67938629377f9cc82b SHA1 3edd2e74f9b26289d95ad7609b838edb3ccb9561 SHA256 76c1d0553f09390397af4354dc653677f25d06828e42e57a60b2f35a869222ac
 MISC metadata.xml 572 RMD160 bc941571413238acb3d77e61d49b959737ed4f5a SHA1 0c05303509c0e2dd21b37fc93c936809db49e530 SHA256 89b9964a9404a95dbb622a91735348da8e66d34d7dd7e7f144ed8c0159c43e31
diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm.patch
index e6163a732..863930e58 100644
--- a/sci-biology/gbrowse/files/GBrowseInstall.pm.patch
+++ b/sci-biology/gbrowse/files/GBrowseInstall.pm.patch
@@ -1,5 +1,5 @@
---- GBrowse-2.03/install_util/GBrowseInstall.pm.ori	2010-11-27 12:01:58.000000000 +0100
-+++ GBrowse-2.03/install_util/GBrowseInstall.pm	2010-11-27 12:02:15.000000000 +0100
+--- GBrowse-2.26/install_util/GBrowseInstall.pm.ori	2010-11-27 12:01:58.000000000 +0100
++++ GBrowse-2.26/install_util/GBrowseInstall.pm	2010-11-27 12:02:15.000000000 +0100
 @@ -436,8 +436,8 @@
  	$self->ownership_warning($databases,$user);
      }
@@ -11,3 +11,62 @@
  
      my $base = basename($self->install_path->{htdocs});
  
+--- GBrowse-2.26/install_util/GBrowseInstall.pm.ori	2011-02-14 13:39:46.000000000 +0100
++++ GBrowse-2.26/install_util/GBrowseInstall.pm	2011-02-14 13:41:50.000000000 +0100
+@@ -438,25 +438,25 @@
+     $gid =~ /^(\d+)$/;
+     $gid = $1;
+     
+-    unless (chown $uid,$gid,$tmp) {
+-	$self->ownership_warning($tmp,$user);
+-    }
++#   unless (chown $uid,$gid,$tmp) {
++#	$self->ownership_warning($tmp,$user);
++#   }
+ 
+     my $htdocs_i = File::Spec->catfile($self->install_path->{htdocs},'i');
+     my $images   = File::Spec->catfile($tmp,'images');
+     my $htdocs = $self->install_path->{htdocs};
+-    chown $uid,-1,$htdocs;
+-    {
+-	local $> = $uid;
+-	symlink($images,$htdocs_i);  # so symlinkifowner match works!
+-    }
+-    chown $>,-1,$self->install_path->{htdocs};
++#    chown $uid,-1,$htdocs;
++#    {
++#	local $> = $uid;
++#	symlink($images,$htdocs_i);  # so symlinkifowner match works!
++#    }
++#    chown $>,-1,$self->install_path->{htdocs};
+ 
+     my $databases = $self->install_path->{'databases'};
+     
+-    unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) {
+-	$self->ownership_warning($databases,$user);
+-    }
++#    unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) {
++#	$self->ownership_warning($databases,$user);
++#    }
+ 
+     # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave');
+     # $self->fix_selinux;
+--- GBrowse-2.26/install_util/GBrowseInstall.pm.ori	2011-02-14 13:50:41.000000000 +0100
++++ GBrowse-2.26/install_util/GBrowseInstall.pm	2011-02-14 13:51:46.000000000 +0100
+@@ -470,11 +470,11 @@
+     my @inc           = map{"-I$_"} split ':',$self->added_to_INC;
+     system $perl,@inc,$metadb_script;
+ 
+-    if (Module::Build->y_n(
+-	    "It is recommended that you restart Apache. Shall I try this for you?",'y'
+-	)) {
+-	system "sudo /etc/init.d/apache2 restart";
+-    }
++#    if (Module::Build->y_n(
++#	    "It is recommended that you restart Apache. Shall I try this for you?",'y'
++#	)) {
++#	system "sudo /etc/init.d/apache2 restart";
++#    }
+     
+     print STDERR "\n***INSTALLATION COMPLETE***\n";
+     print STDERR "Load http://localhost/$base for demo and documentation.\n";
diff --git a/sci-biology/gbrowse/gbrowse-2.03.ebuild b/sci-biology/gbrowse/gbrowse-2.26.ebuild
index 9fc872b3d..b525bcca3 100644
--- a/sci-biology/gbrowse/gbrowse-2.03.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.26.ebuild
@@ -31,6 +31,7 @@ S="${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
 DEPEND=">=dev-lang/perl-5.8.8
+	dev-perl/Capture-Tiny
 	>=sci-biology/bioperl-1.6
 	>=dev-perl/GD-2.07
 	dev-perl/IO-String
@@ -45,6 +46,11 @@ DEPEND=">=dev-lang/perl-5.8.8
 # 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
 
+#    *  Bio::DB::BigFile is not installed
+#    *  Bio::DB::Sam is not installed
+#    *  DBD::Pg is not installed
+
+
 RDEPEND="${DEPEND}
 	>=www-servers/apache-2.0.47
 	www-apache/mod_fastcgi
@@ -54,6 +60,8 @@ RDEPEND="${DEPEND}
 		dev-perl/File-NFSLock
 		dev-perl/FCGI
 		perl-core/Math-BigInt
+		perl-core/Math-BigInt-FastCalc
+		dev-perl/Math-BigInt-GMP
 		dev-perl/Digest-SHA1
 		dev-perl/Crypt-SSLeay
 		dev-perl/Net-SMTP-SSL
@@ -67,6 +75,7 @@ RDEPEND="${DEPEND}
 		dev-perl/XML-Writer
 		dev-perl/XML-Parser
 		dev-perl/Bio-Das
+		dev-perl/Text-Shellwords
 	)"
 
 src_prepare() {
@@ -93,6 +102,7 @@ src_configure() {
 		INSTALLCONF="n" \
 		WWWUSER="apache" \
 		DO_XS=1 \
+		NONROOT=1 \
 		|| die
 }
 
@@ -102,7 +112,7 @@ src_install() {
 
 	# TODO: write our own readme
 	webapp_postinst_txt en "${S}"/INSTALL
-	webapp_src_install
+	webapp_src_install || die "Failed running webapp_src_install"
 
 	# should create a /etc/init.d/ startup script based on this
 	# /var/tmp/portage/sci-biology/gbrowse-2.03/work/GBrowse-2.03/etc/init.d/gbrowse-slave
@@ -118,6 +128,10 @@ src_install() {
 	einfo "Make sure you compiled apache with +cgi and copy ${FILESDIR}/gbrowse.conf.vhosts.d to /etc/apache2/vhosts.d/"
 }
 
+pkg_postinst() {
+	webapp_pkg_postinst || die "webapp_pkg_postinst failed"
+}
+
 src_test() {
 	mysql -uroot -p password -e 'create database yeast'
 	mysql -uroot -p password -e 'grant all privileges on yeast.* to gbrowse@localhost'