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-rw-r--r--profiles/package.mask2
-rw-r--r--sci-biology/gbrowse/Manifest13
-rw-r--r--sci-biology/gbrowse/files/GBrowseInstall.pm-2.39.patch32
-rw-r--r--sci-biology/gbrowse/files/GBrowseInstall.pm-2.45.patch32
-rw-r--r--sci-biology/gbrowse/files/destdir.patch92
-rw-r--r--sci-biology/gbrowse/files/disable-gbrowse_metadb_config.pl.patch19
-rw-r--r--sci-biology/gbrowse/files/fix-PNG-export.patch11
-rw-r--r--sci-biology/gbrowse/files/gbrowse-slave.default12
-rw-r--r--sci-biology/gbrowse/files/gbrowse-slave.init.d94
-rw-r--r--sci-biology/gbrowse/files/gbrowse.conf.vhosts.d26
-rw-r--r--sci-biology/gbrowse/files/gbrowse_metadb_config.pl.patch55
-rw-r--r--sci-biology/gbrowse/files/symlink.patch11
-rw-r--r--sci-biology/gbrowse/gbrowse-2.39.ebuild169
-rw-r--r--sci-biology/gbrowse/gbrowse-2.45.ebuild200
-rw-r--r--sci-biology/gbrowse/gbrowse-2.48.ebuild201
-rw-r--r--sci-biology/gbrowse/metadata.xml16
16 files changed, 0 insertions, 985 deletions
diff --git a/profiles/package.mask b/profiles/package.mask
index 306c5be55..20ff196b6 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -55,11 +55,9 @@ sci-mathematics/scilab
# bigdft moved from sci-libs to sci-physics
# sci-physics/abinit now uses sci-libs/bigdft-abi instead
# sci-libs/bigdft should be deleted in 30 days
-sci-libs/bigdft
# Justin Lecher <jlec@gentoo.org> (03 March 2013)
# Missing deps
-sci-biology/gbrowse
sci-mathematics/surfer
dev-python/pymvpa
sci-biology/artemis-bin
diff --git a/sci-biology/gbrowse/Manifest b/sci-biology/gbrowse/Manifest
deleted file mode 100644
index 0dcb760e2..000000000
--- a/sci-biology/gbrowse/Manifest
+++ /dev/null
@@ -1,13 +0,0 @@
-DIST GBrowse-2.39.tar.gz 11969088 SHA256 b4e76acfa1d8f64d5f227c3ba0258666928b4f357428549be85f05c944337d44 SHA512 4297192236a297a4f6a25892e245e3f5a4951b561ae167d7d402ff09b50a9a8a0d924094136d191d9068f735f77795a166e37aac67cd964d70cc805a15f8c26d WHIRLPOOL a0fc2c882d9e11f76d739a824152f9b5482f2b352583dc2e92fcfb60cf1b19ff1a9684c543ee6b8e69b3ed441548d5dd9b1d2da9e8779f0d157a7fe73f6e7af8
-DIST GBrowse-2.45.tar.gz 11954151 SHA256 8f8c9054d48199ccfe0a536ef892461a9e197d49ac99dd67381f9ad45377c35c SHA512 8b330ccb5468a4dd6b2f409a97350578788eb857a8db79715314f12875a69c5f37c6679b1efa23aaae77b978f93f35dbe8113a2714e3bbd45fb02273edf1a119 WHIRLPOOL 2bd2e7a47788b31861dc0d0f8654f56c5e078b9a99b9bab74c89422800b8e9a8bfb3e0b64e99dc9eb53bcfe04f3106322f8da2c978ad2873adc3ef06e64d37a4
-DIST GBrowse-2.48.tar.gz 11958127 SHA256 02772c5a7a31ed87733e21278efec2edd3bd6ee8a4bec9b002233e57f6dc9681 SHA512 d5a07caf1517fb15741e8e6056669763eb04678a42637a9e90788c91e74fb34515b5f86aac10a00f29d8848aceb19d6f5f7258d2dda0e281feee550e9e2fb3db WHIRLPOOL 5a3ec31de1582c4c551c76908ca8e8024c8d3311404f0c94f7b75a391c340da0ededd80df34be3f10f581902ba1408d84e3e65218f46322546623e15a1020135
-DIST README-gff-files 5309 SHA256 21f4f026b212698c5aac0e82045670f8397ab50fdfe74b938fcbc71a1d36c82a SHA512 b591d269400c28f8908e5cc7bd27815b35b1750661cd4bb2c34e94f712ce100f71c7e9934800477425747e75fdd487192c3a2c05cf7249e28006c986feb54cca WHIRLPOOL f4080b582ac52adc76536cb7dcd646e4ce85b0f8210ef2010e037db7d114b436077f3b7d7d84216030e92130ad5be649442ece1e281273b13c39c537542270b6
-DIST Refseq_Genome_TBLASTX.tar.gz 56482234 SHA256 7036bdd9aefbf44e384df83f4c1e973c1ab3eac8fe74b37499c4a3f1c55a18af SHA512 d49dc91f1246a881acf1b4fa0f336fe25ee0317f04a5bc42f2750509f95af3768eabfa0d4517f97ee14bb5de9e59700e0a7ef9018e577d2a87874809d313fdfb WHIRLPOOL 0cc86c1987d5399b952ba05cb441035a03ef5e47242e7f2ce95a73cc5420ff8b581ab6b097b66c96d65dc73b9ef4e301473b89a29c60413dd4d4d5e39508b6df
-DIST fly.fasta.gz 37349852 SHA256 892ed03e17edd3469f1ed00cb9967fb905bbac57c1cb7858667381f34a6bfeea SHA512 f3c0864d82be03c5e06a2e420ecd42df254318b7ee18f7dbb982b1c716ff5db465da69991ab009cf157b6a3601220fadd58d91d68732570af453e2bd329e09b7 WHIRLPOOL e914a4082913fff82687b0282e9ddcb01cfdd50712dbc30dba9ba697fcacc2b4b168f2b6b587479c84e2b51370ea7285fb6c5a8ce3961a55f3ee2ee29f27d169
-DIST fly.gff.gz 18687640 SHA256 db03b56993b739dd6e6df92dcb94163f04ca03a1911c99dd4df4fe65e16b6d44 SHA512 7f4ac316c4028d0e15c4b304169c7225379ad0857d4e66a0c03c1479eabe9beac84098786725b2895a12c607e2895492c24c920d85ba8c589c0d2e65d88bf687 WHIRLPOOL 4b2d66953afb33e9d6cafc7f6220a573129a8cdca49cadee089ed528faf55209d25bf5a8c82592c38248a5fa9bed205060d68dec853fe7b141b9bb1f00b816fa
-DIST human.gff.tar.gz 40362676 SHA256 7d0ea6363e6dda8618f53b42dea72d6ef6034b4f2fb541b94b4800383009f6b0 SHA512 c757d3573774a4328c4dbc564a3f9d0e415265fec788fbfcd1b1adcb93f4c58aebd02c26a01cad27de4d23a2b9a27f9099192580269e5c499e681336b056a648 WHIRLPOOL ed7847f7b7db34071ec4224b9f6d9fa70b42e0f15af2e5dc2df5b96520addc0cd6edfd106a6d6e1dec42f944de768ddd0a80929645f0e0d682cc6c625d165e2d
-DIST saccharomyces_cerevisiae.gff.bz2 4000445 SHA256 fb41705b64f0e36cbb46fb6b7557c2f36e517db582f1472d852f89b46ca750d4 SHA512 128c33a956e6b01b704bd37d21eebb123283fe3e2b1b7097158b4e0f6d951bca473d4dba5f03c902bf03d7a25e1ee2fdb22e2d829cfe39ee89d4c772825a41b4 WHIRLPOOL 1e1dc5114f22db8641feb933f5718b07afb8718e40afe8c9cd347280d598a12104c4396859f3a6dce96a12a640ca5452a08701f72126d9877eefab29b5177f2c
-DIST worm.fasta.gz 30593662 SHA256 dbd6dcc44a8960e0e475b0be31b03caa3d97f4ddfc36ba566862732880f7dbc0 SHA512 2518970a420d8f18cde0271fc9f1fe81cbce0f888bec9afe98497cc5389ea7a5a9d232a102ad776b2ecad8e29839f468ca06db3fc6babd13b6af5afa5843f0d1 WHIRLPOOL 744651e5f1ea1e7f5893db9b7e1114c42686fa70e27735c96ff828e4a061cba5cd95ddeba9f81dd0279213485d12c373ea0eb06dc8d0367cfdcb82556ea4101d
-DIST worm.gff.gz 65789458 SHA256 afd63c65c3fdb0ba8a1cf455bd4477a2d5d27d5b0e88c6a5a10d156d0567374f SHA512 9fde867eb2e676904bc79432ec3e293d69e6795fd7f18fa1de409c48417ba974dfe1ebc1c1c07c4825b83cd738c153de7b192da77b2c4a518131797984a608ca WHIRLPOOL 38d8c9965341824dcc561acc7670d21c5dba93c52efc0b1022f28e9f37eb986799a9e368537ce3a7c40c890a21b237025132012a43ebb860bbceb59624bd193d
-DIST yeast.fasta.gz 3801757 SHA256 bf51cbced31aa6a30bca43cc72fdb53194fbb403407e2ebb9d70c901ab072e6d SHA512 5dc0a0ca99ff7fab859eec60df896dbdf6e6c20352ed2b88bf331b351442136a71a5d4adc0654be090e322c35ae20e1ea74286410b3c0f90dce6d89ad5170381 WHIRLPOOL 92e192cc027045ffbbfbc78fffa7a1f190b75026d4f1bd0061f1b3e3eb15c8b724ce566abd6f7bda48f5f941f870288a0a394625177d66beabd251bcfd479985
-DIST yeast.gff.gz 249814 SHA256 20c93e6ba9457896a693d13e8fd8fa00d77acbb55aee9b19a31c2b29c4b7e9b1 SHA512 2a4257569145a9d0d4c9d6b91e01c4f88771d2cc3c16ece9d0d86106903528e8c5386d51298c9360e9d59cfec21a6f61c6bc0b464d0561af6c18f6b2094fba8a WHIRLPOOL e17689198aa3710e02e090ddc38c6f7286d1e09e11ee88248e760053e23b33e0aacf88fcc594fec904fa520e3df55008db568147517c1a059ed7fe22896f8e1c
diff --git a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.39.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.39.patch
deleted file mode 100644
index e91fe1634..000000000
--- a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.39.patch
+++ /dev/null
@@ -1,32 +0,0 @@
---- install_util/GBrowseInstall.pm.ori 2010-11-27 12:01:58.000000000 +0100
-+++ install_util/GBrowseInstall.pm 2010-11-27 12:02:15.000000000 +0100
-@@ -436,8 +436,8 @@
- $self->ownership_warning($databases,$user);
- }
-
-- chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave');
-- $self->fix_selinux;
-+ # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave');
-+ # $self->fix_selinux;
-
- my $base = basename($self->install_path->{htdocs});
-
---- install_util/GBrowseInstall.pm.ori 2011-02-14 13:50:41.000000000 +0100
-+++ 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/files/GBrowseInstall.pm-2.45.patch b/sci-biology/gbrowse/files/GBrowseInstall.pm-2.45.patch
deleted file mode 100644
index e91fe1634..000000000
--- a/sci-biology/gbrowse/files/GBrowseInstall.pm-2.45.patch
+++ /dev/null
@@ -1,32 +0,0 @@
---- install_util/GBrowseInstall.pm.ori 2010-11-27 12:01:58.000000000 +0100
-+++ install_util/GBrowseInstall.pm 2010-11-27 12:02:15.000000000 +0100
-@@ -436,8 +436,8 @@
- $self->ownership_warning($databases,$user);
- }
-
-- chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave');
-- $self->fix_selinux;
-+ # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave');
-+ # $self->fix_selinux;
-
- my $base = basename($self->install_path->{htdocs});
-
---- install_util/GBrowseInstall.pm.ori 2011-02-14 13:50:41.000000000 +0100
-+++ 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/files/destdir.patch b/sci-biology/gbrowse/files/destdir.patch
deleted file mode 100644
index 655158c04..000000000
--- a/sci-biology/gbrowse/files/destdir.patch
+++ /dev/null
@@ -1,92 +0,0 @@
---- install_util/GBrowseInstall.pm.ori 2011-07-30 16:06:18.000000000 +0200
-+++ install_util/GBrowseInstall.pm 2011-07-30 16:06:28.000000000 +0200
-@@ -419,6 +419,7 @@
- sub ACTION_install {
- my $self = shift;
- my $prefix = $self->install_base || $self->prefix || '';
-+ my $destdir = $self->destdir || '';
- GBrowseGuessDirectories->prefix($prefix);
-
- $self->depends_on('config_data');
-@@ -445,7 +446,7 @@
-
- # fix some directories so that www user can write into them
- my $tmp = $self->config_data('tmp') || GBrowseGuessDirectories->tmp;
-- mkpath($tmp);
-+ mkpath($destdir.$tmp);
- my ($uid,$gid) = (getpwnam($user))[2,3];
-
- # taint check issues
-@@ -454,29 +455,29 @@
- $gid =~ /^(\d+)$/;
- $gid = $1;
-
-- unless (chown $uid,$gid,$tmp) {
-+ unless (chown $uid,$gid,$destdir.$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;
-+ chown $uid,-1,$destdir.$htdocs;
- {
- local $> = $uid;
- symlink($images,$htdocs_i); # so symlinkifowner match works!
- }
-- chown $>,-1,$self->install_path->{htdocs};
-+ chown $>,-1,$destdir.$self->install_path->{htdocs};
-
- my $persistent = $self->install_path->{'persistent'};
- my $sessions = File::Spec->catfile($persistent,'sessions');
- my $userdata = File::Spec->catfile($persistent,'userdata');
-- mkpath([$sessions,$userdata],0711);
-+ mkpath([$destdir.$sessions,$destdir.$userdata],0711);
-
- 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($destdir.File::Spec->catfile($databases,'').'*')) {
-+ $self->ownership_warning($destdir.$databases,$user);
- }
-
- # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave');
-@@ -490,7 +491,7 @@
- my $perl = $self->perl;
- my @inc = map{"-I$_"} split ':',$self->added_to_INC;
- system $perl,@inc,$metadb_script;
-- system 'sudo','chown','-R',"$uid.$gid",$sessions,$userdata;
-+ system 'sudo','chown','-R',"$uid.$gid",$destdir.$sessions,$destdir.$userdata;
-
- # if (Module::Build->y_n(
- # "It is recommended that you restart Apache. Shall I try this for you?",'y'
-@@ -600,6 +601,7 @@
- my $self = shift;
-
- my $prefix = $self->install_base || $self->prefix || '';
-+ my $destdir = $self->destdir || '';
- GBrowseGuessDirectories->prefix($prefix);
- my $install_path = GBrowseGuessDirectories->etc;
-
-@@ -647,7 +649,7 @@
- if ($self->config_data('installconf') =~ /^[yY]/ && !-e "${includes}/$file") {
- warn "Creating include file for Apache config: $target\n";
- my $dir = dirname($target);
-- mkpath([$dir]);
-+ mkpath([$destdir.$dir]);
- if (my $f = IO::File->new("blib${includes}/$file",'>')) {
- $f->print($self->apache_conf);
- $f->close;
-@@ -935,8 +937,9 @@
- sub ownership_warning {
- my $self = shift;
- my ($path,$owner) = @_;
-+ my $destdir = $self->destdir || '';
- warn "*** WARNING: Using sudo to change ownership of $path to '$owner'. You may be prompted for your login password ***\n";
-- system "sudo chown -R $owner $path";
-+ system "sudo chown -R $owner $destdir.$path";
- }
-
- sub cgiurl {
diff --git a/sci-biology/gbrowse/files/disable-gbrowse_metadb_config.pl.patch b/sci-biology/gbrowse/files/disable-gbrowse_metadb_config.pl.patch
deleted file mode 100644
index 1e96bb8c6..000000000
--- a/sci-biology/gbrowse/files/disable-gbrowse_metadb_config.pl.patch
+++ /dev/null
@@ -1,19 +0,0 @@
---- install_util/GBrowseInstall.pm.ori 2011-07-30 20:42:02.000000000 +0200
-+++ install_util/GBrowseInstall.pm 2011-07-30 20:42:19.000000000 +0200
-@@ -486,11 +486,11 @@
- my $base = basename($self->install_path->{htdocs});
-
- # Configure the databases, if needed.
-- print STDERR "Updating user account database...\n";
-- my $metadb_script = File::Spec->catfile("bin", "gbrowse_metadb_config.pl");
-- my $perl = $self->perl;
-- my @inc = map{"-I$_"} split ':',$self->added_to_INC;
-- system $perl,@inc,$metadb_script;
-+# print STDERR "Updating user account database...\n";
-+# my $metadb_script = File::Spec->catfile("bin", "gbrowse_metadb_config.pl");
-+# my $perl = $self->perl;
-+# my @inc = map{"-I$_"} split ':',$self->added_to_INC;
-+# system $perl,@inc,$metadb_script;
- system 'sudo','chown','-R',"$uid.$gid",$destdir.$sessions,$destdir.$userdata;
-
- # if (Module::Build->y_n(
diff --git a/sci-biology/gbrowse/files/fix-PNG-export.patch b/sci-biology/gbrowse/files/fix-PNG-export.patch
deleted file mode 100644
index 469f75202..000000000
--- a/sci-biology/gbrowse/files/fix-PNG-export.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm.ori 2011-07-30 17:14:28.000000000 +0200
-+++ lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm 2011-07-30 17:13:13.000000000 +0200
-@@ -30,7 +30,7 @@
- sub setting {
- my $self = shift;
- my ($label,$option,@rest) = @_ >= 2 ? @_ : ('general',@_);
-- $label = 'general' if lc $label eq 'general'; # buglet
-+ $label = 'general' if lc($label) eq 'general'; # buglet
- $self->SUPER::setting($label,$option,@rest);
- }
-
diff --git a/sci-biology/gbrowse/files/gbrowse-slave.default b/sci-biology/gbrowse/files/gbrowse-slave.default
deleted file mode 100644
index 46457c2dc..000000000
--- a/sci-biology/gbrowse/files/gbrowse-slave.default
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/bin/sh
-
-export PERL5LIB=$PERL5LIB
-
-DAEMON=$INSTALLSCRIPT/gbrowse_slave
-USER=$WWWUSER
-PRELOAD=$CONF/slave_preload.conf
-RUNDIR=/var/run/gbrowse
-LOGDIR=/var/log/gbrowse
-PORT="8101 8102 8103"
-VERBOSITY=3
-NICE=0
diff --git a/sci-biology/gbrowse/files/gbrowse-slave.init.d b/sci-biology/gbrowse/files/gbrowse-slave.init.d
deleted file mode 100644
index c298faf3c..000000000
--- a/sci-biology/gbrowse/files/gbrowse-slave.init.d
+++ /dev/null
@@ -1,94 +0,0 @@
-#!/bin/sh
-### BEGIN INIT INFO
-# Provides: gbrowse_slave
-# Required-Start: $local_fs
-# Required-Stop: $local_fs
-# Default-Start: 28
-# Default-Stop: S
-# Short-Description: Start/Stop the gbrowse_slave rendering server.
-### END INIT INFO
-
-PATH=/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin
-DAEMON=$INSTALLSCRIPT/gbrowse_slave
-NAME="gbrowse-slave"
-DESC="GBrowse slave track rendering server"
-
-test -x $DAEMON || exit 0
-set -e
-
-USER=$WWWUSER
-PRELOAD=""
-RUNDIR=/var/run/gbrowse
-LOGDIR=/var/log/gbrowse
-PORT='8101'
-VERBOSITY=1
-NICE=0
-
-if [ -f /etc/default/gbrowse-slave ]; then
- . /etc/default/gbrowse-slave
-fi
-
-mkdir -p $RUNDIR
-chown -R $USER $RUNDIR
-mkdir -p $LOGDIR
-chown -R $USER $LOGDIR
-
-case "$1" in
- start)
- echo -n "Starting $DESC: $NAME "
- for port in $PORT; do
- if test -e $RUNDIR/$NAME.$port.pid ; then
- echo "$NAME already running, use restart instead."
- else
- PRELOAD_DB=""
- if [ "$PRELOAD" != "" ]; then
- PRELOAD_DB="--preload $PRELOAD"
- fi
- ARGS="--port $port --verbose $VERBOSITY --log $LOGDIR/gbrowse_slave --pid $RUNDIR/$NAME.$port.pid $PRELOAD_DB"
- su $USER -s /bin/sh -c "nice -n $NICE $DAEMON $ARGS"
- echo -n "$port "
- fi
- done
- echo "."
- ;;
- stop)
- echo -n "Stopping $DESC: $NAME "
- killed=0
- for port in $PORT; do
- if test -e $RUNDIR/$NAME.$port.pid ; then
- kill -TERM `cat $RUNDIR/$NAME.$port.pid`
- killed=1
- fi
- echo -n "$port "
- done
- if [ "$killed" -ne 1 ]; then
- base=`basename $DAEMON`
- killall -q -r $base || true
- fi
- echo "."
- ;;
- status)
- for port in $PORT; do
- if test -e $RUNDIR/$NAME.$port.pid ; then
- kill -0 `cat $RUNDIR/$NAME.$port.pid`
- if [ "$?" -eq 0 ]; then
- echo "$NAME is running on port $port."
- fi
- else
- echo "$NAME is not running on port $port."
- fi
- done
- ;;
- restart|force-reload)
- $0 stop
- sleep 3
- $0 start
- ;;
- *)
- N=/etc/init.d/$NAME
- echo "Usage: $N {start|stop|restart|force-reload|status}" >&2
- exit 1
- ;;
-esac
-
-exit 0
diff --git a/sci-biology/gbrowse/files/gbrowse.conf.vhosts.d b/sci-biology/gbrowse/files/gbrowse.conf.vhosts.d
deleted file mode 100644
index a3966ea19..000000000
--- a/sci-biology/gbrowse/files/gbrowse.conf.vhosts.d
+++ /dev/null
@@ -1,26 +0,0 @@
-ScriptAlias /gbrowse/cgi-bin/gbrowse "/var/www/localhost/htdocs/gbrowse/cgi-bin/gbrowse"
-ScriptAlias /gbrowse/cgi-bin/ "/var/www/localhost/htdocs/gbrowse/cgi-bin/"
-
-<Directory "/var/www/localhost/htdocs/gbrowse/cgi-bin/">
- Options ExecCGI
- AllowOverride None
- <IfModule mod_access.c>
- Order allow,deny
- Allow from all
- </IfModule>
-</Directory>
-
-Alias /gbrowse/i "/var/www/localhost/htdocs/gbrowse/images"
-Alias /gbrowse "/var/www/localhost/htdocs/gbrowse"
-Alias /gbrowse2 "/var/www/localhost/htdocs/gbrowse"
-
-<Directory "/var/www/localhost/htdocs/gbrowse">
- Options FollowSymlinks
- AllowOverride None
- <IfModule mod_access.c>
- Order allow,deny
- Allow from all
- </IfModule>
-</Directory>
-
-
diff --git a/sci-biology/gbrowse/files/gbrowse_metadb_config.pl.patch b/sci-biology/gbrowse/files/gbrowse_metadb_config.pl.patch
deleted file mode 100644
index 0f7d5d373..000000000
--- a/sci-biology/gbrowse/files/gbrowse_metadb_config.pl.patch
+++ /dev/null
@@ -1,55 +0,0 @@
---- bin/gbrowse_metadb_config.pl.ori 2011-07-30 19:57:33.000000000 +0200
-+++ bin/gbrowse_metadb_config.pl 2011-07-30 20:04:51.000000000 +0200
-@@ -703,9 +703,9 @@
- local $database->{AutoCommit} = 0;
- local $database->{RaiseError} = 1;
- eval {
-- $database->do("delete from $table");
-- $database->do("insert into $table (schema_version) values ($version)");
-- $database->commit();
-+ $database->do("delete from $table") or warn "delete from $table failed with: $database->errstr";
-+ $database->do("insert into $table (schema_version) values ($version)") or warn "insert into $table (schema_version) values ($version) failed with: $database->errstr";
-+ $database->commit() or warn "commitfailed with: $database->errstr";
- };
- if ($@) {
- warn "update failed due to $@. Rolling back";
-@@ -768,11 +768,11 @@
- $insert_user->finish;
- # rename the current users table
- $database->do('drop table users')
-- or die "Couldn't drop old users table";
-+ or die "Couldn't drop old users table: $database->errstr";
- $database->do('alter table users_new rename to users')
-- or die "Couldn't rename new users table";
-+ or die "Couldn't rename new users table: $database->errstr";
- $database->do('create index index_session on session(username)')
-- or die "Couldn't index sessions table";
-+ or die "Couldn't index sessions table: $database->errstr";
-
- # now do the uploads table
- # this upgrades to latest version 0
-@@ -808,9 +808,9 @@
- $insert->finish();
-
- $database->do('drop table uploads')
-- or die "Couldn't drop old uploads table";
-+ or die "Couldn't drop old uploads table: $database->errstr";
- $database->do('alter table uploads_new rename to uploads')
-- or die "Couldn't rename new uploads table";
-+ or die "Couldn't rename new uploads table: $database->errstr";
-
- # now do the openid_users table
- # this creates the new one
-@@ -916,10 +916,10 @@
- $select->finish;
- $insert->finish;
- $database->do('drop table users')
-- or die "Couldn't drop old users table";
-+ or die "Couldn't drop old users table: $database->errstr";
-
- $database->do('alter table users_new rename to users')
-- or die "Couldn't rename new users table";
-+ or die "Couldn't rename new users table: $database->errstr";
- $database->commit();
- };
-
diff --git a/sci-biology/gbrowse/files/symlink.patch b/sci-biology/gbrowse/files/symlink.patch
deleted file mode 100644
index e6df771ee..000000000
--- a/sci-biology/gbrowse/files/symlink.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- install_util/GBrowseInstall.pm.ori 2011-07-30 19:41:55.000000000 +0200
-+++ install_util/GBrowseInstall.pm 2011-07-30 19:42:31.000000000 +0200
-@@ -465,7 +465,7 @@
- chown $uid,-1,$destdir.$htdocs;
- {
- local $> = $uid;
-- symlink($images,$htdocs_i); # so symlinkifowner match works!
-+ symlink($images,$destdir.$htdocs_i) or warn "symlink($images,$destdir.$htdocs_i) failed: $!\n"; # so symlinkifowner match works!
- }
- chown $>,-1,$destdir.$self->install_path->{htdocs};
-
diff --git a/sci-biology/gbrowse/gbrowse-2.39.ebuild b/sci-biology/gbrowse/gbrowse-2.39.ebuild
deleted file mode 100644
index ed43aae98..000000000
--- a/sci-biology/gbrowse/gbrowse-2.39.ebuild
+++ /dev/null
@@ -1,169 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils perl-module webapp
-
-MY_P="GBrowse-${PV}"
-
-DESCRIPTION="Display of genomic annotations on interactive web pages"
-HOMEPAGE="http://gmod.org/"
-# mirror://sourceforge/gmod/${MY_P}.tar.gz
-# mirror://cpan/authors/id/L/LD/LDS/GBrowse-2.33.tar.gz
-SRC_URI="
- mirror://cpan/authors/id/L/LD/LDS/${MY_P}.tar.gz
- test? (
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )"
-
-LICENSE="Artistic"
-# webapp ebuilds do not set SLOT
-KEYWORDS="~x86 ~amd64"
-IUSE="cgi fastcgi minimal mysql pdf 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)
-# how about mod_fcgi and dev-libs/fcgi and mod_scgi?
-DEPEND="
- >=virtual/perl-Module-Build-0.380.0
- >=dev-lang/perl-5.8.8:=
- dev-perl/Capture-Tiny
- >=sci-biology/bioperl-1.6.901
- >=dev-perl/GD-2.07
- dev-perl/IO-String
- virtual/perl-Digest-MD5
- >=dev-perl/CGI-Session-4.03
- dev-perl/Statistics-Descriptive
- >=dev-perl/Bio-Graphics-1.97
- >=dev-perl/JSON-2.510.0
- dev-perl/TermReadKey
- dev-perl/libwww-perl
- svg? ( dev-perl/GD-SVG )
- pdf? ( media-gfx/inkscape )
- 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
-
-RDEPEND="${DEPEND}
- >=www-servers/apache-2.0.47
- fastcgi? ( dev-libs/fcgi )
- www-apache/mod_fastcgi
- dev-perl/DBI
- || ( dev-perl/DBD-Pg dev-perl/DBD-mysql )
- !minimal? (
- dev-perl/File-NFSLock
- dev-perl/FCGI
- virtual/perl-Math-BigInt
- virtual/perl-Math-BigInt-FastCalc
- dev-perl/Math-BigInt-GMP
- dev-perl/Digest-SHA1
- dev-perl/Crypt-SSLeay
- dev-perl/Net-SMTP-SSL
- dev-perl/Net-OpenID-Consumer
- virtual/perl-DB_File
- dev-perl/DB_File-Lock
- dev-perl/GD-SVG
- dev-perl/Text-Shellwords
- dev-perl/XML-Twig
- dev-perl/XML-DOM
- dev-perl/XML-Writer
- dev-perl/XML-Parser
- dev-perl/Bio-Das
- dev-perl/Text-Shellwords
- postgres? ( >=dev-perl/Bio-DB-Das-Chado-0.32 )
- >=dev-perl/Bio-SamTools-1.29
- >=dev-perl/Bio-BigFile-1.06
- )"
-
-src_prepare() {
- sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die
- sed -i 's/process_/bp_process_/g' INSTALL || die
- epatch \
- "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch \
- "${FILESDIR}"/destdir.patch \
- "${FILESDIR}"/fix-PNG-export.patch \
- "${FILESDIR}"/symlink.patch \
- "${FILESDIR}"/gbrowse_metadb_config.pl.patch \
- "${FILESDIR}"/disable-gbrowse_metadb_config.pl.patch
-}
-
-src_configure() {
- # GBROWSE_ROOT is the root path in SRC_URI to be prepended
- # /usr/share/webapps/gbrowse/2.03/htdocs/etc/gbrowse/GBrowse.conf
- webapp_src_preinst
- perl Makefile.PL \
- HTDOCS="${MY_HTDOCSDIR}" \
- CGIBIN="${MY_HTDOCSDIR}"/cgi-bin \
- CONF="${MY_HTDOCSDIR}"/etc/gbrowse \
- PACKAGE_DIR="${D}" \
- INSTALLDIRS=vendor \
- GBROWSE_ROOT="gbrowse" \
- DESTDIR="${D}" \
- DATABASES="/var/www/gbrowse2/databases/" \
- TMP="/var/tmp/gbrowse2" \
- INSTALLETC="n" \
- INSTALLCONF="n" \
- WWWUSER="apache" \
- DO_XS=1 \
- NONROOT=1 \
- || die
-}
-
-src_install() {
- mydoc="Changes README TODO INSTALL"
- perl-module_src_install
-
- # TODO: write our own readme
- webapp_postinst_txt en "${S}"/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
-
- chown -R apache.apache "${D}"/var/www/gbrowse2/databases || die
-
- mkdir -p "${D}"/var/www/localhost/htdocs/gbrowse || die
- ln -s "${D}"/var/tmp/gbrowse2/images "${D}"/var/www/localhost/htdocs/gbrowse/i || die
-
- einfo "Probably you want to install a cron job to remove the generated temporary images:"
- einfo "find /var/tmp/gbrowse2/images -type f -atime +20 -print -exec rm {}"
-
- einfo "Make sure you compiled apache with +cgi and copy ${FILESDIR}/gbrowse.conf.vhosts.d to /etc/apache2/vhosts.d/"
-
- sed -i "s#"${D}"##g" "${S}"/install_util/GBrowseInstall.pm || die
- sed -i "s#"${D}"##" "${S}"/blib/conf/GBrowse.conf* || die
- sed -i 's#DBI:SQLite:'${D}'/var/www/gbrowse2/databases/#DBI:SQLite:/var/www/gbrowse2/databases/#' "${S}"/install_util/GBrowseInstall.pm || die
-}
-
-pkg_postinst() {
- webapp_pkg_postinst || die "webapp_pkg_postinst failed"
-
- einfo "Please run gbrowse_metadb_config.pl to update SQLite flatfiles of the live database."
-}
-
-src_test() {
- mysql -uroot -p password -e 'create database yeast'
- mysql -uroot -p password -e 'grant all privileges on yeast.* to gbrowse@localhost'
- mysql -uroot -p password -e 'grant file on *.* to gbrowse@localhost'
- mysql -uroot -p password -e 'grant select on yeast.* to nobody@localhost'
-
- cd /usr/portage/distfiles || die
- gzip -d yeast.fasta.gz || die
- gzip -d yeast.gff.gz || die
- #gzip -d fly.fasta.gz
- #gzip -d fly.gff.gz
- bp_bulk_load_gff.pl -d yeast -fasta yeast.fasta yeast.gff || die
-}
diff --git a/sci-biology/gbrowse/gbrowse-2.45.ebuild b/sci-biology/gbrowse/gbrowse-2.45.ebuild
deleted file mode 100644
index dec4791d7..000000000
--- a/sci-biology/gbrowse/gbrowse-2.45.ebuild
+++ /dev/null
@@ -1,200 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils perl-module webapp
-
-MY_P="GBrowse-${PV}"
-
-DESCRIPTION="Display of genomic annotations on interactive web pages"
-HOMEPAGE="http://gmod.org/"
-# mirror://sourceforge/gmod/${MY_P}.tar.gz
-# mirror://cpan/authors/id/L/LD/LDS/GBrowse-2.33.tar.gz
-SRC_URI="
- mirror://cpan/authors/id/L/LD/LDS/${MY_P}.tar.gz
- test? (
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )"
-
-LICENSE="Artistic"
-# webapp ebuilds do not set SLOT
-KEYWORDS="~x86 ~amd64"
-IUSE="cgi fastcgi minimal mysql pdf 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)
-# how about mod_fcgi and dev-libs/fcgi and mod_scgi?
-DEPEND="!!sci-biology/GBrowse
- >=virtual/perl-Module-Build-0.380.0
- >=dev-lang/perl-5.8.8:=
- dev-perl/Capture-Tiny
- >=sci-biology/bioperl-1.6.901
- >=dev-perl/GD-2.07
- dev-perl/IO-String
- virtual/perl-Digest-MD5
- >=dev-perl/CGI-Session-4.03
- dev-perl/Statistics-Descriptive
- >=dev-perl/Bio-Graphics-2.26
- >=dev-perl/JSON-2.510.0
- dev-perl/TermReadKey
- dev-perl/libwww-perl
- svg? ( dev-perl/GD-SVG )
- pdf? ( media-gfx/inkscape )
- 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
-
-RDEPEND="${DEPEND}
- >=www-servers/apache-2.0.47
- fastcgi? ( dev-libs/fcgi )
- www-apache/mod_fastcgi
- dev-perl/DBI
- || ( dev-perl/DBD-Pg dev-perl/DBD-mysql )
- !minimal? (
- dev-perl/File-NFSLock
- dev-perl/FCGI
- virtual/perl-Math-BigInt
- virtual/perl-Math-BigInt-FastCalc
- dev-perl/Math-BigInt-GMP
- dev-perl/Digest-SHA1
- dev-perl/Crypt-SSLeay
- dev-perl/Net-SMTP-SSL
- dev-perl/Net-OpenID-Consumer
- virtual/perl-DB_File
- dev-perl/DB_File-Lock
- dev-perl/GD-SVG
- dev-perl/Text-Shellwords
- dev-perl/XML-Twig
- dev-perl/XML-DOM
- dev-perl/XML-Writer
- dev-perl/XML-Parser
- dev-perl/Bio-Das
- dev-perl/Text-Shellwords
- postgres? ( >=dev-perl/Bio-DB-Das-Chado-0.32 )
- >=dev-perl/Bio-SamTools-1.29
- >=dev-perl/Bio-BigFile-1.06
- )"
-
-src_prepare() {
- sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die "Failed to kill the interactive behavior of install_util/GBrowseInstall.pm"
- sed -i 's/process_/bp_process_/g' INSTALL || die "Failed to prepend bp_ prefix to INSTALL file"
- epatch \
- "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch \
- "${FILESDIR}"/destdir.patch \
- "${FILESDIR}"/fix-PNG-export.patch \
- "${FILESDIR}"/symlink.patch \
- "${FILESDIR}"/gbrowse_metadb_config.pl.patch \
- "${FILESDIR}"/disable-gbrowse_metadb_config.pl.patch
- for f in conf/synteny/wild_rice_synteny.conf conf/synteny/rice_synteny.conf conf/GBrowse.conf \
- htdocs/tutorial/tutorial.html htdocs/index.html lib/Bio/Graphics/Browser2/Action.pm \
- Changes; do
- sed -i 's#/var/lib/gbrowse2#/var/db/gbrowse2#' $f || die "Failed to rewrite /var/lib/gbrowse2 to /var/db/gbrowse2 in $f"
- done
- for f in htdocs/index.html; do
- sed -i 's#/usr/lib/cgi-bin/gb2#/usr/share/webapps/gbrowse/"${PV}"/htdocs/cgi-bin#' $f || die "Failed to rewrite /usr/lib/cgi-bin/gb2 to /usr/share/webapps/gbrowse/"${PV}"/htdocs/cgi-bin in $f"
- done
-}
-
-src_configure() {
- # GBROWSE_ROOT is the root path in SRC_URI to be prepended
- # /usr/share/webapps/gbrowse/2.03/htdocs/etc/gbrowse/GBrowse.conf
- webapp_src_preinst
- perl Makefile.PL \
- HTDOCS="${MY_HTDOCSDIR}" \
- CGIBIN="${MY_HTDOCSDIR}"/cgi-bin \
- CONF="${MY_HTDOCSDIR}"/etc/gbrowse \
- PACKAGE_DIR="${D}" \
- INSTALLDIRS=vendor \
- GBROWSE_ROOT="gbrowse" \
- DESTDIR="${D}" \
- DATABASES="/var/db/gbrowse2/databases" \
- PERSISTENT="/var/db/gbrowse2" \
- TMP="/var/tmp/gbrowse2" \
- INSTALLETC="n" \
- INSTALLCONF="n" \
- WWWUSER="apache" \
- DO_XS=1 \
- NONROOT=1 \
- || die
-}
-
-src_install() {
- mydoc="Changes README TODO INSTALL"
- perl-module_src_install
-
- # TODO: write our own readme
- webapp_postinst_txt en "${S}"/INSTALL
- webapp_src_install || die "Failed running webapp_src_install"
-
- # should create a /etc/init.d/ startup script based on this
- # /var/tmp/portage/sci-biology/gbrowse-2.03/work/GBrowse-2.03/etc/init.d/gbrowse-slave
-
- mkdir -p "${D}"/var/tmp/gbrowse2/images
- chown -R apache.apache "${D}"/var/tmp/gbrowse2
-
- # mkdir -p "${D}"/var/www/localhost/htdocs/gbrowse || die
- # ln -s "${D}"/var/tmp/gbrowse2/images "${D}"/usr/share/webapps/gbrowse/"${PV}"/htdocs/i || die
-
- # whole "${D}"/var/db/gbrowse2 has to be owned by apache.apache otherwise:
- # 1. you hit an error that /var/db/gbrowse2/sessions/cgisess.db.lck
- # [no, it is not enough chown -R apache.apache /var/db/gbrowse2/sessions, the parent dir has to be apapche.apache as well]
- # 2. even if you set /var/db/gbrowse2 to apache.apache still it is not enough, you will get
- # [Tue Jan 17 14:59:40 2012] [error] [client 127.0.0.1] Use of uninitialized value $label in lc at /usr/lib/perl5/vendor_perl/5.12.4/i686-linux-thread-multi/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm line 34., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse/yeast/
-
- mkdir -p "${D}"/var/db/gbrowse2
- mkdir -p "${D}"/var/db/gbrowse2/databases
- mkdir -p "${D}"/var/db/gbrowse2/sessions "${D}"/var/db/gbrowse2/userdata
- chown -R apache.apache "${D}"/var/db/gbrowse2 # it has to be owned by apache.apache otherwise /var/db/gbrowse2/sessions/cgisess.db.lck cannot be created although /var/db/gbrowse2/sessions is owner by apache.apache
-
- einfo "Dropping trailing 'databases' from db_variable in conf/GBrowse.conf"
- sed -i 's#/var/db/gbrowse2/databases#/var/db/gbrowse2#' conf/GBrowse.conf || die "Failed to dropping trailing 'databases' from db_variable in conf/GBrowse.conf"
-
- einfo "Probably you want to install a cron job to remove the generated temporary images:"
- einfo "find /var/tmp/gbrowse2/images -type f -atime +20 -print -exec rm {}"
-
- einfo "Make sure you compiled apache with +cgi and do"
- einfo "cp -i ${FILESDIR}/gbrowse.conf.vhosts.d /etc/apache2/vhosts.d/gbrowse.conf"
-
- sed -i "s#"${D}"##g" "${S}"/install_util/GBrowseInstall.pm || die
- sed -i "s#"${D}"##" "${S}"/blib/conf/GBrowse.conf*
- sed -i 's#DBI:SQLite:'${D}'/var/lib/gbrowse2/databases/#DBI:SQLite:/var/db/gbrowse2/databases/#' "${S}"/install_util/GBrowseInstall.pm || die
-}
-
-pkg_postinst() {
- webapp_pkg_postinst || die "webapp_pkg_postinst failed"
-
- einfo "Please run gbrowse_metadb_config.pl to update SQLite flatfiles of the live database."
- einfo "d='/usr/share/webapps/gbrowse/${PV}/htdocs/etc/gbrowse'; for f in \$d/*.conf.new; do \ "
- einfo " mv -i \$f \$d/\`basename \$f .new\`; done"
-
- einfo "Fix also the other copy of the file:"
- einfo "d='/var/www/localhost/htdocs/gbrowse/etc/gbrowse'; for f in \$d/*.conf.new; do \ "
- einfo " mv -i \$f \$d/\`basename \$f .new\`; done"
-}
-
-src_test() {
- mysql -uroot -p password -e 'create database yeast'
- mysql -uroot -p password -e 'grant all privileges on yeast.* to gbrowse@localhost'
- mysql -uroot -p password -e 'grant file on *.* to gbrowse@localhost'
- mysql -uroot -p password -e 'grant select on yeast.* to nobody@localhost'
-
- cd /usr/portage/distfiles || die
- gzip -d yeast.fasta.gz || die
- gzip -d yeast.gff.gz || die
- #gzip -d fly.fasta.gz
- #gzip -d fly.gff.gz
- bp_bulk_load_gff.pl -d yeast -fasta yeast.fasta yeast.gff || die
-}
diff --git a/sci-biology/gbrowse/gbrowse-2.48.ebuild b/sci-biology/gbrowse/gbrowse-2.48.ebuild
deleted file mode 100644
index aecc9bc31..000000000
--- a/sci-biology/gbrowse/gbrowse-2.48.ebuild
+++ /dev/null
@@ -1,201 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils perl-module webapp
-
-MY_P="GBrowse-${PV}"
-
-DESCRIPTION="Display of genomic annotations on interactive web pages"
-HOMEPAGE="http://gmod.org/"
-# mirror://sourceforge/gmod/${MY_P}.tar.gz
-# mirror://cpan/authors/id/L/LD/LDS/GBrowse-2.33.tar.gz
-SRC_URI="
- mirror://cpan/authors/id/L/LD/LDS/${MY_P}.tar.gz
- test? (
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/saccharomyces_cerevisiae.gff.bz2
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/Refseq_Genome_TBLASTX.tar.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/README-gff-files
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/human.gff.tar.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.fasta.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/yeast.gff.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.fasta.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/worm.gff.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.fasta.gz
- http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/Sample%20Data%20Files/fly.gff.gz )"
-
-LICENSE="Artistic"
-# webapp ebuilds do not set SLOT
-KEYWORDS="~x86 ~amd64"
-IUSE="cgi fastcgi minimal mysql pdf postgres svg test" # lwp moby scf
-
-S="${WORKDIR}/${MY_P}"
-
-# TODO: dev-perl/MOBY, dev-perl/Bio-SCF, dev-perl/Safe-World (not compatible w/perl-5.10)
-# how about mod_fcgi and dev-libs/fcgi and mod_scgi?
-DEPEND="!!sci-biology/GBrowse
- >=virtual/perl-Module-Build-0.380.0
- >=dev-lang/perl-5.8.8:=
- dev-perl/Capture-Tiny
- >=sci-biology/bioperl-1.6.901
- >=dev-perl/GD-2.07
- dev-perl/IO-String
- virtual/perl-Digest-MD5
- >=dev-perl/CGI-Session-4.03
- dev-perl/Statistics-Descriptive
- >=dev-perl/Bio-Graphics-2.26
- >=dev-perl/JSON-2.510.0
- dev-perl/TermReadKey
- dev-perl/libwww-perl
- svg? ( dev-perl/GD-SVG )
- pdf? ( media-gfx/inkscape )
- mysql? ( dev-perl/DBD-mysql )
- postgres? ( dev-perl/DBD-Pg )
- sci-biology/ucsc-genome-browser" # that provides bigWig.h and jkweb.a, aka Jim Kent's src
-
-# TODO: based on the following message in apache/error_log the list of deps should be longer
-# GBROWSE NOTICE: To enable PDF generation, please enter the directory "/home/httpd" and run the commands: "sudo mkdir .inkscape .gnome2" and "sudo chown apache .inkscape .gnome2". To turn off this message add "generate pdf = 0" to the [GENERAL] section of your GBrowse.conf configuration file., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse_details/yeast?ref=chrII;start=90739;end=92028;name=YBL069W;class=Sequence;feature_id=881;db_id=annotations%3Adatabase
-
-RDEPEND="${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 )
- !minimal? (
- dev-perl/File-NFSLock
- dev-perl/FCGI
- virtual/perl-Math-BigInt
- virtual/perl-Math-BigInt-FastCalc
- dev-perl/Math-BigInt-GMP
- dev-perl/Digest-SHA1
- dev-perl/Crypt-SSLeay
- dev-perl/Net-SMTP-SSL
- dev-perl/Net-OpenID-Consumer
- virtual/perl-DB_File
- dev-perl/DB_File-Lock
- dev-perl/GD-SVG
- dev-perl/Text-Shellwords
- dev-perl/XML-Twig
- dev-perl/XML-DOM
- dev-perl/XML-Writer
- 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
- <=sci-biology/primer3-2
- )"
-
-src_prepare() {
- sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die "Failed to kill the interactive behavior of install_util/GBrowseInstall.pm"
- sed -i 's/process_/bp_process_/g' INSTALL || die "Failed to prepend bp_ prefix to INSTALL file"
- epatch \
- "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch \
- "${FILESDIR}"/destdir.patch \
- "${FILESDIR}"/fix-PNG-export.patch \
- "${FILESDIR}"/symlink.patch \
- "${FILESDIR}"/gbrowse_metadb_config.pl.patch \
- "${FILESDIR}"/disable-gbrowse_metadb_config.pl.patch
- for f in conf/synteny/wild_rice_synteny.conf conf/synteny/rice_synteny.conf conf/GBrowse.conf \
- htdocs/tutorial/tutorial.html htdocs/index.html lib/Bio/Graphics/Browser2/Action.pm \
- Changes; do
- sed -i 's#/var/lib/gbrowse2#/var/db/gbrowse2#' $f || die "Failed to rewrite /var/lib/gbrowse2 to /var/db/gbrowse2 in $f"
- done
- for f in htdocs/index.html; do
- sed -i 's#/usr/lib/cgi-bin/gb2#/usr/share/webapps/gbrowse/"${PV}"/htdocs/cgi-bin#' $f || die "Failed to rewrite /usr/lib/cgi-bin/gb2 to /usr/share/webapps/gbrowse/"${PV}"/htdocs/cgi-bin in $f"
- done
-}
-
-src_configure() {
- # GBROWSE_ROOT is the root path in SRC_URI to be prepended
- # /usr/share/webapps/gbrowse/2.03/htdocs/etc/gbrowse/GBrowse.conf
- webapp_src_preinst
- perl Makefile.PL \
- HTDOCS="${MY_HTDOCSDIR}" \
- CGIBIN="${MY_HTDOCSDIR}"/cgi-bin \
- CONF="${MY_HTDOCSDIR}"/etc/gbrowse \
- PACKAGE_DIR="${D}" \
- INSTALLDIRS=vendor \
- GBROWSE_ROOT="gbrowse" \
- DESTDIR="${D}" \
- DATABASES="/var/db/gbrowse2/databases" \
- PERSISTENT="/var/db/gbrowse2" \
- TMP="/var/tmp/gbrowse2" \
- INSTALLETC="n" \
- INSTALLCONF="n" \
- WWWUSER="apache" \
- DO_XS=1 \
- NONROOT=1 \
- || die
-}
-
-src_install() {
- mydoc="Changes README TODO INSTALL"
- perl-module_src_install
-
- # TODO: write our own readme
- webapp_postinst_txt en "${S}"/INSTALL
- webapp_src_install || die "Failed running webapp_src_install"
-
- # should create a /etc/init.d/ startup script based on this
- # /var/tmp/portage/sci-biology/gbrowse-2.03/work/GBrowse-2.03/etc/init.d/gbrowse-slave
-
- mkdir -p "${D}"/var/tmp/gbrowse2/images
- chown -R apache.apache "${D}"/var/tmp/gbrowse2
-
- # mkdir -p "${D}"/var/www/localhost/htdocs/gbrowse || die
- # ln -s "${D}"/var/tmp/gbrowse2/images "${D}"/usr/share/webapps/gbrowse/"${PV}"/htdocs/i || die
-
- # whole "${D}"/var/db/gbrowse2 has to be owned by apache.apache otherwise:
- # 1. you hit an error that /var/db/gbrowse2/sessions/cgisess.db.lck
- # [no, it is not enough chown -R apache.apache /var/db/gbrowse2/sessions, the parent dir has to be apapche.apache as well]
- # 2. even if you set /var/db/gbrowse2 to apache.apache still it is not enough, you will get
- # [Tue Jan 17 14:59:40 2012] [error] [client 127.0.0.1] Use of uninitialized value $label in lc at /usr/lib/perl5/vendor_perl/5.12.4/i686-linux-thread-multi/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm line 34., referer: http://127.0.0.1/gbrowse/cgi-bin/gbrowse/yeast/
-
- mkdir -p "${D}"/var/db/gbrowse2
- mkdir -p "${D}"/var/db/gbrowse2/databases
- mkdir -p "${D}"/var/db/gbrowse2/sessions "${D}"/var/db/gbrowse2/userdata
- chown -R apache.apache "${D}"/var/db/gbrowse2 # it has to be owned by apache.apache otherwise /var/db/gbrowse2/sessions/cgisess.db.lck cannot be created although /var/db/gbrowse2/sessions is owner by apache.apache
-
- einfo "Dropping trailing 'databases' from db_variable in conf/GBrowse.conf"
- sed -i 's#/var/db/gbrowse2/databases#/var/db/gbrowse2#' conf/GBrowse.conf || die "Failed to dropping trailing 'databases' from db_variable in conf/GBrowse.conf"
-
- einfo "Probably you want to install a cron job to remove the generated temporary images:"
- einfo "find /var/tmp/gbrowse2/images -type f -atime +20 -print -exec rm {}"
-
- einfo "Make sure you compiled apache with +cgi and do"
- einfo "cp -i ${FILESDIR}/gbrowse.conf.vhosts.d /etc/apache2/vhosts.d/gbrowse.conf"
-
- sed -i "s#"${D}"##g" "${S}"/install_util/GBrowseInstall.pm || die
- sed -i "s#"${D}"##" "${S}"/blib/conf/GBrowse.conf*
- sed -i 's#DBI:SQLite:'${D}'/var/lib/gbrowse2/databases/#DBI:SQLite:/var/db/gbrowse2/databases/#' "${S}"/install_util/GBrowseInstall.pm || die
-}
-
-pkg_postinst() {
- webapp_pkg_postinst || die "webapp_pkg_postinst failed"
-
- einfo "Please run gbrowse_metadb_config.pl to update SQLite flatfiles of the live database."
- einfo "d='/usr/share/webapps/gbrowse/${PV}/htdocs/etc/gbrowse'; for f in \$d/*.conf.new; do \ "
- einfo " mv -i \$f \$d/\`basename \$f .new\`; done"
-
- einfo "Fix also the other copy of the file:"
- einfo "d='/var/www/localhost/htdocs/gbrowse/etc/gbrowse'; for f in \$d/*.conf.new; do \ "
- einfo " mv -i \$f \$d/\`basename \$f .new\`; done"
-}
-
-src_test() {
- mysql -uroot -p password -e 'create database yeast'
- mysql -uroot -p password -e 'grant all privileges on yeast.* to gbrowse@localhost'
- mysql -uroot -p password -e 'grant file on *.* to gbrowse@localhost'
- mysql -uroot -p password -e 'grant select on yeast.* to nobody@localhost'
-
- cd /usr/portage/distfiles || die
- gzip -d yeast.fasta.gz || die
- gzip -d yeast.gff.gz || die
- #gzip -d fly.fasta.gz
- #gzip -d fly.gff.gz
- bp_bulk_load_gff.pl -d yeast -fasta yeast.fasta yeast.gff || die
-}
diff --git a/sci-biology/gbrowse/metadata.xml b/sci-biology/gbrowse/metadata.xml
deleted file mode 100644
index d0116db4a..000000000
--- a/sci-biology/gbrowse/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <longdescription lang="en">
- GBrowse is a generic genome browser written in perl, could run as CGI,
- under mod_perl. Something called Apache::Registry should make it faster.
- It uses mysql or postgres as the storage engine.
- </longdescription>
- <upstream>
- <remote-id type="sourceforge">gmod</remote-id>
- </upstream>
-</pkgmetadata>