Permalink
Browse files

fix conflict

  • Loading branch information...
2 parents d27e23e + 9326ff1 commit 235a60ba8c44b005b7b6d87e03cad8bb42d829d3 @lstein lstein committed Jan 28, 2013
View
@@ -99,7 +99,7 @@ conf/pop_demo.conf
conf/renderfarm.conf
conf/slave_preload.conf
conf/submitter_plugin.conf
-conf/synteny/oryza.synconf.disabled
+conf/synteny/oryza.synconf.disabled.conf
conf/synteny/rice_synteny.conf
conf/synteny/wild_rice_synteny.conf
conf/themes/solid_gray_colors
View
@@ -234,7 +234,7 @@ sub render_image {
my $url = $renderer->source->generate_image($img_data);
my $js = $render->data_source->globals->js_url;
my @scripts = map { {src=>"$js/$_"} }
- qw(balloon.js balloon.config.js yahoo-dom-event.js);
+ qw(balloon.js balloon.config.js prototype.js GBox.js);
print $self->header(-type=>'text/html');
print start_html(-script=>\@scripts),
$render->render_balloon_settings,
@@ -563,13 +563,13 @@ sub usage {
<pre>
- &lt;img src="http://www.wormbase.org/db/gb2/gbrowse_img/c_elegans?name=mec-3;width=400"&gt;
+ &lt;img src="http://www.wormbase.org/tools/genome/gbrowse_img/c_elegans?name=mec-3;width=400"&gt;
<blockquote>
<i>Will generate this picture:</i>
- <img src="http://www.wormbase.org/db/gb2/gbrowse_img/c_elegans?name=mec-3;width=400">
+ <img src="http://www.wormbase.org/tools/genome/gbrowse_img/c_elegans?name=mec-3;width=400">
</blockquote>
- &lt;a href="http://www.wormbase.org/db/gb2/gbrowse_img?list=sources"&gt;list&lt;/a&gt;
+ &lt;a href="http://www.wormbase.org/tools/genome/gbrowse_img?list=sources"&gt;list&lt;/a&gt;
<blockquote>
<i>Will return this document:</i>
## Sources
@@ -591,7 +591,7 @@ sub usage {
yeast
</blockquote>
- &lt;a href="http://www.wormbase.org/db/gb2/gbrowse_img/c_elegans?list=types"&gt;types&lt;/a&gt;
+ &lt;a href="http://www.wormbase.org/tools/genome/gbrowse_img/c_elegans?list=types"&gt;types&lt;/a&gt;
<blockquote>
<i>Will return this document:</i>
## Feature types for source c_elegans
@@ -619,7 +619,7 @@ can be used as the destination of an &lt;img&gt; tag like this:
</p>
<blockquote><pre>
-&lt;img src="http://www.wormbase.org/db/gb2/gbrowse_img/c_elegans?name=III:1..1000"&gt;
+&lt;img src="http://www.wormbase.org/tools/genome/gbrowse_img/c_elegans?name=III:1..1000"&gt;
</pre></blockquote>
<p>
@@ -699,7 +699,7 @@ lengths.
a list of track names separated by spaces ("+" characters when URL-escaped). For example:
<p>
<pre>
- &lt;img src="http://www.wormbase.org/db/gb2/gbrowse_img/c_elegans?name=mec-3;
+ &lt;img src="http://www.wormbase.org/tools/genome/gbrowse_img/c_elegans?name=mec-3;
type=tRNA+NG+WABA+CG+ESTB"&gt;
</pre>
Multiple <i>type=</i> arguments will be combined to form a single space-delimited list.
@@ -759,7 +759,7 @@ lengths.
<dt><b>style</b>
<dd>The style argument can be used to control the rendering of additional features added
with "add". It is a flattened version of the style configuration sections described
- in <a href="http://www.wormbase.org/db/gb2/gbrowse?help=annotation">this document</a>
+ in <a href="http://www.wormbase.org/tools/genome/gbrowse?help=annotation">this document</a>
For example, if you have added a "Blast Hit" annotation, then you can tell the
renderer to use a red arrow for this glyph in this way:
style=%22Blast%20Hit%22+glyph=arrow+fgcolor=red
@@ -832,7 +832,7 @@ lengths.
</dl>
<p>
Putting it all together, here's a working (very long) URL:
-<pre><a href="http://www.wormbase.org/db/gb2/gbrowse_img/c_elegans?name=B0001;add=B0001+pcr+pcr1+20000..333000;add=B0001+%22cool%20knockout%22+kn2+30000..20000,10000..5000;type=add+CG+WTP;style=pcr+glyph=primers;style=%22cool%20knockout%22+glyph=transcript2+bgcolor=orange;abs=1">http://www.wormbase.org/db/gb2/gbrowse_img/c_elegans?name=B0001;add=B0001+pcr+pcr1+20000..333000;add=B0001+%22cool%20knockout%22+kn2+30000..20000,10000..5000;type=add+CG+WTP;style=pcr+glyph=primers;style=%22cool%20knockout%22+glyph=transcript2+bgcolor=orange;abs=1</a>
+<pre><a href="http://www.wormbase.org/tools/genome/gbrowse_img/c_elegans?name=B0001;add=B0001+pcr+pcr1+20000..333000;add=B0001+%22cool%20knockout%22+kn2+30000..20000,10000..5000;type=add+CG+WTP;style=pcr+glyph=primers;style=%22cool%20knockout%22+glyph=transcript2+bgcolor=orange;abs=1">http://www.wormbase.org/tools/genome/gbrowse_img/c_elegans?name=B0001;add=B0001+pcr+pcr1+20000..333000;add=B0001+%22cool%20knockout%22+kn2+30000..20000,10000..5000;type=add+CG+WTP;style=pcr+glyph=primers;style=%22cool%20knockout%22+glyph=transcript2+bgcolor=orange;abs=1</a>
</pre>
<p>
View
@@ -3,18 +3,6 @@
eval 'exec /usr/bin/perl -w -S $0 ${1+"$@"}'
if 0; # not running under some shell
-eval 'exec /usr/bin/perl -w -S $0 ${1+"$@"}'
- if 0; # not running under some shell
-
-eval 'exec /usr/bin/perl -w -S $0 ${1+"$@"}'
- if 0; # not running under some shell
-
-eval 'exec /usr/bin/perl -w -S $0 ${1+"$@"}'
- if 0; # not running under some shell
-
-eval 'exec /usr/bin/perl -w -S $0 ${1+"$@"}'
- if 0; # not running under some shell
-
our $CONF_DIR = "$ENV{GBROWSE_CONF}/synteny";
our $VERSION = '$Id: gbrowse_details,v 1.7 2009-08-27 19:13:18 idavies Exp $';
our $BIOGRAPHICS_VERSION = 1.8;
@@ -91,7 +79,7 @@ unless ($go) {
print p('Please consult '.a({-href=>'http://gmod.org/wiki/GBrowse_syn'},'the documentation'));
print <<END;
-<iframe style="frameborder:0;width:800px;height:2000px" src="/gbrowse2/gbrowse_syn_help.html">
+<iframe style="frameborder:0;width:1280px;height:2000px" src="/gbrowse2/gbrowse_syn_help.html">
</iframe>
END
;
@@ -15,15 +15,15 @@ join = dbi:mysql:database=rice_synteny;host=localhost
source_map = rice rice_synteny "Domesic Rice (O. sativa)"
wild_rice wild_rice_synteny "Wild Rice"
-tmpimages = /tmp/gbrowse2
+tmpimages = $TMP
imagewidth = 800
stylesheet = /gbrowse2/css/gbrowse_transparent.css
cache time = 1
config_extension = conf
# example searches to display
-examples = rice 3:200000..280000
+examples = rice 3:16050173..16064974
wild_rice 3:1..400000
zoom levels = 5000 10000 25000 50000 100000 200000 400000
@@ -14,9 +14,9 @@
for two rice species and blastz-derived whole genome aligment data between
the two species.
<ul>
-<li>/var/lib/gbrowse2/databases/gbrowse_syn/rice/rice.gff3
-<li>/var/lib/gbrowse2/databases/gbrowse_syn/wild_rice/wild_rice.gff3
-<li>/var/lib/gbrowse2/databases/gbrowse_syn/alignments/rice.aln
+<li>$DATABASES/gbrowse_syn/rice/rice.gff3
+<li>$DATABASES/gbrowse_syn/wild_rice/wild_rice.gff3
+<li>$DATABASES/gbrowse_syn/alignments/rice.aln
</ul>
@@ -27,9 +27,9 @@
species. They are already set up to use the in-memory adapter and the GFF3 flat files listed
above.
<ul>
-<li>/etc/gbrowse2/synteny/oryza.synconf.disabled</li>
-<li>/etc/gbrowse2/synteny/rice_synteny.conf</li>
-<li>/etc/gbrowse2/synteny/wild_rice_synteny.conf</li>
+<li>$CONF/synteny/oryza.synconf.disabled</li>
+<li>$CONF/synteny/rice_synteny.conf</li>
+<li>$CONF/synteny/wild_rice_synteny.conf</li>
</ul>
<h2>Activate the Example Data Source</h2>
@@ -42,128 +42,89 @@
mysql> create database rice_synteny;
Query OK, 1 row affected (0.00 sec)
-mysql> grant SELECT on rice_synteny.* to 'www-data'@'localhost';
+mysql> grant SELECT on *.* to 'www-data'@'localhost';
Query OK, 0 rows affected (0.02 sec)
mysql> quit
Bye
</pre>
-<p>
2: populate the database using the <a href="http://gmod.org/wiki/GBrowse_syn_Scripts#load_alignments_msa.pl">
gbrowse_syn_load_alignments_msa.pl script</a> (pre-installed with GBrowse). This will load the
CLUSTALW-formated alignment file above into the database.
<pre>
-<<<<<<< HEAD
-$ cd /var/www/gbrowse2/databases/gbrowse_syn/alignments
-$ sudo gunzip rice.aln.gz
-$ gbrowse_syn_load_alignments_msa.pl -u user -p pass -d rice_synteny -c -v rice.aln
-=======
-$ cd /var/lib/gbrowse2/databases/gbrowse_syn/alignments
-$ gunzip -c rice.aln.gz | gbrowse_syn_load_alignments_msa.pl -u user -p pass -d rice_synteny -c -v -
->>>>>>> master
+$ zcat DATABASES/gbrowse_syn/alignments/rice.aln.gz | gbrowse_syn_load_alignments_msa.pl -u user -p pass -d rice_synteny -v -c -
</pre>
-<i>Where 'user' and 'pass' correspond to a mysql account with root-level privileges</i>
-<p>
-3: activate the oryza gbrwose_syn configuration file by renaming it (root-level acess may be required).
+3: activate the oryza gbrwose_syn configuration file by renaming it (root-level acess required).
<pre>
-<<<<<<< HEAD
# as a sudoer
-$ sudo mv /etc/gbrowse2/synteny/oryza.synconf.disabled /etc/gbrowse2/synteny/oryza.synconf
+$ sudo mv $CONF/synteny/oryza.synconf.disabled $CONF/synteny/oryza.synconf
# or as root
-% mv /etc/gbrowse2/synteny/oryza.synconf.disabled /etc/gbrowse2/synteny/oryza.synconf
-=======
-$ mv /etc/gbrowse2/synteny/oryza.synconf.disabled /etc/gbrowse2/synteny/oryza.synconf
->>>>>>> master
+% mv $CONF/synteny/oryza.synconf.disabled $CONF/synteny/oryza.synconf
</pre>
-<p>
-Now reload this page and view the result!
<h1> Advanced (optional) </h1>
You can speed up the image loading time by putting your species' GFF3 data into relational MySQL databases.
-1: create a database for each of the GFF<p>
- data files (rice.gff3 and wild_rice.gff3).
+1: create a database for each of the GFF data files (rice.gff3 and wild_rice.gff3).
<pre>
# create a mysql database for the rice data
-$ mysql -uuser -ppass
+$ mysql -uuser -ppass
mysql> create database rice;
Query OK, 1 row affected (0.00 sec)
-mysql> grant SELECT on rice.* to 'www-data'@'localhost';
-Query OK, 0 rows affected (0.00 sec)
-
mysql> create database wild_rice;
Query OK, 1 row affected (0.00 sec)
-mysql> grant SELECT on wild_rice.* to 'www-data'@'localhost';
-Query OK, 0 rows affected (0.00 sec)
</pre>
-2: populate the database using the <a
+2: populate the database using the <a
href="http://code.open-bio.org/svnweb/index.cgi/bioperl/view/bioperl-live/trunk/scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS">
bp_seqfeature_load.pl</a> (pre-installed as part of BioPerl with GBrowse). This will load the
-<<<<<<< HEAD
GFF3 data into a mySQL relational database.
<b>Note the mySQL user will need CREATE and INSERT privileges.</b>
<pre>
-$ bp_seqfeature_load.pl -u user -p pass -d rice -c -f /var/www/gbrowse2/$GBROWSE_ROOT/databases/gbrowse_syn/rice/rice.gff3
+$ bp_seqfeature_load.pl -u user -p pass -d rice -c -f /var/www/html/gbrowse/databases/gbrowse_syn/rice/rice.gff3
loading /var/www/html/gbrowse/databases/gbrowse_syn/rice/rice.gff3...
-Building object tree... 1.05s7s
+Building object tree... 1.05s7s
Loading bulk data into database... 0.67s
load time: 31.40s
-$ bp_seqfeature_load.pl -u user -p pass -d wild_rice -c -f /var/www/gbrowse2/$GBROWSE_ROOT/databases/gbrowse_syn/wild_rice/wild_rice.gff3
+$ bp_seqfeature_load.pl -u user -p pass -d wild_rice -c -f /var/www/html/gbrowse/databases/gbrowse_syn/wild_rice/wild_rice.gff3
loading /var/www/html/gbrowse/databases/gbrowse_syn/wild_rice/wild_rice.gff3...
-Building object tree... 1.15s9s
+Building object tree... 1.15s9s
Loading bulk data into database... 0.69s
load time: 31.93s
</pre>
-3: Modify the following stanza in each configurations file (rice_syntency.conf and wild_rice_synteny),
+3: Modify the following stanza in each configurations file (rice_syntency.conf and wild_rice_synteny),
changing the dsn argumant as required for each data source.
-=======
- GFF3 data into a MySQL relational database.
->>>>>>> master
-<b>Note the MySQL user will need CREATE and INSERT privileges.</b>
+You will need to set the permissions so you can edit the files
<pre>
-<<<<<<< HEAD
-
+$ sudo chmod 644 $CONF/synteny/*
+</pre>
-<b>Note the mySQL user will need CREATE and INSERT privileges.</b>
+Change:
<pre>
-$ bp_seqfeature_load.pl -u user -p pass -d rice -c -f /var/www/gbrowse2/$GBROWSE_ROOT/databases/gbrowse_syn/rice/rice.gff3
-=======
-$ bp_seqfeature_load.pl -u user -p pass -d rice -c -f /var/lib/gbrowse2/databases/gbrowse_syn/rice/rice.gff3
->>>>>>> master
-loading /var/www/html/gbrowse/databases/gbrowse_syn/rice/rice.gff3...
-Building object tree... 1.05s7s
-Loading bulk data into database... 0.67s
-load time: 31.40s
+# from
+db_adaptor = Bio::DB::SeqFeature::Store
+db_args = -adaptor memory
+ -dir $DATABASES/gbrowse_syn/rice
-<<<<<<< HEAD
-$ bp_seqfeature_load.pl -u user -p pass -d wild_rice -c -f /var/www/gbrowse2/$GBROWSE_ROOT/databases/gbrowse_syn/wild_rice/wild_rice.gff3
-=======
-$ bp_seqfeature_load.pl -u user -p pass -d wild_rice -c -f /var/lib/gbrowse2/databases/gbrowse_syn/wild_rice/wild_rice.gff3
->>>>>>> master
-loading /var/www/html/gbrowse/databases/gbrowse_syn/wild_rice/wild_rice.gff3...
-Building object tree... 1.15s9s
-Loading bulk data into database... 0.69s
-load time: 31.93s
+# to
+db_adaptor = Bio::DB::SeqFeature::Store
+db_args = -adaptor DBI::mysql
+ -dsn dbi:mysql:rice
+ -user www-data
</pre>
-
-3: Modify the following stanza in each configurations file (rice_syntency.conf and wild_rice_synteny),
-changing the dsn argumant as required for each data source.
-
-<pre>

0 comments on commit 235a60b

Please sign in to comment.