Configuring gbrowse-syn

cnr-ibba · Nov 14, 2017 · 3fd7d11 · 3fd7d11
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diff --git a/compose/gbrowse/README.md b/compose/gbrowse/README.md
@@ -118,3 +118,38 @@ $ chown -R www-data.www-data volvox
 ```
 
 [gbrowse-admin-tutorial]: http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html
+
+Configuring gbrowse_syn
+-----------------------
+
+### Create a MySQL database
+
+Connect to a MySQL instance and create `rice_synteny` database:
+
+```
+$ docker-compose run --no-deps --rm db mysql -h db -u root --password=my-secret-pw
+mysql> CREATE USER gbrowsero IDENTIFIED BY 'gbrowseropass' ;
+mysql> CREATE DATABASE rice_synteny ;
+mysql> GRANT SELECT ON rice_synteny.* TO gbrowsero@'%';
+mysql> exit
+```
+
+### Load alignment into database
+
+Launch a gbrowse container:
+
+```
+$ docker-compose run --no-deps --rm gbrowse /bin/bash
+$ cd /var/lib/gbrowse2/databases/gbrowse_syn/alignments
+$ gzip -d rice.aln.gz
+$ zcat rice.aln.gz perl | /usr/local/bin/gbrowse_syn_load_alignments_msa.pl -u root -p my-secret-pw --dsn='dbi:mysql:database=rice_synteny;host=db' -f clustalw -v -c -
+```
+
+Then reach `gbrowse_syn` from this [link][local-gbrowse_syn]. More information on
+`gbrowse_syn` could be found [here][gbrowse_syn] and [here][gbrowse_syn_help]. More information on loading alignments
+and `gbrowse_syn` scripts in general could be found [here][gbrowse_syn-script]
+
+[local-gbrowse_syn]: http://localhost:10080/gb2/gbrowse_syn/
+[gbrowse_syn]: http://gmod.org/wiki/GBrowse_syn
+[gbrowse_syn_help]: http://gmod.org/wiki/GBrowse_syn_Help
+[gbrowse_syn-script]: http://gmod.org/wiki/GBrowse_syn_Script
diff --git a/compose/gbrowse/gbrowse/conf.d/GBrowse.conf b/compose/gbrowse/gbrowse/conf.d/GBrowse.conf
@@ -4,7 +4,7 @@
 
 [GENERAL]
 config_base            = /etc/gbrowse2 # overridden by environment variable GBROWSE_CONF
-htdocs_base            = /usr/local/apache2/htdocs/gbrowse2
+htdocs_base            = /var/www/html/gbrowse2
 url_base               = /gbrowse2
 tmp_base               = /var/tmp/gbrowse2
 persistent_base        = /var/lib/gbrowse2

diff --git a/...onf.d/synteny/oryza.synconf.disabled.conf → ...owse/gbrowse/conf.d/synteny/oryza.synconf b/...onf.d/synteny/oryza.synconf.disabled.conf → ...owse/gbrowse/conf.d/synteny/oryza.synconf
@@ -2,7 +2,7 @@
 description =  BLASTZ alignments for Oryza sativa
 
 # The synteny database
-join        = dbi:mysql:database=rice_synteny;host=localhost;user='www-data'
+join        = dbi:mysql:database=rice_synteny;host=db;user=gbrowsero;password=gbrowseropass
 
 # This option maps the relationship between the species data sources, names and descriptions
 # The value for "name" (the first column) is the symbolic name that gbrowse_syn users to identify each species.
@@ -15,7 +15,7 @@ join        = dbi:mysql:database=rice_synteny;host=localhost;user='www-data'
 source_map =      rice          rice_synteny          "Domesic Rice (O. sativa)"
                   wild_rice     wild_rice_synteny     "Wild Rice"
 
-tmpimages     = /var/tmp/gbrowse2
+tmpimages     = tmp
 imagewidth    = 800
 stylesheet    = /gbrowse2/css/gbrowse_transparent.css
 cache time    = 1

diff --git a/compose/gbrowse/gbrowse/conf.d/synteny/rice_synteny.conf b/compose/gbrowse/gbrowse/conf.d/synteny/rice_synteny.conf
@@ -6,7 +6,7 @@ db_args       = -adaptor memory
 
 
 # Web site configuration info
-tmpimages   = /var/tmp/gbrowse2
+tmpimages   = tmp
 
 [EG]
 feature      = gene:ensembl

diff --git a/compose/gbrowse/gbrowse/conf.d/synteny/wild_rice_synteny.conf b/compose/gbrowse/gbrowse/conf.d/synteny/wild_rice_synteny.conf
@@ -6,7 +6,7 @@ db_args       = -adaptor memory
 
 
 # Web site configuration info
-tmpimages   = /var/tmp/gbrowse2
+tmpimages   = tmp
 
 ################## TRACK CONFIGURATION ####################
 # the remainder of the sections configure individual tracks