1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/931382e567f5/ changeset: 931382e567f5 user: dan date: 2012-08-22 18:35:23 summary: Refactor GBrowse external display application. Update WormBase with latest builds and to be able to use reference sites. affected #: 6 files

diff -r 7eeee803345e111b9485cc9b9c2b397a6623fa5f -r 931382e567f501ff8529cdd3c7b45c2d08d0ab23 display_applications/gbrowse/gbrowse_gff.xml --- a/display_applications/gbrowse/gbrowse_gff.xml +++ b/display_applications/gbrowse/gbrowse_gff.xml @@ -1,16 +1,24 @@ <display id="gbrowse_gff" version="1.0.0" name="display at GBrowse"><!-- Load links from file: one line to one link --> - <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1"> + <!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/> - <dynamic_param name="gbrowse_link" value="1"/> - <dynamic_param name="builds" value="2" split="True" separator="," /> + <dynamic_param name="site_name" value="1"/> + <dynamic_param name="site_link" value="2"/> + <dynamic_param name="site_dbkeys" value="3" split="True" separator="," /> + <dynamic_param name="site_organisms" value="4" split="True" separator="," /> + <!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey --><filter>${site_id in $APP.config.gbrowse_display_sites}</filter> - <filter>${dataset.dbkey in $builds}</filter> + <filter>${dataset.dbkey in $site_dbkeys}</filter> + <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --> - <url>${gbrowse_link}/?${position}eurl=${gff_file.qp}</url> + <url>${site_link}${site_organism}/?${position}eurl=${gff_file.qp}</url><param type="data" name="gff_file" url="galaxy_${DATASET_HASH}.gff" /> + <param type="template" name="site_organism" strip="True" > + $site_organisms[ $site_dbkeys.index( $gff_file.dbkey ) ] + </param><param type="template" name="position" strip="True" > #set chrom, start, end = $gff_file.datatype.get_estimated_display_viewport( $gff_file ) #if $chrom is not None:

diff -r 7eeee803345e111b9485cc9b9c2b397a6623fa5f -r 931382e567f501ff8529cdd3c7b45c2d08d0ab23 display_applications/gbrowse/gbrowse_interval_as_bed.xml --- a/display_applications/gbrowse/gbrowse_interval_as_bed.xml +++ b/display_applications/gbrowse/gbrowse_interval_as_bed.xml @@ -1,16 +1,24 @@ <display id="gbrowse_interval_as_bed" version="1.0.0" name="display at GBrowse"><!-- Load links from file: one line to one link --> - <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1"> + <!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/> - <dynamic_param name="gbrowse_link" value="1"/> - <dynamic_param name="builds" value="2" split="True" separator="," /> + <dynamic_param name="site_name" value="1"/> + <dynamic_param name="site_link" value="2"/> + <dynamic_param name="site_dbkeys" value="3" split="True" separator="," /> + <dynamic_param name="site_organisms" value="4" split="True" separator="," /> + <!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey --><filter>${site_id in $APP.config.gbrowse_display_sites}</filter> - <filter>${dataset.dbkey in $builds}</filter> + <filter>${dataset.dbkey in $site_dbkeys}</filter> + <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --> - <url>${gbrowse_link}/?${position}eurl=${bed_file.qp}</url> + <url>${site_link}${site_organism}/?${position}eurl=${bed_file.qp}</url><param type="data" name="bed_file" url="galaxy_${DATASET_HASH}.bed" format="bedstrict"/><!-- Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, gbrowse does not(?): force use of converter which will make strict BED6+ file --> + <param type="template" name="site_organism" strip="True" > + $site_organisms[ $site_dbkeys.index( $bed_file.dbkey ) ] + </param><param type="template" name="position" strip="True" > #set chrom, start, end = $bed_file.datatype.get_estimated_display_viewport( $bed_file ) #if $chrom is not None:

diff -r 7eeee803345e111b9485cc9b9c2b397a6623fa5f -r 931382e567f501ff8529cdd3c7b45c2d08d0ab23 display_applications/gbrowse/gbrowse_wig.xml --- a/display_applications/gbrowse/gbrowse_wig.xml +++ b/display_applications/gbrowse/gbrowse_wig.xml @@ -1,16 +1,24 @@ <display id="gbrowse_wig" version="1.0.0" name="display at GBrowse"><!-- Load links from file: one line to one link --> - <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="0"> + <dynamic_links from_file="tool-data/shared/gbrowse/gbrowse_build_sites.txt" skip_startswith="#" id="0" name="1"> + <!-- Define parameters by column from file, allow splitting on builds --><dynamic_param name="site_id" value="0"/> - <dynamic_param name="gbrowse_link" value="1"/> - <dynamic_param name="builds" value="2" split="True" separator="," /> + <dynamic_param name="site_name" value="1"/> + <dynamic_param name="site_link" value="2"/> + <dynamic_param name="site_dbkeys" value="3" split="True" separator="," /> + <dynamic_param name="site_organisms" value="4" split="True" separator="," /> + <!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey --><filter>${site_id in $APP.config.gbrowse_display_sites}</filter> - <filter>${dataset.dbkey in $builds}</filter> + <filter>${dataset.dbkey in $site_dbkeys}</filter> + <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --> - <url>${gbrowse_link}/?${position}eurl=${wig_file.qp}</url> + <url>${site_link}${site_organism}/?${position}eurl=${wig_file.qp}</url><param type="data" name="wig_file" url="galaxy_${DATASET_HASH}.wig" format="wig"/> + <param type="template" name="site_organism" strip="True" > + $site_organisms[ $site_dbkeys.index( $wig_file.dbkey ) ] + </param><param type="template" name="position" strip="True" > #set chrom, start, end = $wig_file.datatype.get_estimated_display_viewport( $wig_file ) #if $chrom is not None:

diff -r 7eeee803345e111b9485cc9b9c2b397a6623fa5f -r 931382e567f501ff8529cdd3c7b45c2d08d0ab23 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -132,7 +132,7 @@ self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) ) self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) ) self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") - self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "wormbase,tair,modencode_worm,modencode_fly,sgd_yeast" ).lower().split(",") + self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225" ).lower().split(",") self.genetrack_display_sites = kwargs.get( 'genetrack_display_sites', "main,test" ).lower().split(",") self.brand = kwargs.get( 'brand', None ) self.support_url = kwargs.get( 'support_url', 'http://wiki.g2.bx.psu.edu/Support' )

diff -r 7eeee803345e111b9485cc9b9c2b397a6623fa5f -r 931382e567f501ff8529cdd3c7b45c2d08d0ab23 tool-data/shared/gbrowse/gbrowse_build_sites.txt --- a/tool-data/shared/gbrowse/gbrowse_build_sites.txt +++ b/tool-data/shared/gbrowse/gbrowse_build_sites.txt @@ -1,14 +1,24 @@ -# wormbase sites / supported genomes -wormbase http://www.wormbase.org/db/gb2/gbrowse/c_elegans ce8,ce7,ce6,ce5,ce4,ce3,ce2,cb3,cb2,cb1,caeRem3,caeRem2,caeRem1,caePb2,caePb1,caeJap2,caeJap1 -#test http://dev.wormbase.org/db/seq/gbrowse/c_elegans/ ce8,ce7,ce6,ce5,ce4,ce3,ce2,cb3,cb2,cb1,caeRem3,caeRem2,caeRem1,caePb2,caePb1,caeJap2,caeJap1 +#GBrowse Sites +#site_id site_name site_link site_dbkeys site_organisms

-# UCSC mirror that includes arabidopsis -tair http://arabidopsis.org/cgi-bin/gbrowse/ arabidopsis_tair8,arabidopsis +#WormBase +wormbase WormBase current http://www.wormbase.org/db/gb2/gbrowse/ ce10,ce9,ce8,ce7,ce6,ce5,ce4,ce3,ce2,cb4,cb3,cb2,cb1,caeRem4,caeRem3,caeRem2,caeRem1,caePb2,caePb1,caeJap4,caeJap3,caeJap2,caeJap1,caeAng1 c_elegans,c_elegans,c_elegans,c_elegans,c_elegans,c_elegans,c_elegans,c_elegans,c_elegans,c_briggsae,c_briggsae,c_briggsae,c_briggsae,c_remanei,c_remanei,c_remanei,c_remanei,c_brenneri,c_brenneri,c_japonica,c_japonica,c_japonica,c_japonica,c_angaria +wormbase_ws120 WormBase WS120 http://ws120.wormbase.org/db/seq/gbrowse/ ce2 wormbase +wormbase_ws140 WormBase WS140 http://ws140.wormbase.org/db/seq/gbrowse/ ce3 wormbase +wormbase_ws170 WormBase WS170 http://ws170.wormbase.org/db/seq/gbrowse/ ce4 wormbase +wormbase_ws180 WormBase WS180 http://ws180.wormbase.org/db/seq/gbrowse/ ce5 elegans +wormbase_ws190 WormBase WS190 http://ws190.wormbase.org/db/seq/gbrowse/ ce6 elegans +wormbase_ws200 WormBase WS200 http://ws200.wormbase.org/db/seq/gbrowse/ ce7 c_elegans +wormbase_ws204 WormBase WS204 http://ws204.wormbase.org/db/seq/gbrowse/ ce8 c_elegans +wormbase_ws210 WormBase WS210 http://ws210.wormbase.org/db/seq/gbrowse/ ce9 c_elegans +wormbase_ws220 WormBase WS220 http://ws220.wormbase.org/db/gb2/gbrowse/ ce10,caeRem4 c_elegans,c_remanei +wormbase_ws225 WormBase WS225 http://ws225.wormbase.org/db/gb2/gbrowse/ caeAng1,cb4 c_angaria,c_briggsae

-# modENCODE worm and fly -modencode_worm http://modencode.oicr.on.ca/fgb2/gbrowse/worm ce6 -modencode_fly http://modencode.oicr.on.ca/fgb2/gbrowse/fly dm2 +#The Arabidopsis Information Resource (tair) +tair tair http://arabidopsis.org/cgi-bin/gbrowse/ arabidopsis_tair8,arabidopsis,Arabidopsis_thaliana_TAIR10 arabidopsis_tair8,arabidopsis_tair9,arabidopsis

-#SGD -sgd_yeast http://browse.yeastgenome.org/fgb2/gbrowse/scgenome Saccharomyces_cerevisiae_S288C_SGD2010 +#modENCODE +modencode modENCODE http://modencode.oicr.on.ca/fgb2/gbrowse/ ce6,dm2 worm,fly

+#Saccharomyces Genome Database (SGD) +sgd_yeast Saccharomyces Genome Database http://browse.yeastgenome.org/fgb2/gbrowse/ Saccharomyces_cerevisiae_S288C_SGD2010 scgenome

diff -r 7eeee803345e111b9485cc9b9c2b397a6623fa5f -r 931382e567f501ff8529cdd3c7b45c2d08d0ab23 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -218,7 +218,7 @@ #ucsc_display_sites = main,test,archaea,ucla

# GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt -#gbrowse_display_sites = wormbase,tair,modencode_worm,modencode_fly,yeast_sgd +#gbrowse_display_sites = modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225

# GeneTrack servers: tool-data/shared/genetrack/genetrack_sites.txt #genetrack_display_sites = main,test

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