2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4456e0cf7721/ Changeset: 4456e0cf7721 Branch: igv-local-dbkey User: lance_parsons Date: 2014-09-04 21:22:10 Summary: Allow local IGV users to visualize custom genomes Affected #: 2 files diff -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 -r 4456e0cf7721386a728e9cb05ef7463bbd477d5b display_applications/igv/bam.xml --- a/display_applications/igv/bam.xml +++ b/display_applications/igv/bam.xml @@ -12,15 +12,19 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /><!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey --> - <filter>${dataset.dbkey in $site_dbkeys}</filter> - + <filter>${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}</filter> + <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --><url>${redirect_url}</url><param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" /><param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" /><param type="template" name="site_organism" strip="True" > - $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ] + #if ($dataset.dbkey in $site_dbkeys) + $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ] + #else: + $bam_file.dbkey + #end if </param><param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><?xml version="1.0" encoding="utf-8"?> diff -r 9b6cccb3af2d6b13a1a1da7def87dcc19172be88 -r 4456e0cf7721386a728e9cb05ef7463bbd477d5b display_applications/igv/vcf.xml --- a/display_applications/igv/vcf.xml +++ b/display_applications/igv/vcf.xml @@ -12,15 +12,19 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /><!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey --> - <filter>${dataset.dbkey in $site_dbkeys}</filter> - + <filter>${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}</filter> + <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --><url>${redirect_url}</url><param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" /><param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" /><param type="template" name="site_organism" strip="True" > - $site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ] + #if ($dataset.dbkey in $site_dbkeys) + $site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ] + #else: + $bgzip_file.dbkey + #end if </param><param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><?xml version="1.0" encoding="utf-8"?> https://bitbucket.org/galaxy/galaxy-central/commits/f8465681a19d/ Changeset: f8465681a19d User: dannon Date: 2014-09-12 19:10:52 Summary: Merged in lance_parsons/galaxy-central-pull-requests/igv-local-dbkey (pull request #488) Allow local IGV users to visualize custom genomes Affected #: 2 files diff -r 2346e098b27e0141fdd3e9821895413e27bc2c2f -r f8465681a19d189317fabebbc3c400c2418e8776 display_applications/igv/bam.xml --- a/display_applications/igv/bam.xml +++ b/display_applications/igv/bam.xml @@ -12,15 +12,19 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /><!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey --> - <filter>${dataset.dbkey in $site_dbkeys}</filter> - + <filter>${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}</filter> + <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --><url>${redirect_url}</url><param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" /><param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" /><param type="template" name="site_organism" strip="True" > - $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ] + #if ($dataset.dbkey in $site_dbkeys) + $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ] + #else: + $bam_file.dbkey + #end if </param><param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><?xml version="1.0" encoding="utf-8"?> diff -r 2346e098b27e0141fdd3e9821895413e27bc2c2f -r f8465681a19d189317fabebbc3c400c2418e8776 display_applications/igv/vcf.xml --- a/display_applications/igv/vcf.xml +++ b/display_applications/igv/vcf.xml @@ -12,15 +12,19 @@ <dynamic_param name="site_organisms" value="4" split="True" separator="," /><!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey --> - <filter>${dataset.dbkey in $site_dbkeys}</filter> - + <filter>${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}</filter> + <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --><url>${redirect_url}</url><param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" /><param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" /><param type="template" name="site_organism" strip="True" > - $site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ] + #if ($dataset.dbkey in $site_dbkeys) + $site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ] + #else: + $bgzip_file.dbkey + #end if </param><param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><?xml version="1.0" encoding="utf-8"?> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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