commit/galaxy-central: 2 new changesets
2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/aab39d3344e2/ Changeset: aab39d3344e2 Branch: stable User: dan Date: 2014-04-16 16:50:23 Summary: Manually graft IGB updates to stable, since the old display applications now no longer work properly. Affected #: 8 files diff -r 1ad62c7727285084e46ee3572835483e34c551a5 -r aab39d3344e2fbe83c209f33d7e69fea2350709d datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -26,6 +26,7 @@ </datatype><datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true"><converter file="bedgraph_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="igb/bedgraph.xml" /></datatype><datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" /><datatype extension="bed6" type="galaxy.datatypes.interval:Bed6"> @@ -98,6 +99,7 @@ <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"><converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/><converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="igb/gtf.xml" /></datatype><datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /><datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /> diff -r 1ad62c7727285084e46ee3572835483e34c551a5 -r aab39d3344e2fbe83c209f33d7e69fea2350709d display_applications/igb/bam.xml --- a/display_applications/igb/bam.xml +++ b/display_applications/igb/bam.xml @@ -1,58 +1,14 @@ <display id="igb_bam" version="0.0.0" name="display in IGB"> - <link id="Local" name="Local"> - <url>http://localhost:7085/UnibrowControl?version=${bam_file.dbkey}&feature_url_0=${bam_file.url}&sym_name_0=${thenicename}&sym_method_0=${bam_file.url}&query_url=${bam_file.url}&server_url=galaxy</url> - <param type="data" name="bam_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bam_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="bai_file" url="${thenicename}_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /> - <param type="data" name="bam_file" url="${thenicename}_${DATASET_HASH}.bam" strip_https="True" /> - </link> + <link id="View" name="View"> + <url>http://bioviz.org/igb/galaxy.html?version=${bam_file.dbkey}&feature_url_0=${bam_file.url}&sym_name_0=${niceName}&sym_method_0=${bam_file.url}&query_url=${bam_file.url}&server_url=galaxy</url> + <param type="data" name="bam_file_for_name" viewable="False"/> + <param type="template" name="niceName" viewable="False" strip="True"> + #import re + #set nm=$bam_file_for_name.name + ${re.sub('\W',"_",nm)} + </param> + <param type="data" name="bai_file" url="${niceName}.bam.bai" metadata="bam_index" strip_https="True" /> + <param type="data" name="bam_file" url="${niceName}.bam" strip_https="True" /> + </link> - <link id="Web" name="Web"> - <url>$jnlp.url</url> - <param type="data" name="bam_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bam_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="bai_file" url="${thenicename}_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /> - <param type="data" name="bam_file" url="${thenicename}_${DATASET_HASH}.bam" strip_https="True" /> - <param type="template" name="jnlp" url="${thenicename}_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file"> -<?xml version="1.0" encoding="utf-8"?> -<jnlp spec="6.0+" version="" codebase="http://www.bioviz.org/igb/releases/current/"; > - <information> - <title>IGB</title> - <vendor>Genoviz Project</vendor> - <homepage href="http://genoviz.sourceforge.net/"; /> - <description>Integrated Genome Browser</description> - <icon href="igb.gif"/> - <offline-allowed/> - <shortcut online="true"> - <desktop/> - <menu submenu="IGB" /> - </shortcut> - </information> - <security> - <all-permissions/> - </security> - <resources> - <java version="1.6+" initial-heap-size="32m" max-heap-size="1024m"/> - <jar href="igb_exe.jar" main="true" /> - <jar href="igb-i18n.jar" /> - <property name="apple.laf.useScreenMenuBar" value="true" /> - <property name="http.agent" value="IGB (Webstart)" /> - </resources> - <application-desc main-class="com.affymetrix.main.Main"> - <argument>-prefs</argument> - <argument>http://www.bioviz.org/igb/releases/current/igb_prefs.xml</argument>; - <argument>-href</argument> - <argument>http://localhost:7085/UnibrowControl?version=${bam_file.dbkey}&feature_url_0=${bam_file.url}&sym_name_0=${thenicename}&sym_method_0=${bam_file.url}&query_url=${bam_file.url}&server_url=galaxy </argument> - </application-desc> -</jnlp> - </param> - </link></display> diff -r 1ad62c7727285084e46ee3572835483e34c551a5 -r aab39d3344e2fbe83c209f33d7e69fea2350709d display_applications/igb/bb.xml --- a/display_applications/igb/bb.xml +++ b/display_applications/igb/bb.xml @@ -1,58 +1,14 @@ <display id="igb_bb" version="1.0.0" name="display in IGB"> - <link id="Local" name="Local"> - <url>http://localhost:7085/UnibrowControl?version=${bigbed_file.dbkey}&loadresidues=false&feature_url_0=${bigbed_file.url}&sym_name_0=${thenicename}&sym_method_0=${bigbed_file.url}&query_url=${bigbed_file.url}&server_url=galaxy</url> + <link id="View" name="View"> + <url>http://bioviz.org/igb/galaxy.html?version=${bigbed_file.dbkey}&loadresidues=false&feature_url_0=${bigbed_file.url}&sym_name_0=${niceName}&sym_method_0=${bigbed_file.url}&query_url=${bigbed_file.url}&server_url=galaxy</url><param type="data" name="bigbed_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> + <param type="template" name="niceName" viewable="False" strip="True"> #import re #set nm=$bigbed_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="bigbed_file" url="${thenicename}_${DATASET_HASH}.bigbed" strip_https="True" /> - </link> - - <link id="Web" name="Web"> - <url>$jnlp.url</url> - <param type="data" name="bigbed_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bigbed_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="bigbed_file" url="${thenicename}_${DATASET_HASH}.bigbed" strip_https="True" /> - <param type="template" name="jnlp" url="${thenicename}_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file"> -<?xml version="1.0" encoding="utf-8"?> -<jnlp spec="6.0+" version="" codebase="http://www.bioviz.org/igb/releases/current/"; > - <information> - <title>IGB</title> - <vendor>Genoviz Project</vendor> - <homepage href="http://genoviz.sourceforge.net/"; /> - <description>Integrated Genome Browser</description> - <icon href="igb.gif"/> - <offline-allowed/> - <shortcut online="true"> - <desktop/> - <menu submenu="IGB" /> - </shortcut> - </information> - <security> - <all-permissions/> - </security> - <resources> - <java version="1.6+" initial-heap-size="32m" max-heap-size="1024m"/> - <jar href="igb_exe.jar" main="true" /> - <jar href="igb-i18n.jar" /> - <property name="apple.laf.useScreenMenuBar" value="true" /> - <property name="http.agent" value="IGB (Webstart)" /> - </resources> - <application-desc main-class="com.affymetrix.main.Main"> - <argument>-prefs</argument> - <argument>http://www.bioviz.org/igb/releases/current/igb_prefs.xml</argument>; - <argument>-href</argument> - <argument>http://localhost:7085/UnibrowControl?version=${bigbed_file.dbkey}&loadresidues=false&feature_url_0=${bigbed_file.url}&sym_name_0=${thenicename}&sym_method_0=${bigbed_file.url}&query_url=${bigbed_file.url}&server_url=galaxy </argument> - </application-desc> -</jnlp> - </param> + <param type="data" name="bigbed_file" url="${niceName}.bigbed" strip_https="True" /></link></display> diff -r 1ad62c7727285084e46ee3572835483e34c551a5 -r aab39d3344e2fbe83c209f33d7e69fea2350709d display_applications/igb/bed.xml --- a/display_applications/igb/bed.xml +++ b/display_applications/igb/bed.xml @@ -1,73 +1,17 @@ <display id="igb_bed" version="1.0.0" name="display in IGB"> - <link id="Local" name="Local"> - <url>http://localhost:7085/UnibrowControl?version=${bed_file.dbkey}&${position}&loadresidues=false&feature_url_0=${bed_file.url}&sym_name_0=${thenicename}&sym_method_0=${bed_file.url}&query_url=${bed_file.url}&server_url=galaxy</url> - <param type="data" name="bed_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bed_file_for_name.name - ${re.sub('\W',"_",nm)} + <link id="View" name="View"> + <url>$bioviz</url> + <param type="data" name="bed_file_for_name" viewable="False"/> + <param type="template" name="niceName" viewable="False" strip="True"> + #import re + #set nm=$bed_file_for_name.name + ${re.sub('\W',"_",nm)} + </param> + <param type="data" name="bed_file" url="${niceName}.bed" strip_https="True" /> + + <param type="template" name="bioviz" strip="True" > + http://bioviz.org/igb/galaxy.html?version=${bed_file.dbkey}&loadresidues=false&feature_url_0=${bed_file.url}&sym_name_0=${niceName}&sym_method_0=${bed_file.url}&query_url=${bed_file.url}&server_url=galaxy </param> - <param type="data" name="bed_file" url="${thenicename}_${DATASET_HASH}.bed" strip_https="True" /> - <param type="template" name="position" strip="True" > - #set chrom, start, end = $bed_file.datatype.get_estimated_display_viewport( $bed_file ) - #if $chrom is not None: - seqid=${chrom}&start=${start}&end=${int(end) + 1} - #else: - seqid=&start=&end= - #end if - </param> - </link> - - <link id="Web" name="Web"> - <url>$jnlp.url</url> - <param type="data" name="bed_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bed_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="bed_file" url="${thenicename}_${DATASET_HASH}.bed" strip_https="True" /> - <param type="template" name="position" strip="True" > - #set chrom, start, end = $bed_file.datatype.get_estimated_display_viewport( $bed_file ) - #if $chrom is not None: - seqid=${chrom}&start=${start}&end=${int(end) + 1} - #else: - seqid=&start=&end= - #end if - </param> - <param type="template" name="jnlp" url="${thenicename}_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file"> -<?xml version="1.0" encoding="utf-8"?> -<jnlp spec="6.0+" version="" codebase="http://www.bioviz.org/igb/releases/current/"; > - <information> - <title>IGB</title> - <vendor>Genoviz Project</vendor> - <homepage href="http://genoviz.sourceforge.net/"; /> - <description>Integrated Genome Browser</description> - <icon href="igb.gif"/> - <offline-allowed/> - <shortcut online="true"> - <desktop/> - <menu submenu="IGB" /> - </shortcut> - </information> - <security> - <all-permissions/> - </security> - <resources> - <java version="1.6+" initial-heap-size="32m" max-heap-size="1024m"/> - <jar href="igb_exe.jar" main="true" /> - <jar href="igb-i18n.jar" /> - <property name="apple.laf.useScreenMenuBar" value="true" /> - <property name="http.agent" value="IGB (Webstart)" /> - </resources> - <application-desc main-class="com.affymetrix.main.Main"> - <argument>-prefs</argument> - <argument>http://www.bioviz.org/igb/releases/current/igb_prefs.xml</argument>; - <argument>-href</argument> - <argument>http://localhost:7085/UnibrowControl?version=${bed_file.dbkey}&${position}&loadresidues=false&feature_url_0=${bed_file.url}&sym_name_0=${thenicename}&sym_method_0=${bed_file.url}&query_url=${bed_file.url}&server_url=galaxy </argument> - </application-desc> -</jnlp> - </param> - </link> + </link></display> diff -r 1ad62c7727285084e46ee3572835483e34c551a5 -r aab39d3344e2fbe83c209f33d7e69fea2350709d display_applications/igb/bedgraph.xml --- /dev/null +++ b/display_applications/igb/bedgraph.xml @@ -0,0 +1,17 @@ +<display id="igb_bedgraph" version="1.0.0" name="display in IGB"> + + <link id="View" name="View"> + <url>$bioviz</url> + <param type="data" name="bedgraph_file_for_name" viewable="False"/> + <param type="template" name="niceName" viewable="False" strip="True"> + #import re + #set nm=$bedgraph_file_for_name.name + ${re.sub('\W',"_",nm)} + </param> + <param type="data" name="bedgraph_file" url="${niceName}.bed.bedgraph" strip_https="True" /> + + <param type="template" name="bioviz" strip="True" > + http://bioviz.org/igb/galaxy.html?version=${bedgraph_file.dbkey}&loadresidues=false&feature_url_0=${bedgraph_file.url}&sym_name_0=${niceName}&sym_method_0=${bedgraph_file.url}&query_url=${bedgraph_file.url}&server_url=galaxy + </param> + </link> +</display> diff -r 1ad62c7727285084e46ee3572835483e34c551a5 -r aab39d3344e2fbe83c209f33d7e69fea2350709d display_applications/igb/bigwig.xml --- a/display_applications/igb/bigwig.xml +++ b/display_applications/igb/bigwig.xml @@ -1,14 +1,14 @@ <display id="igb_bigwig" version="1.0.0" name="display in IGB"> - <link id="Local" name="Local"> - <url>http://localhost:7085/UnibrowControl?version=${bigwig_file.dbkey}&loadresidues=false&feature_url_0=${bigwig_file.url}&sym_name_0=${thenicename}&sym_method_0=${bigwig_file.url}&query_url=${bigwig_file.url}&server_url=galaxy</url> + <link id="View" name="View"> + <url>http://bioviz.org/igb/galaxy.html?version=${bigwig_file.dbkey}&loadresidues=false&feature_url_0=${bigwig_file.url}&sym_name_0=${niceName}&sym_method_0=${bigwig_file.url}&query_url=${bigwig_file.url}&server_url=galaxy</url><param type="data" name="bigwig_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> + <param type="template" name="niceName" viewable="False" strip="True"> #import re #set nm=$bigwig_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="bigwig_file" url="${thenicename}_${DATASET_HASH}.bigwig" strip_https="True" /> + <param type="data" name="bigwig_file" url="${niceName}.bigwig" strip_https="True" /><!--<param type="template" name="position" strip="True" > #set chrom, start, end = $bigwig_file.datatype.get_estimated_display_viewport( $bigwig_file ) #if $chrom is not None: @@ -19,47 +19,4 @@ </param>--></link> - <link id="Web" name="Web"> - <url>$jnlp.url</url> - <param type="data" name="bigwig_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$bigwig_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="bigwig_file" url="${thenicename}_${DATASET_HASH}.bigwig" strip_https="True" /> - <param type="template" name="jnlp" url="${thenicename}_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file"> -<?xml version="1.0" encoding="utf-8"?> -<jnlp spec="6.0+" version="" codebase="http://www.bioviz.org/igb/releases/current/"; > - <information> - <title>IGB</title> - <vendor>Genoviz Project</vendor> - <homepage href="http://genoviz.sourceforge.net/"; /> - <description>Integrated Genome Browser</description> - <icon href="igb.gif"/> - <offline-allowed/> - <shortcut online="true"> - <desktop/> - <menu submenu="IGB" /> - </shortcut> - </information> - <security> - <all-permissions/> - </security> - <resources> - <java version="1.6+" initial-heap-size="32m" max-heap-size="1024m"/> - <jar href="igb_exe.jar" main="true" /> - <jar href="igb-i18n.jar" /> - <property name="apple.laf.useScreenMenuBar" value="true" /> - <property name="http.agent" value="IGB (Webstart)" /> - </resources> - <application-desc main-class="com.affymetrix.main.Main"> - <argument>-prefs</argument> - <argument>http://www.bioviz.org/igb/releases/current/igb_prefs.xml</argument>; - <argument>-href</argument> - <argument>http://localhost:7085/UnibrowControl?version=${bigwig_file.dbkey}&loadresidues=false&feature_url_0=${bigwig_file.url}&sym_name_0=${thenicename}&sym_method_0=${bigwig_file.url}&query_url=${bigwig_file.url}&server_url=galaxy </argument> - </application-desc> -</jnlp> - </param> - </link></display> diff -r 1ad62c7727285084e46ee3572835483e34c551a5 -r aab39d3344e2fbe83c209f33d7e69fea2350709d display_applications/igb/gtf.xml --- /dev/null +++ b/display_applications/igb/gtf.xml @@ -0,0 +1,17 @@ +<display id="igb_gtf" version="1.0.0" name="display in IGB"> + + <link id="View" name="View"> + <url>$bioviz</url> + <param type="data" name="gtf_file_for_name" viewable="False"/> + <param type="template" name="niceName" viewable="False" strip="True"> + #import re + #set nm=$gtf_file_for_name.name + ${re.sub('\W',"_",nm)} + </param> + <param type="data" name="gtf_file" url="${niceName}.gtf" strip_https="True" /> + + <param type="template" name="bioviz" strip="True" > + http://bioviz.org/igb/galaxy.html?version=${gtf_file.dbkey}&loadresidues=false&feature_url_0=${gtf_file.url}&sym_name_0=${niceName}&sym_method_0=${gtf_file.url}&query_url=${gtf_file.url}&server_url=galaxy + </param> + </link> +</display> \ No newline at end of file diff -r 1ad62c7727285084e46ee3572835483e34c551a5 -r aab39d3344e2fbe83c209f33d7e69fea2350709d display_applications/igb/wig.xml --- a/display_applications/igb/wig.xml +++ b/display_applications/igb/wig.xml @@ -1,14 +1,14 @@ <display id="igb_wig" version="1.0.0" name="display in IGB"> - <link id="Local" name="Local"> - <url>http://localhost:7085/UnibrowControl?version=${wig_file.dbkey}&${position}&loadresidues=false&feature_url_0=${wig_file.url}&sym_name_0=${thenicename}&sym_method_0=${wig_file.url}&query_url=${wig_file.url}&server_url=galaxy</url> + <link id="View" name="View"> + <url>http://bioviz.org/igb/galaxy.html?version=${wig_file.dbkey}&${position}&loadresidues=false&feature_url_0=${wig_file.url}&sym_name_0=${niceName}&sym_method_0=${wig_file.url}&query_url=${wig_file.url}&server_url=galaxy</url><param type="data" name="wig_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> + <param type="template" name="niceName" viewable="False" strip="True"> #import re #set nm=$wig_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="wig_file" url="${thenicename}_${DATASET_HASH}.wig" strip_https="True" /> + <param type="data" name="wig_file" url="${niceName}.wig" strip_https="True" /><param type="template" name="position" strip="True" > #set chrom, start, end = $wig_file.datatype.get_estimated_display_viewport( $wig_file ) #if $chrom is not None: @@ -18,57 +18,5 @@ #end if </param></link> - - <link id="Web" name="Web"> - <url>$jnlp.url</url> - <param type="data" name="wig_file_for_name" viewable="False"/> - <param type="template" name="thenicename" viewable="False" strip="True"> - #import re - #set nm=$wig_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="wig_file" url="${thenicename}_${DATASET_HASH}.wig" strip_https="True" /> - <param type="template" name="position" strip="True" > - #set chrom, start, end = $wig_file.datatype.get_estimated_display_viewport( $wig_file ) - #if $chrom is not None: - seqid=${chrom}&start=${start}&end=${int(end) + 1} - #else: - seqid=&start=&end= - #end if - </param> - <param type="template" name="jnlp" url="${thenicename}_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file"> -<?xml version="1.0" encoding="utf-8"?> -<jnlp spec="6.0+" version="" codebase="http://www.bioviz.org/igb/releases/current/"; > - <information> - <title>IGB</title> - <vendor>Genoviz Project</vendor> - <homepage href="http://genoviz.sourceforge.net/"; /> - <description>Integrated Genome Browser</description> - <icon href="igb.gif"/> - <offline-allowed/> - <shortcut online="true"> - <desktop/> - <menu submenu="IGB" /> - </shortcut> - </information> - <security> - <all-permissions/> - </security> - <resources> - <java version="1.6+" initial-heap-size="32m" max-heap-size="1024m"/> - <jar href="igb_exe.jar" main="true" /> - <jar href="igb-i18n.jar" /> - <property name="apple.laf.useScreenMenuBar" value="true" /> - <property name="http.agent" value="IGB (Webstart)" /> - </resources> - <application-desc main-class="com.affymetrix.main.Main"> - <argument>-prefs</argument> - <argument>http://www.bioviz.org/igb/releases/current/igb_prefs.xml</argument>; - <argument>-href</argument> - <argument>http://localhost:7085/UnibrowControl?version=${wig_file.dbkey}&${position}&loadresidues=false&feature_url_0=${wig_file.url}&sym_name_0=${thenicename}&sym_method_0=${wig_file.url}&query_url=${wig_file.url}&server_url=galaxy </argument> - </application-desc> -</jnlp> - </param> - </link></display> https://bitbucket.org/galaxy/galaxy-central/commits/bd1abde45a41/ Changeset: bd1abde45a41 User: dan Date: 2014-04-16 16:51:00 Summary: merge stable Affected #: 8 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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