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October 2009

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172 discussions

[hg] galaxy 2778: Added Cite to masthead
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/40f58d95a051 changeset: 2778:40f58d95a051 user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Fri Sep 25 13:58:15 2009 -0400 description: Added Cite to masthead 5 file(s) affected in this change: templates/base_panels.mako tools/fastx_toolkit/fastq_to_fasta.xml tools/samtools/pileup_parser.xml tools/samtools/sam_pileup.xml universe_wsgi.ini.sample diffs (80 lines): diff -r 6a86a558f405 -r 40f58d95a051 templates/base_panels.mako --- a/templates/base_panels.mako Fri Sep 25 11:32:47 2009 -0400 +++ b/templates/base_panels.mako Fri Sep 25 13:58:15 2009 -0400 @@ -167,11 +167,16 @@ <div class="submenu"> <ul> <li><a href="${app.config.get( "bugs_email", "mailto:galaxy-bugs@bx.psu.edu" )}">Email comments, bug reports, or suggestions</a></li> - <li><a target="_blank" href="${app.config.get( "wiki_url", "http://g2.trac.bx.psu.edu/" )}">Galaxy Wiki</a></li> - <li><a target="_blank" href="${app.config.get( "screencasts_url", "http://g2.trac.bx.psu.edu/wiki/ScreenCasts" )}">Video tutorials (screencasts)</a></li> + <li><a target="_blank" href="${app.config.get( "wiki_url", "http://bitbucket.org/galaxy/galaxy-central/wiki" )}">Galaxy Wiki</a></li> + <li><a target="_blank" href="${app.config.get( "screencasts_url", "http://galaxycast.org" )}">Video tutorials (screencasts)</a></li> </ul> </div> </td> + + <td class="tab"> + <a target="_blank" href="${app.config.get( "citation_url", "http://bitbucket.org/galaxy/galaxy-central/wiki/Citations" )}">Cite</a> + </td> + <td class="tab"> <a>User</a> @@ -282,7 +287,7 @@ </head> <body scroll="no" class="${self.body_class}"> - <div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; min-width: 600px;"> + <div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; min-width: 960px;"> ## Background displays first <div id="background"></div> ## Layer iframes over backgrounds diff -r 6a86a558f405 -r 40f58d95a051 tools/fastx_toolkit/fastq_to_fasta.xml --- a/tools/fastx_toolkit/fastq_to_fasta.xml Fri Sep 25 11:32:47 2009 -0400 +++ b/tools/fastx_toolkit/fastq_to_fasta.xml Fri Sep 25 13:58:15 2009 -0400 @@ -3,7 +3,7 @@ <command>gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v </command> <inputs> - <param format="fastqsolexa" name="input" type="data" label="FASTQ Library to convert" /> + <param format="fastqsolexa,fastqsanger" name="input" type="data" label="FASTQ Library to convert" /> <param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases "> <option value="">yes</option> diff -r 6a86a558f405 -r 40f58d95a051 tools/samtools/pileup_parser.xml --- a/tools/samtools/pileup_parser.xml Fri Sep 25 11:32:47 2009 -0400 +++ b/tools/samtools/pileup_parser.xml Fri Sep 25 13:58:15 2009 -0400 @@ -1,5 +1,5 @@ -<tool id="pileup_parser" name="Parse pileup"> - <description>to find variants</description> +<tool id="pileup_parser" name="Filter pileup"> + <description>on coverage and SNPs</description> <command interpreter="perl"> #if $pileup_type.type_select == "six": #pileup_parser.pl $input "3" "5" "6" "4" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1 #elif $pileup_type.type_select == "ten": #pileup_parser.pl $input "3" "9" "10" "8" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1 diff -r 6a86a558f405 -r 40f58d95a051 tools/samtools/sam_pileup.xml --- a/tools/samtools/sam_pileup.xml Fri Sep 25 11:32:47 2009 -0400 +++ b/tools/samtools/sam_pileup.xml Fri Sep 25 13:58:15 2009 -0400 @@ -1,5 +1,5 @@ -<tool id="sam_pileup" name="SAM Pileup Format" version="1.0.0"> - <description>generates the pileup format for a provided BAM file</description> +<tool id="sam_pileup" name="Generate pileup" version="1.0.0"> + <description>from BAM dataset</description> <command interpreter="python"> sam_pileup.py --input1=$input1 diff -r 6a86a558f405 -r 40f58d95a051 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample Fri Sep 25 11:32:47 2009 -0400 +++ b/universe_wsgi.ini.sample Fri Sep 25 13:58:15 2009 -0400 @@ -102,9 +102,11 @@ ## Brand: appends "/[brand]" to the "Galaxy" text in the masthead ## wiki_url: replaces the default galaxy main wiki ## bugs_email: replaces the default galaxy bugs email list +##citation_url: point to a URL listing citations #brand = Private local mirror #wiki_url = /path/to/my/local/wiki #bugs_email = mailto:galaxy-bugs@example.org +#citation_url = /path/to/my/citations # ---- Logging and Debugging ------------------------------------------------

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bowtie and bwa
by Mark Garner 01 Oct '09

01 Oct '09

Hello, we're in the process of installing bowtie and bwa to get them working with Galaxy and have a question. Looking at left hand menu item "NGS: Mapping" on the home page of Galaxy that we have just installed we see: NGS: Mapping Megablast compare short reads against nt and wgs databases Parse blast XML output Digging in tools_config.xml we see: <section name="NGS: Mapping" id="solexa_tools">  <tool file="metag_tools/megablast_wrapper.xml" /> <tool file="metag_tools/megablast_xml_parser.xml" /> <tool file="sr_mapping/bowtie_wrapper.xml" /> <tool file="sr_mapping/bwa_wrapper.xml" /> </section> Looking in .../tools/sr_mapping we see both: bowtie_wrapper.xml bwa_wrapper.xml And checking say bowtie_wrapper.xml we see <tool id="bowtie_wrapper" name="Bowtie" version="1.0.0"> <description> fast alignment of reads against reference sequence </ description > Everything looks good so why do we not see sub-menu items for bowtie and bwa? All we see under NGS: Mapping are the two items I listed initially, "Megablast compare short reads against nt and wgs databases" and "Parse blast XML output". Thanks for your help. Mark.

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