1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/b6beb68c36b0/
changeset: r5364:b6beb68c36b0
user: greg
date: 2011-04-11 16:37:14
summary: Fix for rating a tool in the tool shed.
affected #: 1 file (206 bytes)
--- a/templates/webapps/community/common/rate_tool.mako Mon Apr 11 09:39:55 2011 -0400
+++ b/templates/webapps/community/common/rate_tool.mako Mon Apr 11 10:37:14 2011 -0400
@@ -146,7 +146,13 @@
</div><div class="form-row"><label>Your Rating:</label>
- ${render_star_rating( 'rating', tra.rating )}
+ <%
+ if tra and tra.rating:
+ rating = tra.rating
+ else:
+ rating = 0
+ %>
+ ${render_star_rating( 'rating', rating )}
<div style="clear: both"></div></div><div class="form-row">
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/a77c1ea48451/
changeset: r5361:a77c1ea48451
user: james_taylor
date: 2011-04-08 22:43:45
summary: trackster: remove condition that sets mode to squish when less than four features in tile. mode selection must not change across tiles at the same level.
affected #: 1 file (72 bytes)
--- a/static/scripts/trackster.js Fri Apr 08 14:14:58 2011 -0400
+++ b/static/scripts/trackster.js Fri Apr 08 16:43:45 2011 -0400
@@ -2153,8 +2153,9 @@
//if ( (result.message && result.message.match(/^Only the first [\d]+/)) ||
// (result.data && result.data.length > 2000) ||
var data = result.data;
- if ( (data.length && data.length < 4) ||
- (this.view.high - this.view.low > MIN_SQUISH_VIEW_WIDTH) ) {
+ // if ( (data.length && data.length < 4) ||
+ // (this.view.high - this.view.low > MIN_SQUISH_VIEW_WIDTH) ) {
+ if ( this.view.high - this.view.low > MIN_SQUISH_VIEW_WIDTH ) {
mode = "Squish";
} else {
mode = "Pack";
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/61b493011087/
changeset: r5359:61b493011087
user: kellyv
date: 2011-04-08 18:06:28
summary: Removed unnecessary size check on BAM file produce in view step of sam-to-bam
affected #: 1 file (560 bytes)
--- a/tools/samtools/sam_to_bam.py Fri Apr 08 09:45:38 2011 -0400
+++ b/tools/samtools/sam_to_bam.py Fri Apr 08 12:06:28 2011 -0400
@@ -125,8 +125,6 @@
tmp_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir )
tmp_aligns_file_name = tmp_aligns_file.name
tmp_aligns_file.close()
- # IMPORTANT NOTE: for some reason the samtools view command gzips the resulting bam file without warning,
- # and the docs do not currently state that this occurs ( very bad ).
command = 'samtools view -bt %s -o %s %s' % ( fai_index_file_path, tmp_aligns_file_name, options.input1 )
tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
tmp_stderr = open( tmp, 'wb' )
@@ -147,8 +145,6 @@
tmp_stderr.close()
if returncode != 0:
raise Exception, stderr
- if len( open( tmp_aligns_file_name ).read() ) == 0:
- raise Exception, 'Initial BAM file empty'
except Exception, e:
#clean up temp files
if os.path.exists( tmp_dir ):
@@ -188,11 +184,6 @@
stop_err( 'Error sorting alignments from (%s), %s' % ( tmp_aligns_file_name, str( e ) ) )
# Move tmp_aligns_file_name to our output dataset location
sorted_bam_file = '%s.bam' % tmp_sorted_aligns_file_name
- if os.path.getsize( sorted_bam_file ) == 0:
- #clean up temp files
- if os.path.exists( tmp_dir ):
- shutil.rmtree( tmp_dir )
- stop_err( 'Error creating sorted version of BAM file' )
shutil.move( sorted_bam_file, options.output1 )
#clean up temp files
if os.path.exists( tmp_dir ):
@@ -201,6 +192,6 @@
if os.path.getsize( options.output1 ) > 0:
sys.stdout.write( 'SAM file converted to BAM' )
else:
- stop_err( 'The output file is empty, there may be an error with your input file or settings.' )
+ stop_err( 'Error creating sorted version of BAM file.' )
if __name__=="__main__": __main__()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/8a43c7a39dd1/
changeset: r5356:8a43c7a39dd1
user: jgoecks
date: 2011-04-07 22:28:56
summary: Fix hyperlinks in Cuffcompare and Cuffdiff documentation.
affected #: 2 files (36 bytes)
--- a/tools/ngs_rna/cuffcompare_wrapper.xml Thu Apr 07 08:39:07 2011 -0400
+++ b/tools/ngs_rna/cuffcompare_wrapper.xml Thu Apr 07 16:28:56 2011 -0400
@@ -130,9 +130,9 @@
**Input format**
-Cuffcompare takes Cufflinks' GTF output as input, and optionally can take a "reference" annotation (such as from Ensembl___)
+Cuffcompare takes Cufflinks' GTF output as input, and optionally can take a "reference" annotation (such as from Ensembl_)
-.. ___: http://www.todo.org
+.. _Ensembl: http://www.ensembl.org
------
--- a/tools/ngs_rna/cuffdiff_wrapper.xml Thu Apr 07 08:39:07 2011 -0400
+++ b/tools/ngs_rna/cuffdiff_wrapper.xml Thu Apr 07 16:28:56 2011 -0400
@@ -198,8 +198,6 @@
Cuffdiff takes Cufflinks or Cuffcompare GTF files as input along with two SAM files containing the fragment alignments for two or more samples.
-.. ___: http://www.todo.org
-
------
**Outputs**
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/b1657489f16c/
changeset: r5354:b1657489f16c
user: kellyv
date: 2011-04-06 22:28:33
summary: Added BWA for SOLiD to tool_conf.xml.main
affected #: 1 file (53 bytes)
--- a/tool_conf.xml.main Wed Apr 06 12:44:58 2011 -0400
+++ b/tool_conf.xml.main Wed Apr 06 16:28:33 2011 -0400
@@ -358,6 +358,7 @@
<tool file="metag_tools/megablast_xml_parser.xml" /><label text="AB-SOLiD" id="ab_solid"/><tool file="sr_mapping/bowtie_color_wrapper.xml" />
+ <tool file="sr_mapping/bwa_color_wrapper.xml" /></section><section name="NGS: SAM Tools" id="samtools"><tool file="samtools/sam_bitwise_flag_filter.xml" />
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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