1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/0af3b79ea5ea/
changeset: r5271:0af3b79ea5ea
user: jgoecks
date: 2011-03-24 22:36:06
summary: Change default value for Tophat coverage search to true.
affected #: 1 file (8 bytes)
--- a/tools/ngs_rna/tophat_wrapper.xml Thu Mar 24 17:12:16 2011 -0400
+++ b/tools/ngs_rna/tophat_wrapper.xml Thu Mar 24 17:36:06 2011 -0400
@@ -251,8 +251,8 @@
<!-- Coverage search. --><conditional name="coverage_search"><param name="use_search" type="select" label="Use Coverage Search">
- <option value="No">No</option>
- <option value="Yes">Yes</option>
+ <option value="Yes">Yes</option>
+ <option value="No">No</option></param><when value="Yes"><param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" />
@@ -357,8 +357,8 @@
<!-- Coverage search. --><conditional name="coverage_search"><param name="use_search" type="select" label="Use Coverage Search">
- <option value="No">No</option>
- <option value="Yes">Yes</option>
+ <option value="Yes">Yes</option>
+ <option value="No">No</option></param><when value="Yes"><param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" />
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/b41ea12642ad/
changeset: r5267:b41ea12642ad
user: natefoo
date: 2011-03-24 19:33:05
summary: Update the check_galaxy script for the recent changes to the User controller
affected #: 1 file (14 bytes)
--- a/scripts/check_galaxy.py Thu Mar 24 13:52:04 2011 -0400
+++ b/scripts/check_galaxy.py Thu Mar 24 14:33:05 2011 -0400
@@ -274,7 +274,7 @@
self.get("/root/delete?id=%s" % did)
def check_if_logged_in(self):
- self.get("/user")
+ self.get("/user?cntrller=user")
p = loggedinParser()
p.feed(tc.browser.get_html())
return p.logged_in
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/c0330af57060/
changeset: r5266:c0330af57060
user: jgoecks
date: 2011-03-24 18:52:04
summary: Trackster: small fix for read drawing and added note about larger issue.
affected #: 1 file (213 bytes)
--- a/static/scripts/trackster.js Thu Mar 24 11:45:50 2011 -0400
+++ b/static/scripts/trackster.js Thu Mar 24 13:52:04 2011 -0400
@@ -2782,8 +2782,10 @@
// Keep list of items that need to be drawn on top of initial drawing layer.
var draw_last = [];
+ // Gap is needed so that read is offset and hence first base can be drawn on read.
+ // TODO-FIX: using this gap offsets reads so that their start is not visually in sync with other tracks.
if ((mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > CHAR_WIDTH_PX) {
- gap = Math.round(w_scale/2);
+ gap = Math.ceil(CHAR_WIDTH_PX/2 + 1);
}
if (!cigar) {
// If no cigar string, then assume all matches
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/acf9c73836f3/
changeset: r5265:acf9c73836f3
user: dan
date: 2011-03-24 16:45:50
summary: Add more verbose error reporting to FASTQ Groomer tool.
affected #: 2 files (2.3 KB)
--- a/lib/galaxy_utils/sequence/fastq.py Wed Mar 23 19:32:32 2011 -0400
+++ b/lib/galaxy_utils/sequence/fastq.py Thu Mar 24 11:45:50 2011 -0400
@@ -455,6 +455,44 @@
while True:
yield self.next()
+class ReadlineCountFile( object ):
+ def __init__( self, f ):
+ self.__file = f
+ self.readline_count = 0
+ def readline( self, *args, **kwds ):
+ self.readline_count += 1
+ return self.__file.readline( *args, **kwds )
+ def __getattr__( self, name ):
+ return getattr( self.__file, name )
+
+class fastqVerboseErrorReader( fastqReader ):
+ MAX_PRINT_ERROR_BYTES = 1024
+ def __init__( self, fh, **kwds ):
+ super( fastqVerboseErrorReader, self ).__init__( ReadlineCountFile( fh ), **kwds )
+ self.last_good_identifier = None
+ def next( self ):
+ last_good_end_offset = self.file.tell()
+ last_readline_count = self.file.readline_count
+ try:
+ block = super( fastqVerboseErrorReader, self ).next()
+ self.last_good_identifier = block.identifier
+ return block
+ except StopIteration, e:
+ raise e
+ except Exception, e:
+ print "There was an error reading your input file. Your input file is likely malformed.\nIt is suggested that you double-check your original input file for errors -- helpful information for this purpose has been provided below.\nHowever, if you think that you have encountered an actual error with this tool, please do tell us by using the bug reporting mechanism.\n\nThe reported error is: '%s'." % e
+ if self.last_good_identifier is not None:
+ print "The last valid FASTQ read had an identifier of '%s'." % self.last_good_identifier
+ else:
+ print "The error occurred at the start of your file and no valid FASTQ reads were found."
+ error_offset = self.file.tell()
+ error_byte_count = error_offset - last_good_end_offset
+ print_error_bytes = min( self.MAX_PRINT_ERROR_BYTES, error_byte_count )
+ print "The error in your file occurs between lines '%i' and '%i', which corresponds to byte-offsets '%i' and '%i', and contains the text (%i of %i bytes shown):\n" % ( last_readline_count + 1, self.file.readline_count, last_good_end_offset, error_offset, print_error_bytes, error_byte_count )
+ self.file.seek( last_good_end_offset )
+ print self.file.read( print_error_bytes )
+ raise e
+
class fastqNamedReader( object ):
def __init__( self, fh, format = 'sanger' ):
self.file = fh
--- a/tools/fastq/fastq_groomer.py Wed Mar 23 19:32:32 2011 -0400
+++ b/tools/fastq/fastq_groomer.py Thu Mar 24 11:45:50 2011 -0400
@@ -1,6 +1,6 @@
#Dan Blankenberg
import sys
-from galaxy_utils.sequence.fastq import fastqReader, fastqAggregator, fastqWriter
+from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter
def main():
input_filename = sys.argv[1]
@@ -15,7 +15,11 @@
aggregator = fastqAggregator()
out = fastqWriter( open( output_filename, 'wb' ), format = output_type, force_quality_encoding = force_quality_encoding )
read_count = None
- for read_count, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
+ if summarize_input:
+ reader = fastqVerboseErrorReader
+ else:
+ reader = fastqReader
+ for read_count, fastq_read in enumerate( reader( open( input_filename ), format = input_type ) ):
if summarize_input:
aggregator.consume_read( fastq_read )
out.write( fastq_read )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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