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Switch to regular dictionary instead of ordered dictionary.
[htsworkflow.git]
/
htsworkflow
/
pipelines
/
2012-07-06
Diane Trout
Switch to regular dictionary instead of ordered dictionary.
tree
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commitdiff
2012-07-05
Diane Trout
Massively rework eland file finding and indexing.
tree
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commitdiff
2012-07-05
Diane Trout
Rename chromosome in hiseq test set to match our fake...
tree
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commitdiff
2012-06-30
Diane Trout
Disable debug messages for each scanned eland file...
tree
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commitdiff
2012-06-30
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
tree
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commitdiff
2012-06-30
Diane Trout
Support multiple having an eland file split into multip...
tree
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commitdiff
2012-06-30
Diane Trout
Some minor tweaks to rta 1.12 testing.
tree
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commitdiff
2012-06-30
Diane Trout
Properly code in tabs for simulated hiseq export files
tree
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commitdiff
2012-06-30
Diane Trout
Use different tags indicating gerald or casava style...
tree
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commitdiff
2012-06-21
Diane Trout
Merge ssh://jumpgate.caltech.edu/var/htsworkflow/htswor...
tree
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commitdiff
2012-06-12
Diane Trout
Add a software (name) property to firecrest, ipar,...
tree
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commitdiff
2012-06-11
Diane Trout
Return a gerald version number as a number and not...
tree
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commitdiff
2012-06-02
Diane Trout
Split lane parameters into seperate classes for GA...
tree
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commitdiff
2012-05-25
Diane Trout
Merge ssh://jumpgate.caltech.edu/var/htsworkflow/htswor...
tree
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commitdiff
2012-05-25
Diane Trout
Merge ssh://jumpgate.caltech.edu/var/htsworkflow/htswor...
tree
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commitdiff
2012-05-16
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
tree
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commitdiff
2012-05-16
Diane Trout
update summary.py to extract data from HiSeq runs.
tree
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commitdiff
2012-05-15
Diane Trout
Fix bugs introduduced by the improved HiSeq runfolder...
tree
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commitdiff
2012-05-12
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
tree
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commitdiff
2012-05-10
Diane Trout
Minimal changes needed to get raw data archived for...
tree
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commitdiff
2012-04-13
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
tree
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commitdiff
2012-04-12
Diane Trout
Extend the adapter id field to support the dual indexed...
tree
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commitdiff
2012-03-27
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
tree
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commitdiff
2012-03-26
Diane Trout
Switch to lxml for parsing the summary file.
tree
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commitdiff
2012-03-23
Diane Trout
Apparently I forgot to remove a parameter why creating...
tree
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commitdiff
2012-03-08
Diane Trout
Actually if I provide an output file, I want to write...
tree
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commitdiff
2012-03-07
Diane Trout
Forgot to add split attribute to __eq__ test.
tree
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commitdiff
2012-03-06
Diane Trout
Support scanning for split fastq files generated by...
tree
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commitdiff
2012-03-06
Diane Trout
Add module to convert multiple fastq files into a singl...
tree
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commitdiff
2012-03-05
Diane Trout
Use named tuple for sequence flowcell/start/stop/projec...
tree
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commitdiff
2012-03-02
Diane Trout
Core functions for saving and finding fastq files gener...
tree
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commitdiff
2012-03-01
Diane Trout
Remove some debug prints
tree
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commitdiff
2012-03-01
Diane Trout
Simulate a HiSeq runfolder.
tree
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commitdiff
2011-12-20
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
tree
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commitdiff
2011-12-20
Diane Trout
whitespace reformatting
tree
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commitdiff
2011-12-20
Diane Trout
Remove eXecute bit from modules
tree
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commitdiff
2011-11-22
Diane Trout
Add a method to override command used to convert srf...
tree
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commitdiff
2011-11-05
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
tree
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commitdiff
2011-11-04
Diane Trout
Use a logger initialized to the module name much more...
tree
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commitdiff
2011-10-21
Diane Trout
Yes generate regular gerald config file.
tree
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commitdiff
2011-10-10
Diane Trout
Remove ReadPrep and Thumbnail_Images being generated...
tree
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commitdiff
2011-10-10
Diane Trout
Don't need to duplicate %t tile in srf command
tree
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commitdiff
2011-10-06
Diane Trout
Add the ability to specify a flowcell id instead of...
tree
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commitdiff
2011-10-04
Diane Trout
Add support for flowcells analyzed with Casava 1.7
tree
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commitdiff
2011-09-19
Diane Trout
Output samples that don't have index sequence as well.
tree
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commitdiff
2011-09-19
Diane Trout
Python 2.6's DictWriter doesn't have writeheader, so...
tree
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commitdiff
2011-09-17
Diane Trout
Add support for tracking the multiplex index sequence.
0.5.4
tree
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commitdiff
2011-09-12
Diane Trout
Add support for first-gen HiSeq flowcells (e.g. ABXX)
tree
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commitdiff
2011-06-30
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
tree
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commitdiff
2011-06-23
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
tree
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commitdiff
2011-06-22
Diane Trout
Move parse_flowcell_id out of frontend.samples.results
tree
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commitdiff
2011-06-11
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
tree
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commitdiff
2011-06-11
Diane Trout
Convert Rami's DataRun feature to something useful...
tree
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commitdiff
2011-06-10
Brandon W. King
The srf/qseq --raw-format patch.
tree
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commitdiff
2011-06-09
Diane Trout
Move test srf files to testdata directory so I can...
tree
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commitdiff
2011-06-09
Diane Trout
Add a method to return the runfolder name.
tree
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commitdiff
2011-05-26
Diane Trout
Merge branch 'add-condition'
tree
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commitdiff
2011-05-09
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
tree
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commitdiff
2011-05-09
Diane Trout
Report missing directory names to help diagnose sequenc...
tree
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commitdiff
2011-04-18
Diane Trout
Be more flexible with fastq filenames.
tree
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commitdiff
2011-02-17
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
tree
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commitdiff
2011-02-15
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
tree
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commitdiff
2011-02-07
Diane Trout
Add in a little bit of qseq2fastq testing code. More...
tree
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commitdiff
2011-02-07
Diane Trout
Add documentation about which Phred format we're generating
tree
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commitdiff
2011-02-03
Diane Trout
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
tree
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commitdiff
2011-01-25
Diane Trout
Fix typo in a function name.
tree
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commitdiff
2010-11-01
Diane Trout
Only complane about missing genomes if we _wanted_...
tree
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commitdiff
2010-11-01
Diane Trout
Check for s_${lane}_02_matrix.txt as well as s_${lane...
tree
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commitdiff
2010-10-27
Diane Trout
The WITH_SEQUENCE flag needs to be lower-case "true".
tree
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commitdiff
2010-10-22
Diane Trout
Report version number derived from git tag.
tree
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commitdiff
2010-10-19
Diane Trout
Set WITH_SEQUENCE as both a per-lane AND global parameter
0.4.5
tree
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commitdiff
2010-10-08
Diane Trout
WITH_SEQUENCE is actually a global GERALD option, remov...
tree
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commitdiff
2010-10-07
Diane Trout
Update gerald config file generation.
tree
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commitdiff
2010-09-24
Diane Trout
Handle the case when a sequencing lane lacks any yield...
tree
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commitdiff
2010-09-10
Diane Trout
Add support for CASAVA 1.7
tree
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commitdiff
2010-06-10
Diane Trout
Extend htsworkflow.pipelines.sequences to also try...
tree
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commitdiff
2010-06-10
Diane Trout
Move the code to scan the sequence file archive to...
tree
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commitdiff
2010-06-10
Diane Trout
Move the knowledge of the urls for the REST API to...
tree
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commitdiff
2010-04-23
Diane Trout
Update summary script to read from the GERALD Summary...
tree
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commitdiff
2010-02-22
Diane Trout
there is no such thing as sequence_extended. I was...
tree
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commitdiff
2010-01-21
Diane Trout
Update test code to deal with the switch to storing...
tree
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commitdiff
2009-12-11
Diane Trout
Modify the srf utility to tar.bz2 the qseq files instea...
tree
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commitdiff
2009-11-10
Diane Trout
Don't add the post_run_command unless the option and...
tree
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commitdiff
2009-10-17
Diane Trout
Figure out the absolute path to the runfolder for passi...
tree
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commitdiff
2009-10-08
Diane Trout
Add the ability not to build srf files.
tree
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commitdiff
2009-10-06
Diane Trout
Use eland_extended or eland_pair instead of eland for...
tree
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commitdiff
2009-10-06
Diane Trout
Default to sequencing if we don't have a genome for...
tree
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commitdiff
2009-10-02
Diane Trout
Test the updated version of extract results that builds...
tree
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commitdiff
2009-09-30
Diane Trout
Add building srf files to runfolder as part of --extrac...
tree
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commitdiff
2009-09-26
Diane Trout
The config file should also set the SEQUENCE_FORMAT
tree
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commitdiff
2009-09-26
Diane Trout
HttpRequest.getcode doesn't exist in python 2.4, use...
tree
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commitdiff
2009-09-26
Diane Trout
Implement a client side config file generator.
tree
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commitdiff
2009-09-16
Diane Trout
Replace some prints with logging.info messages and
tree
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commitdiff
2009-09-10
Diane Trout
Don't crash if there are no lane result summary entries...
tree
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commitdiff
2009-09-10
Diane Trout
Report if the Summary.htm file is missing the Lane...
tree
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commitdiff
2009-06-19
Diane Trout
I started using ResultLane, so stop treating it like...
tree
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commitdiff
2009-06-17
Diane Trout
Add support for extracting data out of Illumina's new...
tree
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commitdiff
2009-06-17
Diane Trout
Loading really old run xml files caused the website...
tree
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commitdiff
2009-06-17
Diane Trout
remove spurious debug print statements
tree
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commitdiff
2009-05-11
Diane Trout
Fix parameter list for base class.
tree
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commitdiff
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