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Merge branch 'master' into debianized
[htsworkflow.git]
/
scripts
/
2011-02-07
Diane Trout
Merge branch 'master' into debianized
debianized
tree
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commitdiff
2011-01-25
root
Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
tree
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commitdiff
2011-01-21
Diane Trout
Merge branch 'master' of gitosis@mus.cacr.caltech.edu...
tree
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commitdiff
2011-01-08
Diane Trout
Add validation script
0.5.0
tree
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commitdiff
2011-01-04
Diane Trout
Rename all the scripts to start with htsw-
tree
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commitdiff
2010-10-22
Diane Trout
Report version number derived from git tag.
tree
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commitdiff
2010-10-07
Diane Trout
Update gerald config file generation.
tree
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commitdiff
2010-09-24
Diane Trout
Remind myself that dry-run doesn't work with the extrac...
tree
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commitdiff
2010-08-24
Diane Trout
Better detect which program ids generated CNF4 srf...
tree
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commitdiff
2010-07-08
Diane Trout
Update srf2named_fastq to try to detect if the srf...
tree
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commitdiff
2010-07-07
Diane Trout
If a quality score started with an @ sign it was treate...
tree
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commitdiff
2010-06-22
Diane Trout
Fix srf2named_fastq to output the proper /2 in paired...
tree
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commitdiff
2010-06-15
Diane Trout
Make it easier to run srf2named_fastq.py
tree
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commitdiff
2010-06-15
Diane Trout
Wrapper script that helps convert srf files to fastq...
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
2010-05-29
Diane Trout
Do not insert anything into the header if there is...
tree
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commitdiff
2010-05-08
Diane Trout
Always return a count from carefully_make_hardlinks
tree
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commitdiff
2010-04-23
Diane Trout
Add support for generating fasta files in addition...
tree
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commitdiff
2010-03-22
Diane Trout
Extend qseq2fastq to write to two fastq files,
tree
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commitdiff
2010-03-05
Diane Trout
Use the HTS workflow API to figure out the library...
tree
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commitdiff
2010-02-04
Diane Trout
Actually implement the code to loop over a list of...
tree
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commitdiff
2010-01-30
Diane Trout
Update the inventory tracker code for the split from...
tree
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commitdiff
2010-01-13
Diane Trout
Modify qseq2fastq to also read from compressed tar...
tree
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commitdiff
2010-01-07
Diane Trout
Update the usage string for qseq2fastq
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
2009-12-01
Diane Trout
Replace '.' with 'N' in the sequence from qseq files.
tree
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commitdiff
2009-12-01
Diane Trout
Fix typo in srf command
tree
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commitdiff
2009-12-01
Diane Trout
Also include the read ID in the fastq header
tree
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commitdiff
2009-12-01
Diane Trout
Add a simple utility to convert qseq to fastq files.
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
Default to sequencing if we don't have a genome for...
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
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
2009-08-12
Diane Trout
Converted Brandon's scripts into a single python script...
tree
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commitdiff
2009-08-12
Diane Trout
Move Brandon's upgrade script in with all the other...
tree
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commitdiff
2009-08-11
Brandon King
Making it more clear what the script does.
tree
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commitdiff
2009-08-11
Brandon King
Script for conversion of db; start of fixes brought...
tree
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commitdiff
2009-08-10
Brandon King
print killing wsgi; minor fix.
tree
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commitdiff
2009-08-07
Brandon King
New Lane Table migration progress.
tree
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commitdiff
2009-06-16
Brandon King
Icon added.
tree
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commitdiff
2009-06-16
Brandon King
Managed to use a urllib python 2.6 feature... convertin...
tree
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commitdiff
2009-06-10
Brandon King
Improved debugging output.
tree
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commitdiff
2009-06-10
Brandon King
Moved hardcoded URL to it's proper place in the setting...
tree
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commitdiff
2009-06-10
Brandon King
Track which flowcells are archived on which long term...
tree
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commitdiff
2009-05-06
Diane Trout
Update htsworkflow.util.fctracker module to work with...
tree
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commitdiff
2009-04-24
Diane Trout
add --clean option to runfolder
tree
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commitdiff
2009-04-24
Diane Trout
Allow picking runfolder variant we should be trying...
tree
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commitdiff
2009-03-31
Diane Trout
provide an error message if no run is found with the...
tree
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commitdiff
2009-03-30
Diane Trout
Allow specifying a run instead of just scanning the...
tree
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commitdiff
2009-03-30
Diane Trout
Add some logging code to report what the program is...
tree
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commitdiff
2009-03-28
Diane Trout
For pipeline 1.1rc1 or 1.3.2, look for the matrix files...
tree
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commitdiff
2009-03-18
Diane Trout
provide more options for picking how much logging info...
tree
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commitdiff
2009-02-27
Diane Trout
Only configure logging if we're being run as a script
tree
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commitdiff
2009-02-13
Diane Trout
use the compression handling auto-opener for our eland...
tree
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commitdiff
2009-01-30
Diane Trout
extended command line configuration parsing and add...
tree
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commitdiff
2009-01-30
Diane Trout
Try to make runfolder results extraction more robust
tree
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commitdiff
2009-01-24
Diane Trout
insert code to do ~ home directory expansion
tree
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commitdiff
2008-12-22
Diane Trout
update make-tree-library script with new default location
tree
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commitdiff
2008-12-22
Diane Trout
clean up the logic for deciding the output filename...
tree
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commitdiff
2008-12-03
Diane Trout
make-library-tree is a tool to maintain caltech's versi...
tree
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commitdiff
2008-11-21
Diane Trout
Use the get_runs from htsworkflow.pipelines.runfolder
tree
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commitdiff
2008-10-30
Diane Trout
The htsworkflow.pipelines.gerald module was getting...
tree
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commitdiff
2008-10-21
Diane Trout
update scripts for the pipeline to pipelines module...
tree
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commitdiff
2008-10-15
Diane Trout
Rename trunk from gaworkflow to htsworkflow (and update...
tree
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commitdiff
2008-09-25
Diane Trout
use _ for field seperator in srf file names. (Using...
tree
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commitdiff
2008-09-18
Diane Trout
Use queuecommands.run not queuecommands.start_job to...
tree
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commitdiff
2008-08-29
Diane Trout
Add support for converting mutli-eland files from pipel...
tree
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commitdiff
2008-08-15
Diane Trout
Improve code to extract runfolder name from the path...
tree
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commitdiff
2008-08-14
Diane Trout
Utility to create srf files from a bustard directory
tree
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commitdiff
2008-08-11
Diane Trout
A bit of refactoring toward making the run progress...
tree
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commitdiff
2008-06-05
Diane Trout
add --extract-results to scripts/runfolder
tree
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commitdiff
2008-05-28
Diane Trout
Compute all the details needed to create our 25bp rerun...
tree
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commitdiff
2008-05-23
Diane Trout
add --run-xml to runfolder so you can generate summary...
tree
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commitdiff
2008-05-15
Diane Trout
add rerun_eland.py which extracts sub-sequences from...
tree
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commitdiff
2008-05-13
Diane Trout
logging.basicConfig should only be in top level scripts.
tree
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commitdiff
2008-05-09
Diane Trout
Move runfolder analysis classes out of scripts/runfolde...
tree
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commitdiff
2008-04-24
Diane Trout
Add a script that takes a set of eland_result files...
tree
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commitdiff
2008-04-24
Diane Trout
Report cluster results with the rest of the lane summar...
tree
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commitdiff
2008-04-22
Diane Trout
oops forgot to remove some debugging statements from...
tree
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commitdiff
2008-04-22
Diane Trout
Extend makebed to lookup metadata out of a copy of...
tree
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commitdiff
2008-04-21
Diane Trout
split the library script into a reusable database/repor...
tree
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commitdiff
2008-04-09
Diane Trout
Add library.py, a script to extract a useful descriptio...
tree
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commitdiff
2008-04-01
Diane Trout
Don't die if Config/FlowcellId.xml is missing warn...
tree
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commitdiff
2008-04-01
Diane Trout
report statistics on the various eland_result sequence...
tree
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commitdiff
2008-03-28
Diane Trout
Don't die if Summary.htm isn't present
tree
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commitdiff
2008-03-28
Diane Trout
rename the summary report to summary_report to distingu...
tree
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commitdiff
2008-03-28
Diane Trout
make the mapped reads summary report more robust
tree
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commitdiff
2008-03-26
Diane Trout
sort the sample mapped reads output
tree
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commitdiff
2008-03-25
Diane Trout
Add documentation about what runfolder.py does
tree
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commitdiff
2008-03-22
Diane Trout
Store the firecrest/bustard/gerald tuple in a new class...
tree
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commitdiff
2008-03-21
Diane Trout
Summarize information from the runfolder.
tree
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commitdiff
2008-03-06
Diane Trout
convert a single-match eland result file into a bed...
tree
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commitdiff
2008-03-06
Diane Trout
Add script to extract some subset of sequence from...
tree
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commitdiff
2008-01-16
Brandon King
Fix for tickets #45 & #47
tree
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commitdiff
2008-01-15
Diane Trout
move the autotmation scripts into gaworkflow.automation
tree
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commitdiff
2008-01-08
Diane Trout
Add script to make it easier to launch runner
tree
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commitdiff
2008-01-04
Brandon King
Runner seems to work with running the pipeline when...
tree
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commitdiff
2008-01-03
Brandon King
Work towards disabling command-line parsing outside...
tree
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commitdiff
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