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Add script to convert current caltech v0.1.x database to the trunk schema
2009-02-17
Diane Trout
Add script to convert current caltech v0.1.x database...
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2009-02-17
Diane Trout
Merge flowcell 'paired_end' flag from v0.1 branch
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2009-02-17
Diane Trout
remove cfg_defaults. It was part of an idea I was starting...
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2009-02-13
Diane Trout
Reverse a mistake. DataRuns is from Rami and should...
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2009-02-13
Diane Trout
enable sort of library view by descending library_id
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2009-02-13
Diane Trout
save longer comment describing change
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2009-02-13
Diane Trout
Aparently some more recent version of multi eland stopped
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2009-02-13
Diane Trout
Merge in the library list, detail, and results downloading...
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2009-02-13
Diane Trout
use the compression handling auto-opener for our eland...
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2009-02-12
Diane Trout
make our API docstrings more epydoc friendly
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2009-02-12
Diane Trout
Add load_pipeline_run_xml, a little function that feeds...
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2009-02-05
Diane Trout
Drop 'using %s as cwd' down to just debug level.
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2009-01-30
Diane Trout
extended command line configuration parsing and add...
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2009-01-30
Diane Trout
Try to make runfolder results extraction more robust
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2009-01-30
Diane Trout
Update to not hard code the config file name and the...
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2009-01-24
Diane Trout
insert code to do ~ home directory expansion
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2009-01-23
Diane Trout
Add in Rami's report template, and adjust the paths...
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2009-01-23
Diane Trout
Add id as an AutoNumber(primary_key=True) field and...
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2009-01-21
Diane Trout
Merge in Rami's changes from last friday.
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2009-01-14
Diane Trout
add some testing code for the runner daemon
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2009-01-14
Diane Trout
add empty admin.py for eland_config app
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2009-01-14
Diane Trout
Merged much of the stanford htsworkflow frontend into...
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2009-01-08
Diane Trout
This is a partial merge of the stanford branch with...
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2009-01-06
Diane Trout
Look in Temp directories for some of the files we have...
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2008-12-24
Diane Trout
Handle paired-end eland files.
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2008-12-24
Diane Trout
remove a debug print statement
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2008-12-24
Diane Trout
Add test cases for alphanum sort
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2008-12-24
Diane Trout
Support sorting numbers along with the alphanumeric...
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2008-12-23
Diane Trout
change from hand coded formatting functions to the...
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2008-12-23
Diane Trout
Use the right URLError attribute names for error messages
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2008-12-22
Diane Trout
update make-tree-library script with new default location
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2008-12-22
Diane Trout
fix the multi-eland parser to strip off extensions...
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2008-12-22
Diane Trout
clean up the logic for deciding the output filename...
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2008-12-19
Diane Trout
Add command to report path to make figuring out which...
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2008-12-18
Diane Trout
rename config file to something that doesn't include...
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2008-12-10
Diane Trout
The summary parsing code now seems to handle paired...
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2008-12-09
Diane Trout
Test 1.1rc1 style runs, which unfortunately require...
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2008-12-03
Diane Trout
make-library-tree is a tool to maintain caltech's version...
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2008-12-03
Diane Trout
Add test code to see if runfolder can handle something...
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2008-12-03
Diane Trout
Add code to create a paired end Summary.htm file
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2008-12-03
Diane Trout
Store the bustard pathname when searching for run folders
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2008-11-21
Diane Trout
Use the get_runs from htsworkflow.pipelines.runfolder
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2008-11-14
Diane Trout
Forgot to change a import htsworkflow.pipeline to htsworflow...
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2008-11-06
Diane Trout
Updated ipar_100 test case to deal with the using U0...
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2008-11-06
Diane Trout
Process eland extended (or multi) read files.
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2008-10-30
Diane Trout
The htsworkflow.pipelines.gerald module was getting...
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2008-10-30
Diane Trout
Add support for scanning for results in the IPAR directory.
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2008-10-30
Diane Trout
Add "_slow" to the end of the queuecommand test functions
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2008-10-28
Diane Trout
update setup.py for some package renames and some missing...
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2008-10-21
Diane Trout
Merge in new modules from htsworkflow branch.
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2008-10-21
Diane Trout
Merge in model changes to fctracker from htsworkflow...
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2008-10-21
Diane Trout
update scripts for the pipeline to pipelines module...
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2008-10-15
Diane Trout
rename pipeline to pipelines to imply that we can process...
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2008-10-15
Diane Trout
Rename trunk from gaworkflow to htsworkflow (and update...
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2008-09-25
Diane Trout
solexa2srf likes to produce output, so my trick of...
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2008-09-25
Diane Trout
use _ for field seperator in srf file names. (Using...
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2008-09-18
Diane Trout
Use queuecommands.run not queuecommands.start_job to...
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2008-09-18
Diane Trout
Be a little more informative about how many process...
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2008-09-05
Diane Trout
extract status field out of flowcell name.
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2008-08-29
Diane Trout
Add support for converting mutli-eland files from pipeline...
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2008-08-29
Diane Trout
insert stub clean_runs function to list roughly what...
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2008-08-15
Diane Trout
Improve code to extract runfolder name from the path...
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2008-08-14
Diane Trout
In trying to get scripts/srf to work I needed to set...
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2008-08-14
Diane Trout
refactor code to make a runfolder out of the UnitTest...
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2008-08-14
Diane Trout
we might as well automatically save the Summary.htm...
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2008-08-14
Diane Trout
Utility to create srf files from a bustard directory
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2008-08-11
Diane Trout
A bit of refactoring toward making the run progress...
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2008-07-16
Diane Trout
The older pipeline runs had a Phi-X control lane which...
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2008-07-15
Diane Trout
Provide cross referencing information to the libraries...
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2008-07-07
Diane Trout
Finish updating the Summary parsing file to handle...
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2008-07-03
Diane Trout
Partially handle the changed Summary.htm file from...
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2008-06-24
Diane Trout
Detect if our watch is on a mount point.
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2008-06-17
Diane Trout
Add QueueCommands, a class that allows controlling...
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2008-06-06
Diane Trout
don't use os.path.normpath when pathname is null in...
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2008-06-05
Diane Trout
add --extract-results to scripts/runfolder
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2008-05-29
Diane Trout
Some of the older flow cells used a default genome...
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2008-05-28
Diane Trout
Compute all the details needed to create our 25bp rerun...
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2008-05-27
Diane Trout
ignore more *.py[co~] files in some of our test directories
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2008-05-23
Diane Trout
add --run-xml to runfolder so you can generate summary...
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2008-05-23
Diane Trout
Update pipeline.gerald to handle eland_result files...
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2008-05-15
Diane Trout
add rerun_eland.py which extracts sub-sequences from...
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2008-05-14
Diane Trout
separate computing the sample/lane_id names from calculating...
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2008-05-13
Diane Trout
add additional debugging logging to retrieve_config...
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2008-05-13
Diane Trout
logging.basicConfig should only be in top level scripts.
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2008-05-10
Diane Trout
make it possible to include all alignments, not just...
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2008-05-10
Diane Trout
makebed is a script too
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2008-05-10
Diane Trout
Keep track of sample_name and lane_id computed from...
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2008-05-09
Diane Trout
Make the runfolder splitting patch a bit more python...
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2008-05-09
Diane Trout
update the setup.py file to the new name for the runfolder...
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2008-05-09
Diane Trout
Move runfolder analysis classes out of scripts/runfolder...
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2008-04-24
Diane Trout
Add a script that takes a set of eland_result files...
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2008-04-24
Diane Trout
Report cluster results with the rest of the lane summary...
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2008-04-22
Diane Trout
also since nothing is currently using the pipelineFinished...
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2008-04-22
Diane Trout
oops forgot to remove some debugging statements from...
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2008-04-22
Diane Trout
Extend makebed to lookup metadata out of a copy of...
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2008-04-21
Diane Trout
split the library script into a reusable database/reporting...
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2008-04-21
Diane Trout
Ignore binary files generated by python (*.py[co])
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2008-04-09
Diane Trout
Add library.py, a script to extract a useful description...
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2008-04-01
Diane Trout
Don't die if Config/FlowcellId.xml is missing warn...
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2008-04-01
Diane Trout
report statistics on the various eland_result sequence...
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