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update scripts for the pipeline to pipelines module rename
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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2008-03-28
Diane Trout
Don't die if Summary.htm isn't present
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2008-03-28
Diane Trout
rename the summary report to summary_report to distingush...
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2008-03-28
Diane Trout
make the mapped reads summary report more robust
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2008-03-27
Diane Trout
Add runfolder.py to the list of scripts
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2008-03-26
Diane Trout
sort the sample mapped reads output
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2008-03-25
Diane Trout
Add documentation about what runfolder.py does
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2008-03-22
Diane Trout
Store the firecrest/bustard/gerald tuple in a new class...
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2008-03-21
Diane Trout
Summarize information from the runfolder.
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2008-03-06
Diane Trout
convert a single-match eland result file into a bed...
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2008-03-06
Diane Trout
Add script to extract some subset of sequence from...
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2008-01-29
Diane Trout
DummyOptions didn't define a genome_dir member before...
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2008-01-23
Diane Trout
return most recent genome build for the pipeline config...
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2008-01-15
Diane Trout
Oops, forgot to provide a null body to my the stub...
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2008-01-15
Diane Trout
pyinotify rm_watch takes a list, not a dictionary.
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2008-01-15
Diane Trout
Update test_copier to reflect copiers move to gaworkflow...
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2008-01-15
Diane Trout
move the autotmation scripts into gaworkflow.automation
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2008-01-11
Diane Trout
Add the xmi file from umbrello documenting our basic...
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2008-01-09
Diane Trout
always trigger a copy when we receive the sequencingFinshed...
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2008-01-08
Diane Trout
tell subversion to ignore *.py[co~] files
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2008-01-08
Diane Trout
make sequencingFinished return something instead of...
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2008-01-08
Diane Trout
Remove unnecessary code from the runner.py module
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2008-01-08
Diane Trout
Add script to make it easier to launch runner
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2008-01-04
Diane Trout
use \w for alphanumeric flow cell IDs
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2007-12-30
Diane Trout
direntry parser wasn't eating a trailing newline
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2007-12-30
Diane Trout
forgot to rename the caller and called when refactoring...
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2007-12-30
Diane Trout
split rsync directory listing correctly
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2007-12-22
Diane Trout
add a , to make customizing list of template dirs easier
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2007-12-11
Diane Trout
[project @ add skeleton for runner]
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2007-12-11
Diane Trout
[project @ send messages to notify_runner not self...
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2007-12-11
Diane Trout
[project @ add a parser to spoolwatcher]
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2007-12-10
Diane Trout
[project @ rename runFinished to sequencingFinished]
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2007-12-10
Diane Trout
[project @ make spoolwatcher a benderjab bot]
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2007-12-10
Diane Trout
[project @ use XmlRpcBot.rpc_send]
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2007-12-10
Diane Trout
[project @ Require a resource for JIDs that are used...
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2007-12-10
Diane Trout
[project @ moved check_option into benderjab]
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2007-12-08
Diane Trout
[project @ update CopierBot to new logging daemonizable...
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2007-11-20
Diane Trout
[project @ move brandon's pipeline handling code into...
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2007-11-20
Diane Trout
[project @ rename python module to gaworkflow from...
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2007-11-09
Diane Trout
[project @ add notes about what we need to do to more...
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2007-10-16
Diane Trout
[project @ handle IOErrors from xsend]
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2007-08-10
Diane Trout
[project @ add script to launch copier daemon]
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2007-08-10
Diane Trout
[project @ make copier a bot with logging abilities]
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2007-08-09
Diane Trout
[project @ start the copier script]
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2007-08-09
Diane Trout
[project @ add __init__.py]
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2007-08-09
Diane Trout
[project @ make a spoolwatcher script]
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2007-08-08
Diane Trout
[project @ add a basic setup.py file]
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2007-08-08
Diane Trout
[project @ Sequencer spool drive watcher]
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2007-08-08
Diane Trout
[project @ tools to handle the illumina sequencer workflow]
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2007-12-21
Diane Trout
This directory will host the upstream sources
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