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Holland Computing Center
chipathlon
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f85c8175b6135f6ec56ccb9ca6ccb9471af16c84
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Created with Raphaël 2.2.0
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Merge branch 'sample-genome-assembly-naming' into 'master'
master
master
Modify chip-meta-import to first try and set the genome type based on the sample file information instead of the experiment
Add non-zero exit code.
Add condition to check if file is empty before uploading it to MongoDB
Merge branch '36-chip-meta-download-should-support-resuming' into 'master'
Add resume option to meta download script.
Updated installation documentation.
Added bridges example. Updated chip-gen doc.
Added sphinx autodoc for email param.
Fixed up a few more minor issues.
Removed unnecessary conf argument from chip-gen.
Added email argument, removed all references to config file.
Removed config files as being necessary. Added chip-bin and idr bin argumens to workflow & chip-gen scripts.
Merge branch '26-zerone' into 'master'
Should be broad & sharp for pepr.
need to include sharp somewhere in peak_call yaml so it gets loaded correctly.
Merge branch '26-zerone' of git.unl.edu:hcc/chipathlon into 26-zerone
Updated pepr yaml files to copy duplicate control / signal files under new name.
Replace narrow with sharp peak type for PePr
Minor doc fixes.
Updated the getting started example to be up-to-date.
Added two missing links to tools.
Updated all of the scripts. Made a convenient script for writing the scripts documentation...
Fixed peak call yaml for pepr.
Fixed a validation error with jobs with non-required arguments. Trying to evaluate numeric types without a value.
Added disclaimers to formatting jobs.
Fixed arguments for pepr peak calling. Updated params in peak_call module to correctly reflect the output files produced by hidden domains.
Added more debug statements and fixed file_list parsing in workflow_job.
Removed non-existant verbose argument. Removed input/output directory options.
Fixed typo in download from gridfs updated localpath to local_path.
Fixed lots of minor bugs to make sure the workflow actually generates! Running tests now.
Finished resolving merge conflicts. There were a lot.
Fixed minor bug with duplicate dependencies being added to the workflow.
Merge branch '34-mongodb-auth-should-be-optional' into 'master'
docs
docs
Updated gen script to use db info as keyword not positional arguments.
Fixed issues with circular dependncy in utils / db.py
Fixed merge conflicts again...?
Initial master merge into optional mongo branch.
Merge branch '35-workflow-job-parsing-update'
Merge branch 'bridges-compatability' into 'master'
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