cycledash
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hammerlab
Variant Caller Analysis Dashboard and Data Management System
There can be a lot of clutter on that runs page, and some (old) projects don't need to be visible all the time. It would be nice if you can...
There are potential race conditions in the RecordStore. One, being triggered in testing, was removed in https://github.com/hammerlab/cycledash/commit/53eeb84c51d32d445845863c17a5bcb1e0503dce#diff-6757f2bcb90aa08e04dad740879709c2L157, but it allows for other race conditions to occur now, in theory. One...
[This run](http://cycledash.demeter.hpc.mssm.edu/runs/232/examine) should have a GT column, which is found in extant_columns in the DB, but doesn't appear in the table. This may be because there is no header in...
If, for example, the VCF is inserted, but the genotypes cannot be, we have a somewhat inconsistent database. We should at least report errors somewhere more obvious.
when I try to upload this BAM file: /datasets/martignetti_ovarian/189/Illumina_DNA/PT189_Normal_Exome/Processed/NGS.2_7_2b.WES/results/PT189_Normal_Exome.PT189_Normal_Exome.clean.dedup.recal.bam `[2015-07-23 12:44:50,816: ERROR/MainProcess] Task workers.indexer.index[05b77263-2324-4c22-a5ee-e6c3fe52d98e] raised unexpected: PyWebHdfsException('{"RemoteException":{"message":"Permission denied: user=username, access=WRITE, inode=\\"\\/\\":hdfs:supergroup:drwxr-xr-x","exception":"AccessControlException","javaClassName":"org.apache.hadoop.security.AccessControlException"}}\n',) Traceback (most recent call last): File "/Users/jaclynperrone/Workspace/cycledash/venv/lib/python2.7/site-packages/celery/app/trace.py", line 240,...
This should be gone in the Resource class/or with the API class, shouldn't show up at try/excepts in the API module's code.
Consider adding more annotation information, depending on the direction we want to take CycleDash. (Or allowing for plugins with this information.) For example, @timodonnell talking about UCSC: ``` it can...
It'll be great to put in some Google Analytics to track clicks and page views throughout CycleDash.