gatk-3.8

Author	SHA1	Message	Date
kshakir	f1f9bd6dcc	Due to recent LSF hiccups put a very brief (.5-2min) retry around getting status. Can't wait too long because statuses are archived an hour after exit. TODO: Switch to bulk status checks and add status archive lookups. Sending SIGTERM(15) instead of SIGKILL(9) to allow for graceful termination of child process. Printing out the name of the QScripts in the compile error text. Added a pipelineretry -PR pass through for the MFCP and MFCPTest. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5295 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-23 18:59:08 +00:00
kshakir	860b172ef1	Defaulting the MFCP to run without a tear script. Added a missing virtual output for the inner FCP, so that Queue can tell a run of the FCP is dot-done. Enabled the MCFPTest for the first time, running without the tear script. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5264 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-17 21:13:14 +00:00
kshakir	d185c2961f	Added pipeline for calling FCP in batches called MultiFullCallingPipeline. Bug smashes for the MCFP: Synchronized access to LSF library and modifications to the QGraph. If values are missing from the graph with -run make sure to exit with a non-zero. Refactored QGraph to pre-generate a unique Int for each QNode speeding up getHashCode/equals inside the graph. Added jobPriority and removed jobLimitSeconds from QFunction. All scatter gather is by default in a single sub directory queueScatterGather. Moved some FCPTest into BaseTest/PipelineTest for use by MFCPTest. Rev'ed the 1000G bams used for validation from v1 to v2 and added code to look for the bams before running other tests. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5247 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-15 18:26:14 +00:00

Author

SHA1

Message

Date

kshakir

Due to recent LSF hiccups put a very brief (.5-2min) retry around getting status. Can't wait too long because statuses are archived an hour after exit.

TODO: Switch to bulk status checks and add status archive lookups.
Sending SIGTERM(15) instead of SIGKILL(9) to allow for graceful termination of child process.
Printing out the name of the QScripts in the compile error text.
Added a pipelineretry -PR pass through for the MFCP and MFCPTest.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5295 348d0f76-0448-11de-a6fe-93d51630548a

2011-02-23 18:59:08 +00:00

kshakir

860b172ef1

Defaulting the MFCP to run without a tear script.

Added a missing virtual output for the inner FCP, so that Queue can tell a run of the FCP is dot-done.
Enabled the MCFPTest for the first time, running without the tear script.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5264 348d0f76-0448-11de-a6fe-93d51630548a

2011-02-17 21:13:14 +00:00

kshakir

d185c2961f

Added pipeline for calling FCP in batches called MultiFullCallingPipeline.

Bug smashes for the MCFP:
  Synchronized access to LSF library and modifications to the QGraph.
  If values are missing from the graph with -run make sure to exit with a non-zero.
  Refactored QGraph to pre-generate a unique Int for each QNode speeding up getHashCode/equals inside the graph.
  Added jobPriority and removed jobLimitSeconds from QFunction.
  All scatter gather is by default in a single sub directory queueScatterGather.
  Moved some FCPTest into BaseTest/PipelineTest for use by MFCPTest.
  Rev'ed the 1000G bams used for validation from v1 to v2 and added code to look for the bams before running other tests.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5247 348d0f76-0448-11de-a6fe-93d51630548a

2011-02-15 18:26:14 +00:00

3 Commits (abf3fcbb72cf7c8f8238f4dac77c7fb6b910874c)