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Add LSF bsub opts to each step #8

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Add LSF bsub opts to each step #8

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ebelter
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@ebelter ebelter commented Aug 13, 2019

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ebelter added 24 commits July 24, 2019 15:37
@ebelter
arrow.sh
2fdce9b 
Add LSF block GRID block
convert SGE qsub commands to LSF
@ebelter
Add LSF GRID blocks to shell scripts
4c90da5
@ebelter
arrow.sh
835a86e 
add GRIDOPTS to allow extra options for grid engines
@ebelter
Correct LSF baseid and cores vars
3511d22
@ebelter
arrow.sh
055233c 
correct LSF job dependency check
@ebelter
arrow.sh
5ca533f 
rename LSF output files
@ebelter
Up memory to 32G when using 8 cores
0ec38f8
@ebelter
arrow.sh
d061644 
clean up comments
@ebelter
merge.sh
8309c17 
add GRID LSF block for checking job status
@ebelter
Remove sourcing ~/.profile from shell scripts
2ecbb79
@ebelter
Merge pull request #1 from hall-lab/lsf
b9e13f0 
Add LSF support
@ebelter
Add arrow.sh bats test
281cf52
@ebelter
arrow.sh
399eb41 
Source CONFIG instead of using cat-ting
@ebelter
subset.sh
edba5ab 
Source CONFIG instead of using cat-ting
@ebelter
filterAndAlign.sh
68e1637 
Source CONFIG instead of using cat-ting
@ebelter
consensus.sh
782adb5 
Source CONFIG instead of using cat-ting
@ebelter
merge.sh
013efe6 
Source CONFIG instead of using cat-ting
@ebelter
coverage.sh
f66d8ec 
Source CONFIG instead of using cat-ting
@ebelter
splitByContig.sh
2d28dc4 
Source CONFIG instead of using cat-ting
@ebelter
Cleanup CONFIG and arrow.sh
5352479 
remove algorithm
rename LD_LIBRARY_PATH to LD_ADDITION
@ebelter
Add .gitignore to skip files created by arrow.sh
c08f9fc
@ebelter
Merge pull request #2 from hall-lab/config
090a123 
Source CONFIG
@ebelter
LSF
825679c 
Move bsub opts for each step together
@ebelter
LSF GRIDOPTS
6e25dfc 
add grid opts for each step retrieved from CONFIG
@ebelter ebelter closed this Aug 13, 2019
@skoren
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skoren commented Aug 13, 2019

These changes seem reasonable, I like the definition of options for each step and might use that in the other grid configs. One questions

  1. The changes in merge.sh don't seem necessary, the output "Finished" comes from arrow when it terminates. There is no need for a grid-specific option and I think you want to check arrow output not what the grid says to make sure the job completed ok.

@skoren skoren reopened this Aug 13, 2019
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@ebelter @skoren