Commit 2eae552c authored by Taylor Hanayik's avatar Taylor Hanayik
Browse files

update readme

parent 59e45589
......@@ -172,3 +172,25 @@ optional arguments:
# Run pheweb process --no-parse
Now that we have run `pheweb parse` (the SGE version) on the cluster we can run pheweb's remaining stages.
I have created a simple script (`sge_pheweb_process.sh`) that can be submitted to the SGE queue.
If there are RAM limits issues then request more slots, or keep the slots and reduce the number of concurrent jobs that pheweb does (in `config.py`).
```
#!/bin/bash
#
#$ -N phewebFinal
#$ -o /gpfs2/well/win/users/jwz430/phewebFull/data/sgelogs/phewebFin.sgeout
#$ -e /gpfs2/well/win/users/jwz430/phewebFull/data/sgelogs/phewebFin.sgeerr
#$ -P win.prjc
#$ -pe shmem 40
source ~/.bashrc
export PHEWEB_DATADIR=/gpfs2/well/win/users/jwz430/phewebFull/data; cd $PHEWEB_DATADIR; /gpfs2/well/win/users/jwz430/pyenvs/pheweb/bin/pheweb conf num_procs=40 process --no-parse
```
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