ENCODE-DCC / atac-seq-pipeline

ENCODE ATAC-seq pipeline
MIT License
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caper init lsf not supported #398

Open cindyli9888 opened 2 years ago

cindyli9888 commented 2 years ago

Hi, Thank you for working on this amazing pipeline! Our institution (MGH)'s cluster is based on lsf job submission, so that is the only option we have. However, when i was trying to run caper init lsf, it indicated that lsf is not supported. I did notice that from a previous thread that LSF is added (https://github.com/ENCODE-DCC/caper/issues/93). However, it was still not running correctly at our end. Is there anything we can do to make it run correctly? Thank you!

Cindy

leepc12 commented 2 years ago

Please check Caper's version.

$ caper -v

It works find on my end.

$ caper init lsf
2022-10-19 14:55:11,678|caper.cromwell|INFO| Installing Cromwell JAR... https://github.com/broadinstitute/cromwell/releases/download/82/cromwell-82.jar
2022-10-19 14:55:11,678|autouri.autouri|INFO| cp: (ae3e034c) started. src=https://github.com/broadinstitute/cromwell/releases/download/82/cromwell-82.jar, dest=/home/leepc12/.caper/cromwell_jar/cromwell-82.jar
2022-10-19 14:55:13,435|autouri.autouri|INFO| cp: (ae3e034c) skipped due to md5_match. md5=836c966872093cf4beba8e22cbf799b0
2022-10-19 14:55:13,436|caper.cromwell|INFO| Installing Womtool JAR... https://github.com/broadinstitute/cromwell/releases/download/82/womtool-82.jar
2022-10-19 14:55:13,436|autouri.autouri|INFO| cp: (13c0ce75) started. src=https://github.com/broadinstitute/cromwell/releases/download/82/womtool-82.jar, dest=/home/leepc12/.caper/womtool_jar/womtool-82.jar
2022-10-19 14:55:15,129|autouri.autouri|INFO| cp: (13c0ce75) skipped due to md5_match. md5=d3717d95d1607c143b8b92718a373982

$ cat ~/.caper/default.conf
backend=lsf

# Local directory for localized files and Cromwell's intermediate files.
# If not defined then Caper will make .caper_tmp/ on CWD or `local-out-dir`.
# /tmp is not recommended since Caper store localized data files here.
local-loc-dir=

cromwell=/home/leepc12/.caper/cromwell_jar/cromwell-82.jar
womtool=/home/leepc12/.caper/womtool_jar/womtool-82.jar