Closed gaow closed 9 months ago
To reproduce:
bash test_jobman.sh
observed, erroneous behavior:
{ while IFS= read -r command; do eval $command || true done <<< '''" sos run xqtl-pipeline/pipeline/cis_workhorse.ipynb susie_twas ... " '''
The correct expected behavior is that in this case there are no " around the command:
"
{ while IFS= read -r command; do eval $command || true done <<< ''' sos run xqtl-pipeline/pipeline/cis_workhorse.ipynb susie_twas ... '''
Otherwise there will be an error when we run it: "No such file or directory" something like that.
However we do need " aroudn the command, when we generate the command for parallel, eg parallel ::: "cmd1" "cmd2"
parallel
parallel ::: "cmd1" "cmd2"
So we need to fix it for when there is only one command to generate. I've posted the test scripts to our slack channel.
To reproduce:
observed, erroneous behavior:
The correct expected behavior is that in this case there are no
"
around the command:Otherwise there will be an error when we run it: "No such file or directory" something like that.
However we do need
"
aroudn the command, when we generate the command forparallel
, egparallel ::: "cmd1" "cmd2"
So we need to fix it for when there is only one command to generate. I've posted the test scripts to our slack channel.