I am trying to perform process substitution within a command passed to Platform LSF via bsub.
On the worker node that I submit my job to, process substitution is not enabled because it is not a POSIX compliant feature.
I therefore need to enable the feature then submit a second process from within the bsub. I have got this working using a here-document, however, it is not without errors. The final EOF marker is not being read i.e.
warning: here-document at line 4 delimited by end-of-file (wanted 'EOF')
set +o posix; bash <<EOF some.program -1 <(gunzip -c some.file) -2 <(gunzip -c some.file); EOF
submitted to bsub as single string, e.g.
set +o posix;\nbash <<EOF\nsome.program -1 <(gunzip -c some.file) -2 <(gunzip -c some.file);\nEOF
Any suggestions on how to get the final EOF to be read correctly? As I say, everything runs fine, so this is just a case of tidying up the code.