Here Document on Platform LSF

Question

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.

Answer 1

The shell needs the EOF string to be alone in a complete line, just add a \n after it (and mybe a do nothing : after could also help) :

set +o posix;\nbash <<EOF\nsome.program -1 <(gunzip -c some.file) -2 <(gunzip -c some.file);\nEOF\n:

Note: I meant this to be a comment, but there is no enough space in a comment to write this in full.