I'm trying to use process substitution for an input file to a program, and it isn't working. Is it because some programs don't allow process substitution for input files?
The following doesn't work:
bash -c "cat meaningless_name"
>sequence1
gattacagattacagattacagattacagattacagattacagattacagattaca
>sequence2
gattacagattacagattacagattacagattacagattacagattacagattaca
bash -c "clustalw -align -infile=<(cat meaningless_name) -outfile=output_alignment.aln -newtree=output_tree.dnd"
(Less verbose output, finishing with:
No sequences in file. No alignment!
But the following controls do work:
bash -c "clustalw -align -infile=meaningless_name -outfile=output_alignment.aln -newtree=output_tree.dnd"
(Verbose output, finishing with:
CLUSTAL-Alignment file created [output_alignment.aln]
bash -c "cat <(cat meaningless_name) > meaningless_name2"
diff meaningless_name meaningless_name2
(No output: the two files are the same)
bash -c "clustalw -align -infile=meaningless_name2 -outfile=output_alignment.aln -newtree=output_tree.dnd"
(Verbose output, finishing with:
CLUSTAL-Alignment file created [output_alignment.aln]
Which suggest that process substitution itself works, but that the clustalw program itself doesn't like process substitution - perhaps because it creates a non-standard file, or creates files with an unusual filename.
Is it common for programs to not accept process substitution? How would I check whether this is the issue?
I'm running GNU bash version 4.0.33(1)-release (x86_64-pc-linux-gnu) on Ubuntu 9.10. Clustalw is version 2.0.10.