Usage of csh in Ensembl
Hi,
currently I'm checking Ensembl sources for the real usage of csh to see
whether we could get rid of csh-considered-harmful warning. I realised
that the most occurences of [t]csh are in the docs which I simply
removed because there is no need to advertise csh to Debian users.
Those who intentionally are using csh will most probably know how to
apply csh syntax to the alternative bash examples to set some
environment variables. The only remaining csh script was trivial enough
and used csh for no reason at all.
However, in current version of Ensembl 65 the file
ensembl-variation/modules/Bio/EnsEMBL/Variation/Pipeline/ProteinFunction/RunSift.pm
contains a cmd call to a file named
ensembl_seqs_chosen_via_median_info.csh [see numbered lines below] - but
there is no such file in the source tarball. Could somebody please contact
upstream authors about this part of code which is bound to fail?
Kind regards
Andreas.
Extract of ensembl-variation/modules/Bio/EnsEMBL/Variation/Pipeline/ProteinFunction/RunSift.pm:
...
99 $self->dbc->disconnect_when_inactive(1);
100
101 my $cmd = "$sift_dir/bin/ensembl_seqs_chosen_via_median_info.csh $fasta_file $blastdb $MEDIAN_CUTOFF";
102
103 $self->dbc->disconnect_when_inactive(0);
104
105 my $exit_code = system($cmd);
106
107 if ($exit_code == 0) {
108 $alignment_ok = 1;
109 }
110 else {
111 # the alignment failed for some reason, what to do?
112 warn "Alignment for $translation_stable_id failed - cmd: $cmd";
113 $alignment_ok = 0;
114 }
...
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