Ramialison-Lab-ARMI / Trawler-2.0

Motif discovery tool
GNU General Public License v2.0
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Invalid hash-bang lines in Perl scripts #1

Open peterjc opened 6 years ago

peterjc commented 6 years ago

The following lists the first line of all the Perl scripts under bin/ at the command line:

$ head -n 1 bin/*.pl 
==> bin/bedtofasta.pl <==
#########################################################################

==> bin/generate_random_background.pl <==
####################################################################################################

==> bin/overrepresentation.pl <==
#!/usr/bin/perl

==> bin/pipeline_trawler_01_som.pl <==
#!/usr/bin/perl

==> bin/pipeline_trawler_01_som_single_strand.pl <==
#!/usr/bin/perl

==> bin/pipeline_trawler_02.pl <==
#!/usr/bin/perl

==> bin/pipeline_trawler_02_no_orthologs.pl <==
#!/usr/bin/perl

==> bin/pipeline_trawler_02_no_orthologs_single_strand.pl <==
#!/usr/bin/perl

==> bin/pipeline_trawler_02_phastcons.pl <==
#! usr/bin/perl

==> bin/pipeline_trawler_02_single_strand.pl <==
#!/usr/bin/perl

==> bin/pipeline_trawler_03.pl <==
#!/usr/bin/perl

==> bin/trawler.pl <==
#!/usr/bin/perl

Problems:

bin/bedtofasta.pl and bin/generate_random_background.pl have comments before the hash-bang line, rendering it non-functional.

pipeline_trawler_02_phastcons.pl (and bin/bedtofasta.pl on top of the above issue) have #! usr/bin/perl -- there is a space instead of a slash, rendering this non-functional.

Also, it would arguably be better to use this rather than assuming /usr/bin/perl is the appropriate installation of Perl to be using:

#!/usr/bin/env perl
peterjc commented 6 years ago

Also, none of the Perl scripts under bin/ have been marked as executable:

chmod a+x bin/*.pl