[Debian-med-packaging] perl path issue with MEME package?

[Faheem Mitha]

On Wed, 16 Jan 2013, Faheem Mitha wrote:

>
> I'm seeing the following problem
>
> $ iupac2meme
> Can't locate MotifUtils.pm in @INC (@INC contains: /usr/lib/perl/5.10.1 
> /usr/lib/perl /etc/perl /usr/local/lib/perl/5.10.1 
> /usr/local/share/perl/5.10.1 /usr/lib/perl5 /usr/share/perl5 
> /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl .) at 
> /usr/bin/iupac2meme line 16.
> BEGIN failed--compilation aborted at /usr/bin/iupac2meme line 16.

I see the patch perl-include.patch makes changes like

  use lib qw(@PERLLIBDIR@);
+use lib qw(/usr/share/perl5/Meme);

I think that many other perl scripts require the same treatment. See the 
following, for example. Perhaps they all need to be patched?

                                                          Regards, Faheem

faheem at orwell:/usr/local/src/meme/meme-4.9.0/scripts$ grep PERLLIBDIR *pl*
beeml2meme.pl.in:use lib qw(@PERLLIBDIR@);
centrimo_webservice.pl.in:use lib qw(@PERLLIBDIR@);
chen2meme.pl.in:use lib qw(@PERLLIBDIR@);
dreme_webservice.pl.in:use lib qw(@PERLLIBDIR@);
fasta-center.pl.in:push(@INC, "@PERLLIBDIR@"); # add in location of 
installed libraries
fimo_webservice.pl.in:use lib qw(@PERLLIBDIR@);
glam2scan_webservice.pl.in:use lib qw(@PERLLIBDIR@);
glam2_webservice.pl.in:use lib qw(@PERLLIBDIR@);
gomo_webservice.pl.in:use lib qw(@PERLLIBDIR@);
iupac2meme.pl.in:use lib qw(@PERLLIBDIR@);
jaspar2meme.pl.in:use lib qw(@PERLLIBDIR@);
mast_webservice.pl.in:use lib qw(@PERLLIBDIR@);
mcast_webservice.pl.in:use lib qw(@PERLLIBDIR@);
meme2meme.pl.in:use lib qw(@PERLLIBDIR@);
meme-chip.pl.in:use lib qw(@PERLLIBDIR@);
meme-chip_webservice.pl.in:use lib qw(@PERLLIBDIR@);
meme_webservice.pl.in:use lib qw(@PERLLIBDIR@);
nmica2meme.pl.in:use lib qw(@PERLLIBDIR@);
priority2meme.pl.in:use lib qw(@PERLLIBDIR@);
rna2meme.pl.in:use lib qw(@PERLLIBDIR@);
scpd2meme.pl.in:use lib qw(@PERLLIBDIR@);
spamo_webservice.pl.in:use lib qw(@PERLLIBDIR@);
taipale2meme.pl.in:use lib qw(@PERLLIBDIR@);
tamo2meme.pl.in:use lib qw(@PERLLIBDIR@);
tomtom_webservice.pl.in:use lib qw(@PERLLIBDIR@);
transfac2meme.pl.in:use lib qw(@PERLLIBDIR@);
uniprobe2meme.pl.in:use lib qw(@PERLLIBDIR@);
update_db.pl.in:    my $rsat_lib = "@PERLLIBDIR@/RSATWS";