On 27/11/2018 15:34, Christian Meesters wrote:
Dear Kenneth,
Thank you.
On 11/23/18 8:32 AM, Kenneth Hoste wrote:
Dear Christian,
On 22/11/2018 08:55, Christian Meesters wrote:
Dear all,
Sites supporting life-science users might have realized, that modules
installed with BLAST+* configfiles carry a glitch. I am writing in
the event that you have not yet realized that:
The installed modules will provide perl scripts, e. g.
update_blastdb.pl (which is a more frequently demanded script). These
show the following interpreter directive: #!/usr/bin/perl . The issue
at our side is, that our system Perl does not provide two of the
libraries which are used by the script. Therefore, I changed the
directive to #!/usr/bin/env perl and made a fitting Perl module a
dependency.
Perhaps this is useful to someone.
I also wanted to raise some attention to the BLAST developers - to no
avail, as there seemingly is no contact given (?).
The question for this community would be: Alter all BLAST+
easyconfigs accordingly? Or do you not face this issue, perhaps due
to a different setup?
I was not aware of this issue yet, probably because our system Perl
does have the required modules.
Do you mind reporting this in our issue tracker, via
https://github.com/easybuilders/easybuild-easyconfigs/issues/new ?
I will do that tomorrow and also include a review of the required
packages (and perhaps a patch, which covers fixes for a current BLAST+ +
current Perl).
The proper way to fix this would indeed be to include Perl as a
dependency in the BLAST+ easyconfigs, and to fix the hashbang line.
Doing that for *all* BLAST+ easyconfigs may not be worth the effort
though...
Right. In my opinion BLAST+ is the canonical implementation of BLAST,
but not a genuine HPC software (it does not run on realistic samples --
or runs for ages -- without a wrapper script, to leverage the task to
HPC). That being said, I still believe that sites need to provide a
recent version of BLAST+ as a reference. So, perhaps it is worth the
effort to fix / provide one current config and keep the fix from thereon?
Sure, I would certainly fix it for the most recent version we have now
(BLAST+ 2.7.1). And maybe also the version before that (2.6.0).
But going further back is unlikely to help many people, and may also
turn out to be a can of worms w.r.t. conflicting dependencies, etc.
regards,
Kenneth
