BLAST search, perl versions and Darwin Port in mac

[Tonu Margus]

Hi T-Coffee users,

I just installed a new version of T-coffee (9.01) in my mac (OS 10.6)
and pretty soon fall into problems with psicoffee and expresso --
network BLAST did not work (no EBI no NCBI). I checked from newsgroups
and nothing new, similar phenomenology has been reported many times.
But, the reasons were different. After some digging and comparing I
found the reason: it was MacPort perl version.

Perl version installed by MacPort was v5.12.3 system perl (/usr/bin/
perl) is v5.10.0

I am still not sure what exactly caused the problem but after
commenting out PATH (/opt/local/bin:/opt/local/sbin:) added by MacPort
everything works fine.

I hope it helps quicker solution in case of similar problem

Tõnu Margus

---------------------------------------------------------------------------------------------------------
Tõnu Margus
Department of Bioinformatics
Institute of Molecular and Cell Biology at Tartu University
Riia 23, 51010
Tartu
Estonia

Web: http://bioinfo.ut.ee/~tmargus
E-mail: tonu....@ut.ee
Phone: +372-7376037

[Paolo Di Tommaso]

Hi Tõnu,

Thank for your feedback. I'm not sure about that, but I think that your problem could be caused by some incompatibility between the MacPorts PERL you have installed on your Mac and the system default one.

It is worth to know that T-Coffee distribution includes some PERL modules that may not be working with the PERL version that your are trying to use.

Does you have solve all the problems downgrading to the system default PERL distribution?

Cheers,

Paolo Di Tommaso
Software Engineer
Comparative Bioinformatics Group
Centre de Regulacio Genomica (CRG)
Dr. Aiguader, 88
08003 Barcelona, Spain

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[Tonu Margus]

Hi Paolo,

I have partially solved the issue by commenting out MacPort's PATH,
but it does mean that I can not use programs and dependencies
installed by MacPort and the T-coffee at the same time. There should
be a possibility to choose which perl version is active by port
command. If you know such a magic syntax it will save me from digging
in port documentation.

Best,
Tõnu

---------------------------------------------------------------------------------------------------------
Tõnu Margus
Department of Bioinformatics
Institute of Molecular and Cell Biology at Tartu University
Riia 23, 51010
Tartu
Estonia

Web: http://bioinfo.ut.ee/~tmargus
E-mail: tonu....@ut.ee
Phone: +372-7376037

> > E-mail: tonu.mar...@ut.ee

[Paolo Di Tommaso]

Hi Tõnu, 

Unfortunately I didn't know much about that. On Linux I think you could be able to do that using the alternatives command, but it seems that it is not available on Mac. 

Cheers,

Paolo