[Bio-Linux] problem with arb setup on some machines

[Bela Tiwari]

Hello

We have recently received reports about problems with the current setup
of Arb on some machines. Whether or not your Bio-Linux installation has
this problem depends on if you upgraded vs. installed, when you upgraded
or installed, etc, etc. So if you believe you or anyone associated with
your machine, will ever use Arb, please can you check and correct the
following:


Please see if you have a directory called /home/db/pt_server

If not, as manager,  go into /home/db and create a directory called
pt_server:

sudo mkdir /home/db/pt_server

You will then need to change the permissions on that directory so that
the user
you want to be be able to alter things in this directory has
permission
to do so. If that is always going to be manager, then change the
ownership to manager for example.


We have also noticed there are two broken links  in
/usr/software/arb/arb/lib. Fixing them may or may not affect
anything, but if you want to fix them, move into
/usr/software/arb/arb/lib and

1) remove the current link to ghostscript and make the link:

sudo ln -s /usr/bin/ghostscript ghostscript

2) copy the Xlib directory from an older arb installation
into /usr/software/arb/arb:

sudo cp -R /usr/software/arb/arb_15.6.02/Xlib /usr/software/arb/arb


Please let us know if you have come across any other problems on
Bio-Linux.


cheers

Bela



*************************
Dr. Bela Tiwari
Lead Bioinformatician

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

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