[BioRuby] command not found: blastall and broken pipe from apache2 and passenger (mod_rails)

[Adam Kraut]

It's possible that 'blastall' is not in the path of the user running the
apache process.  On my system Apache runs as user 'www', so to run blastall
from a rails app I would edit the system-wide profile in /etc/profile.  You
might also want to check how to set the user for Passenger as it may be
different from Apache.  Using the full path (/usr/local/bin/blastall) should
also work for any user but I'm not sure if the bioruby wrapper lets you do
this.

Cheers,
Adam

On Wed, Jun 25, 2008 at 1:53 PM, Matt Scilipoti <mattscilipoti at possiamo.com>
wrote:

> I am attempting to use bioruby (blast) with a rails application.  It
> works on my dev machine (OSX), but not the Production Server (suse
> sles).  When I attempt to perform a blast query on the Production
> server I receive "Errno::EPIPE (Broken pipe)" and "command not found:
> blastall".  The permissions and path look correct to me.  Is it
> possible that there is an apache permission issue?  This occurred
> intermittently when I was using a mongrel_cluster (usually fixed when
> I restarted the cluster manually thru ssh.  If I used capistrano to
> restart the cluster, it would not fix it.
>
> Production server config:
> Apache2
> passenger 2.0.1 (mod_rails)
>
> > which blastall
> /usr/local/bin/blastall
>
> > ls -lsa /usr/local/bin/blastall
> 0 lrwxrwxrwx 1 root root 40 2008-06-25 13:31 /usr/local/bin/blastall
> -> /usr/local/lib/blast-2.2.16/bin/blastall
>
> > ls -lsa /usr/local/lib/blast-2.2.16/bin/blastall
> 4388 -rwxr-xr-x 1 mpr mpr 4488387 2007-03-25 10:28
> /usr/local/lib/blast-2.2.16/bin/blastall
>
> > echo $PATH
>
> /usr/local/bin:/usr/bin:/usr/X11R6/bin:/bin:/usr/games:/opt/gnome/bin:/opt/kde3/bin:/usr/lib/mit/bin:/usr/lib/mit/sbin
>
> Errors:
> production.log:
> Errno::EPIPE (Broken pipe):
>    /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/command.rb:163:in `write'
>    /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/command.rb:163:in `print'
>    /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/command.rb:163:in
> `query_command_popen'
>    /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/command.rb:161:in `popen'
>    /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/command.rb:161:in
> `query_command_popen'
>    /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/command.rb:148:in
> `query_command'
>    /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast.rb:245:in
> `exec_local'
>    /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast.rb:212:in
> `send'
>    /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast.rb:212:in
> `query'
>    /app/models/blast_query.rb:83:in `query'
>
>
> The apache error.log indicates:
> /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast.rb:186:
> command not found: blastall -p blastp -d STYSiteAbstract -p blastp -m
> 7 -e 0.001 -F F -M Blosum62Phosbz -v 100 -b 100 -g F -T F -I T -U F -W
> 3
>
> Thank you,
> Matt
> --
> Matt Scilipoti | Possiamo Consulting LLC | 443-538-8656 | Coaching,
> Training & Development
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