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

Adam Kraut adamnkraut at gmail.com
Wed Jun 25 18:30:19 UTC 2008


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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