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

Wed Jun 25 19:59:59 UTC 2008

One way to test the 'www' user's environment would be to switch to  
that user with 'su www' or 'sudo www'.  That way you can check if  
blastall is actually in $PATH.  Regarding the per-server  
configuration, do you use multiple production servers or do you mean  
the full path will be different between development and production?   
For the latter, you can set variables in development.rb and  
production.rb.  Something like BLAST_PATH = '/path/to/blastall' can be  
set per environment and in your application set (factory.blastall =  
BLAST_PATH).  That's the way I do it but there may be better solutions  
out there.  Also, if you reply through the bioruby list more people  
can follow the discussion and offer advice.

Best,
Adam

On Jun 25, 2008, at 3:41 PM, Matt Scilipoti wrote:

> Thank you.
> I tried adding the path to /etc/profile.local (recommended in SUSE),  
> but I was unsure how to ensure that 'www' was using the new  
> profile.  I tried restarting apache, but the error still occurs.    
> Is a server restart necessary?  This is difficult, but possible.
>
> The problem is solved by assigning the full path for blastall  
> (factory.blastall='/usr/local/bin/blastall').  But this solution  
> requires me to provide some configuration for each server, so a path  
> solution would be best.
>
> Thanks again,
> Matt
>
> On Wed, Jun 25, 2008 at 2:30 PM, Adam Kraut <adamnkraut at gmail.com>  
> wrote:
> 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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>
>
>
> -- 
> Matt Scilipoti | Possiamo Consulting LLC | 443-538-8656 | Coaching,  
> Training & Development