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

[Matt Scilipoti]

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