[BioRuby] command not found: blastall and broken pipe from apache2 and passenger (mod_rails)
Matt Scilipoti
mattscilipoti at possiamo.com
Wed Jun 25 17:53:53 UTC 2008
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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