Hi All,

The short version of my problem is that I often seem to find myself in a 
situation where my tool gets stuck in the "Installing" phase ... and I don't 
know how to get feedback on it to see where it is failing.  What I guess I'm 
after is just the stdout of the tool installation .. but since the tool install 
never completes I can never see this.  What I usually do is try to recreate the 
environment that galaxy sees during tool install in a normal shell .. and then 
run it manually .. which sometimes tells me the problem ... but not always (see 
below).  

The longer version of my problem is below.  

In my case I am struggling with the following tool 

http://testtoolshed.g2.bx.psu.edu/view/iracooke/package_protk_1_2_5

Which uses the new "setup_ruby_environment" tag ... so the tool should do the 
following

(1) Install the dependency .. Ruby 2.0 ... which it does successfully
(2) Install my protk rubygem from rubygems.org .. which it gets stuck doing.

The last few lines from my galaxy server log during the failed install are;

10.0.2.2 - - [28/Oct/2013:21:54:26 +0000] "POST 
/admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - 
"http://localhost:8088/admin_toolshed/prepare_for_install"; "Mozilla/5.0 
(Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) 
Chrome/30.0.1599.101 Safari/537.36"
[localhost] local: touch 
/home/vagrant/tool_dependencies/ruby/2.0/bgruening/package_ruby_2_0/a0494c6e1c63/env.sh
[localhost] local: echo 
'RUBYLIB=/home/vagrant/tool_dependencies/ruby/2.0/bgruening/package_ruby_2_0/a0494c6e1c63/lib/:$RUBYLIB;
 export RUBYLIB' >> 
/home/vagrant/tool_dependencies/ruby/2.0/bgruening/package_ruby_2_0/a0494c6e1c63/env.sh
10.0.2.2 - - [28/Oct/2013:21:54:30 +0000] "POST 
/admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - 
"http://localhost:8088/admin_toolshed/prepare_for_install"; "Mozilla/5.0 
(Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) 
Chrome/30.0.1599.101 Safari/537.36"
[localhost] local: echo 
'PATH=/home/vagrant/tool_dependencies/ruby/2.0/bgruening/package_ruby_2_0/a0494c6e1c63/bin:$PATH;
 export PATH' >> 
/home/vagrant/tool_dependencies/ruby/2.0/bgruening/package_ruby_2_0/a0494c6e1c63/env.sh
[localhost] local: echo 
'GALAXY_RUBY_HOME=/home/vagrant/tool_dependencies/ruby/2.0/bgruening/package_ruby_2_0/a0494c6e1c63/bin;
 export GALAXY_RUBY_HOME' >> 
/home/vagrant/tool_dependencies/ruby/2.0/bgruening/package_ruby_2_0/a0494c6e1c63/env.sh
[localhost] local: rm -rf ./database/tmp/tmp-toolshed-mtdQaLI7O
ruby version 2.0 installed in 
/home/vagrant/tool_dependencies/ruby/2.0/bgruening/package_ruby_2_0/a0494c6e1c63
[localhost] local: touch 
/home/vagrant/tool_dependencies/ruby/2.0/iracooke/package_protk_1_2_5/876e44dd4609/env.sh
[localhost] local: echo 
'RUBYLIB=/home/vagrant/tool_dependencies/ruby/2.0/bgruening/package_ruby_2_0/a0494c6e1c63/lib/:$RUBYLIB;
 export RUBYLIB' >> 
/home/vagrant/tool_dependencies/ruby/2.0/iracooke/package_protk_1_2_5/876e44dd4609/env.sh
[localhost] local: echo 
'PATH=/home/vagrant/tool_dependencies/ruby/2.0/bgruening/package_ruby_2_0/a0494c6e1c63/bin:$PATH;
 export PATH' >> 
/home/vagrant/tool_dependencies/ruby/2.0/iracooke/package_protk_1_2_5/876e44dd4609/env.sh
[localhost] local: echo 
'GALAXY_RUBY_HOME=/home/vagrant/tool_dependencies/ruby/2.0/bgruening/package_ruby_2_0/a0494c6e1c63/bin;
 export GALAXY_RUBY_HOME' >> 
/home/vagrant/tool_dependencies/ruby/2.0/iracooke/package_protk_1_2_5/876e44dd4609/env.sh
[localhost] local: rm -rf ./database/tmp/tmp-toolshed-mtdJYyhO0
10.0.2.2 - - [28/Oct/2013:21:54:34 +0000] "POST 
/admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - 
"http://localhost:8088/admin_toolshed/prepare_for_install"; "Mozilla/5.0 
(Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) 
Chrome/30.0.1599.101 Safari/537.36"
10.0.2.2 - - [28/Oct/2013:21:47:22 +0000] "POST 
/admin_toolshed/manage_repositories HTTP/1.1" 302 - 
"http://localhost:8088/admin_toolshed/prepare_for_install"; "Mozilla/5.0 
(Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) 
Chrome/30.0.1599.101 Safari/537.36"
10.0.2.2 - - [28/Oct/2013:21:54:37 +0000] "GET 
/admin_toolshed/monitor_repository_installation?tool_shed_repository_ids=f597429621d6eb2b&tool_shed_repository_ids=f2db41e1fa331b3e
 HTTP/1.1" 200 - "http://localhost:8088/admin_toolshed/prepare_for_install"; 
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like 
Gecko) Chrome/30.0.1599.101 Safari/537.36"


With a normal tool install I would see the last line of this output repeat lots 
of times as installation is monitored ... but for some reason in this case 
monitoring just shuts down and I don't see any further updates.

If I recreate the situation on the command-line (eg by manually setting the 
RUBYLIB and GEM_HOME environment variables appropriately I can install my gem 
without any errors.

More details on my setup:

I'm using a vagrant VM for testing which is based on Ubuntu precise64 ... with 
a minimal number of packages installed ... 
(My VM is documented in full here:  
https://bitbucket.org/iracooke/protk_vagrant/src/0ef8d86cc3dcec4ee3a9a83edf230bf0f3b969f8/?at=bare_bones
 )

I'm testing based on the current default branch of galaxy-central .... which I 
regularly tear down and re-clone from scratch ... always with the same result.

Any help or pointers to how to resolve this much appreciated.

Cheers
Ira



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