Hi Ira,
I can reproduce that error here, will try to study it tomorrow more
deeply. For the meantime can you try to remove the following lines?
<action type="set_environment_for_install">
<repository name="package_ruby_2_0" owner="bgruening">
<package name="ruby" version="2.0" />
</repository>
</action>
It's not necessary.
Will get back to you tomorrow.
Bjoern
> 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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