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 > > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. 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