Re: [galaxy-dev] What to do with toolshed tools that get stuck "Installing"
> Ahhh ... Thanks .. I can't believe I missed that. Thanks for spotting it. No problem! > I'm not sure I understand enough about how this works to answer your > ruby_home question. Ill play with this more tomorrow and see how things work > with my tools and maybe have more feedback then Sure, thanks for working on that! Here is the promised trello card: https://trello.com/c/l9ZlGa8R Ciao, Bjoern > Cheers > Ira > > > > On 29 Oct 2013, at 7:17 pm, Björn Grüning > > wrote: > > > > Hi Ira, > > > > as far as I can see you missed the tag. That results in no log > > message at all, since no action type is executed. Galaxy should probably > > give an error here. Or better validate that during tool upload. I will > > fill a Trello Card for it. > > > > The following code snipped worked for me: > > > > > > > > > > > > > > > >> name="package_ruby_2_0" owner="bgruening" > > toolshed="http://testtoolshed.g2.bx.psu.edu";> > > > > > > protk=1.2.6.pre1 > > > > > > > > > >Installs version 1.2.5 of the protk rubygem from rubygems.org > > > > > > > > > > Keep in mind that the repository tag should be filled. If you have a > > actions and action tag it will be filled automatically by the TS during > > upload. But better to check :) > > > > To populate the RUBY_HOME env var ... do you think its better to set it > > via the installation automatically? My idea was to just "require" ruby > > in the tool? If you want to set it in your protk definition you need to > > use the $ENV[] construct. > > > > Cheers, > > Bjoern > > > >> Hi Bjoern, > >> > >> Thanks ... I thought I had to do that in order to make the > >> GALAXY_RUBY_HOME variable available ... nice that it's not necessary. > >> > >> I've updated the tool on the test toolshed and have rerun my test but > >> unfortunately the problem is still there. > >> > >> Cheers > >> Ira > >> > >> > >>> On 29/10/2013, at 10:06 AM, Björn Grüning > >>> wrote: > >>> > >>> 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? > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> 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 +] "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 +] "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
Re: [galaxy-dev] What to do with toolshed tools that get stuck "Installing"
Ahhh ... Thanks .. I can't believe I missed that. Thanks for spotting it. I'm not sure I understand enough about how this works to answer your ruby_home question. Ill play with this more tomorrow and see how things work with my tools and maybe have more feedback then Cheers Ira > On 29 Oct 2013, at 7:17 pm, Björn Grüning > wrote: > > Hi Ira, > > as far as I can see you missed the tag. That results in no log > message at all, since no action type is executed. Galaxy should probably > give an error here. Or better validate that during tool upload. I will > fill a Trello Card for it. > > The following code snipped worked for me: > > > > > > > >name="package_ruby_2_0" owner="bgruening" > toolshed="http://testtoolshed.g2.bx.psu.edu";> > > > protk=1.2.6.pre1 > > > > >Installs version 1.2.5 of the protk rubygem from rubygems.org > > > > > Keep in mind that the repository tag should be filled. If you have a > actions and action tag it will be filled automatically by the TS during > upload. But better to check :) > > To populate the RUBY_HOME env var ... do you think its better to set it > via the installation automatically? My idea was to just "require" ruby > in the tool? If you want to set it in your protk definition you need to > use the $ENV[] construct. > > Cheers, > Bjoern > >> Hi Bjoern, >> >> Thanks ... I thought I had to do that in order to make the GALAXY_RUBY_HOME >> variable available ... nice that it's not necessary. >> >> I've updated the tool on the test toolshed and have rerun my test but >> unfortunately the problem is still there. >> >> Cheers >> Ira >> >> >>> On 29/10/2013, at 10:06 AM, Björn Grüning >>> wrote: >>> >>> 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? >>> >>> >>> >>> >>> >>> >>> >>> 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 +] "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 +] "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-toolsh
Re: [galaxy-dev] What to do with toolshed tools that get stuck "Installing"
Hi Ira, as far as I can see you missed the tag. That results in no log message at all, since no action type is executed. Galaxy should probably give an error here. Or better validate that during tool upload. I will fill a Trello Card for it. The following code snipped worked for me: http://testtoolshed.g2.bx.psu.edu";> protk=1.2.6.pre1 Installs version 1.2.5 of the protk rubygem from rubygems.org Keep in mind that the repository tag should be filled. If you have a actions and action tag it will be filled automatically by the TS during upload. But better to check :) To populate the RUBY_HOME env var ... do you think its better to set it via the installation automatically? My idea was to just "require" ruby in the tool? If you want to set it in your protk definition you need to use the $ENV[] construct. Cheers, Bjoern > Hi Bjoern, > > Thanks ... I thought I had to do that in order to make the GALAXY_RUBY_HOME > variable available ... nice that it's not necessary. > > I've updated the tool on the test toolshed and have rerun my test but > unfortunately the problem is still there. > > Cheers > Ira > > > On 29/10/2013, at 10:06 AM, Björn Grüning > wrote: > > > 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? > > > > > > > > > > > > > > > > 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 +] "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 +] "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/irac
Re: [galaxy-dev] What to do with toolshed tools that get stuck "Installing"
Hi Bjoern, Thanks ... I thought I had to do that in order to make the GALAXY_RUBY_HOME variable available ... nice that it's not necessary. I've updated the tool on the test toolshed and have rerun my test but unfortunately the problem is still there. Cheers Ira On 29/10/2013, at 10:06 AM, Björn Grüning wrote: > 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? > > > > > > > > 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 +] "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/:$RUBYLIB; >> export RUBYLIB' >> >> /home/vagrant/tool_dependencies/ruby/2.0/bgruening/package_ruby_2_0/a0494c6e1c63/env.sh >> 10.0.2.2 - - [28/Oct/2013:21:54:30 +] "POST >> /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - >> "http://localhost:8088/admin_toolshed/prepare_for_install"; "Mozilla/5.0 >> (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) >> Chrome/30.0.1599.101 Safari/537.36" >> [localhost] local: echo >> 'PATH=/home/vagrant/tool_dependencies/ruby/2.0/bgruening/package_ruby_2_0/a0494c6e1c63/bin:$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 +] "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 +] "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/3
Re: [galaxy-dev] What to do with toolshed tools that get stuck "Installing"
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? 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 +] "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/:$RUBYLIB; > export RUBYLIB' >> > /home/vagrant/tool_dependencies/ruby/2.0/bgruening/package_ruby_2_0/a0494c6e1c63/env.sh > 10.0.2.2 - - [28/Oct/2013:21:54:30 +] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://localhost:8088/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/30.0.1599.101 Safari/537.36" > [localhost] local: echo > 'PATH=/home/vagrant/tool_dependencies/ruby/2.0/bgruening/package_ruby_2_0/a0494c6e1c63/bin:$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 +] "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 +] "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 +] "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" > >
[galaxy-dev] What to do with toolshed tools that get stuck "Installing"
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 +] "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/:$RUBYLIB; export RUBYLIB' >> /home/vagrant/tool_dependencies/ruby/2.0/bgruening/package_ruby_2_0/a0494c6e1c63/env.sh 10.0.2.2 - - [28/Oct/2013:21:54:30 +] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://localhost:8088/admin_toolshed/prepare_for_install"; "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/30.0.1599.101 Safari/537.36" [localhost] local: echo 'PATH=/home/vagrant/tool_dependencies/ruby/2.0/bgruening/package_ruby_2_0/a0494c6e1c63/bin:$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 +] "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 +] "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 +] "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
