> 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 
> > <bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:
> > 
> > Hi Ira,
> > 
> > as far as I can see you missed the <actions> 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:
> > 
> > <?xml version="1.0"?>
> > <tool_dependency>
> >    <package name="protk" version="1.2.5">
> >        <install version="1.0">
> >            <actions>
> >                <action type="setup_ruby_environment">
> >                   <repository changeset_revision="a0494c6e1c63"
> > name="package_ruby_2_0" owner="bgruening"
> > toolshed="http://testtoolshed.g2.bx.psu.edu";>
> >                        <package name="ruby" version="2.0" />
> >                    </repository>
> >                   <package>protk=1.2.6.pre1</package>
> >                </action>
> >            </actions>
> >        </install>
> >    <readme>
> >        Installs version 1.2.5 of the protk rubygem from rubygems.org
> >    </readme>
> >    </package>
> > </tool_dependency>
> > 
> > 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 
> >>> <bjoern.gruen...@pharmazie.uni-freiburg.de> 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?
> >>> 
> >>>        <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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