Hi Ira,

> Hi Bjoern, 
> 
> I've just done some more testing of my tool with a fresh install and a fresh 
> checkout of galaxy.  After install of this tool
> 
> http://testtoolshed.g2.bx.psu.edu/view/iracooke/package_protk_1_2_5
> 
> I have an env.sh that looks like
> 
> GEM_PATH=/home/vagrant/tool_dependencies/protk/1.2.5/iracooke/package_protk_1_2_5/1100ac98dfd2:$GEM_PATH;
>  export GEM_PATH
> PATH=/home/vagrant/tool_dependencies/protk/1.2.5/iracooke/package_protk_1_2_5/1100ac98dfd2/bin:$PATH;
>  export PATH
> 
> Which seems to be enough for me to run the executables in my gem.    So I 
> must be wrong about GEM_HOME needing to be set ... sorry for the false alarm 
> there.
> 
> The thing that I'm now having trouble with is that all the other 
> set_environment tags in my tool definition are ignored.
> 
> In my tool_dependencies.xml I have
> 
>             <action type="set_environment">
>                     <environment_variable action="prepend_to" 
> name="PATH">$INSTALL_DIR/bin</environment_variable>
>                     <environment_variable action="set_to" 
> name="GEM_HOME">$INSTALL_DIR/</environment_variable>
>                     <environment_variable action="set_to" 
> name="PROTK_BLAST_ROOT">FROMPATH</environment_variable>
>                 </action>
> 
> 
> Admittedly some of that stuff is redundant ( I now realise ) ... but other 
> stuff (eg PROTK_BLAST_ROOT ) is important ... but it gets ignored.
> 
> Is this intended?  Seems like I should be able to use the set_environment 
> action as well as the setup_ruby_environment action in the same tool 
> definition?

It's implemented in:

https://bitbucket.org/galaxy/galaxy-central/pull-request/248/add-more-env-vars-to-the-standard-envsh/diff

If my last PR will be merged, you should be able to do that.
Thanks for spotting that use-case.

Cheers,
Bjoern

> Hope you can clarify.
> 
> Thanks
> 
> Ira
> 
> 
> 
> 
> 
> On 31/10/2013, at 6:06 AM, Ira Cooke <mudflatsoftw...@gmail.com> wrote:
> 
> > Hi Bjoern, 
> > 
> > I saw the same SO post ... but it says that GEM_PATH can be multiple paths 
> > but one of them should be GEM_HOME.  Under your system (I think) GEM_HOME 
> > remains unset?
> > 
> > Anyway ... I'll test again to double check that this is required for my 
> > tool to work.
> > 
> > Cheers
> > Ira
> > 
> > 
> > On 31 Oct 2013, at 6:00 am, Björn Grüning 
> > <bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:
> > 
> >> Hi Ira,
> >> 
> >>> Hi Bjoern, 
> >>> 
> >>> I'll test, 
> >> 
> >> thanks!
> >> 
> >>> but I wonder if the problem is that GEM_PATH is set instead of GEM_HOME.  
> >>>  I think GEM_HOME needs to be set also.  It's  zoo of environment 
> >>> variables out there :)!!
> >> 
> >> Mh according to 
> >> 
> >> http://stackoverflow.com/questions/11277227/whats-the-difference-between-gem-home-and-gem-path
> >> 
> >> GEM_PATH will contain GEM_HOME and GEM_HOME is used for installation,
> >> and I use it for installation of GEMs, See the code. If you think
> >> GEM_HOME is necessary to export I will do so. Otherwise I would not
> >> export to much.
> >> 
> >> Thanks!
> >> Bjoern
> >> 
> >>> Also ... I think GEM_HOME should be set using "set_to" not  "prepend_to" 
> >>> ... 
> >>> 
> >>> I am using the latest galaxy-central (default branch).
> >>> 
> >>> Cheers
> >>> Ira
> >>> 
> >>> 
> >>> 
> >>> 
> >>> On 31 Oct 2013, at 12:33 am, Bjoern Gruening <bjoern.gruen...@gmail.com> 
> >>> wrote:
> >>> 
> >>>> Hi Ira,
> >>>> 
> >>>> that is strange, because PATH and GEM_HOME should be set automatically
> >>>> for you.
> >>>> 
> >>>> Please have a look at
> >>>> https://github.com/bgruening/galaxytools/blob/master/orphan_tool_dependencies/package_ruby2_bioruby_1_4/tool_dependencies.xml
> >>>> http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_ruby2_bioruby_1_4
> >>>>  
> >>>> 
> >>>> That definition results on my test environment in:
> >>>> 
> >>>> GEM_PATH=/home/gruening/projects/code/galaxy-central/tool_deps/bioruby/1.4/bgruening/package_ruby2_bioruby_1_4/0a30368657b1:$GEM_PATH;
> >>>>  export GEM_PATH
> >>>> PATH=/home/gruening/projects/code/galaxy-central/tool_deps/bioruby/1.4/bgruening/package_ruby2_bioruby_1_4/0a30368657b1/bin:$PATH;
> >>>>  export PATH
> >>>> 
> >>>> And the code for that is here:
> >>>> https://bitbucket.org/galaxy/galaxy-central/src/77d58fdd1c2e0dfde374276209279c5e94b1e4c0/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py?at=default#cl-431
> >>>> 
> >>>> Are you using the latest galaxy central?
> >>>> 
> >>>> Regarding RUBYLIB, I think we need to set it to specify the right ruby
> >>>> version, because many can be installed in parallel. Some holds for
> >>>> RUBYHOME or?
> >>>> 
> >>>> I see your point in having it set automatically and came with the
> >>>> attached patch. Here I need to assume that package_ruby_x_x will have
> >>>> RUBYLIB and RUBYHOME specified, but I think that is a save assumption.
> >>>> Nevertheless, we should document it. 
> >>>> 
> >>>> With that new patch you will end up with
> >>>> 
> >>>> RUBYLIB=/home/gruening/projects/code/galaxy-central/tool_deps/ruby/2.0/bgruening/package_ruby_2_0/a0494c6e1c63/lib/;
> >>>>  export RUBYLIB
> >>>> RUBYHOME=/home/gruening/projects/code/galaxy-central/tool_deps/ruby/2.0/bgruening/package_ruby_2_0/a0494c6e1c63;
> >>>>  export RUBYHOME
> >>>> GEM_PATH=/home/gruening/projects/code/galaxy-central/tool_deps/bioruby/1.4/bgruening/package_ruby2_bioruby_1_4/0a30368657b1:$GEM_PATH;
> >>>>  export GEM_PATH
> >>>> PATH=/home/gruening/projects/code/galaxy-central/tool_deps/bioruby/1.4/bgruening/package_ruby2_bioruby_1_4/0a30368657b1/bin:$PATH;
> >>>>  export PATH
> >>>> PATH=/home/gruening/projects/code/galaxy-central/tool_deps/ruby/2.0/bgruening/package_ruby_2_0/a0494c6e1c63/bin:$PATH;
> >>>>  export PATH
> >>>> 
> >>>> 
> >>>> Thanks very much for your feedback. I do not have any ruby repository so
> >>>> I really appropriate your testing!
> >>>> Bjoern
> >>>> 
> >>>> 
> >>>> 
> >>>>> Hi Bjoern, 
> >>>>> 
> >>>>> Ross just gave me some pointers and I realised that I could just set 
> >>>>> these environment variables myself by doing
> >>>>> 
> >>>>> <action type="set_environment">
> >>>>>                  <environment_variable action="prepend_to" 
> >>>>> name="PATH">$INSTALL_DIR/bin</environment_variable>
> >>>>>                  <environment_variable action="set_to" 
> >>>>> name="GEM_HOME">$INSTALL_DIR/</environment_variable>
> >>>>>              </action>
> >>>>> 
> >>>>> In my protk tool definition. 
> >>>>> 
> >>>>> RUBYLIB isn't set ... hopefully this will not be an issue since I guess 
> >>>>> that's mostly just needed for Gem installation/compilation.
> >>>>> 
> >>>>> This part works now :)
> >>>>> 
> >>>>> Thanks
> >>>>> Ira
> >>>>> 
> >>>>> 
> >>>>> On 30/10/2013, at 3:51 PM, Ira Cooke <iraco...@gmail.com> wrote:
> >>>>> 
> >>>>>> Hi Bjoern, 
> >>>>>> 
> >>>>>> Changing the title to reflect the proper topic
> >>>>>> 
> >>>>>> I see now that the gem executables are installed under $INSTALLDIR/bin 
> >>>>>> so I added this to the environment for my protk install. 
> >>>>>> 
> >>>>>> That got me to the point where my executable would run ... but now I'm 
> >>>>>> seeing that in my env.sh file I don't really have my ruby environment 
> >>>>>> setup properly (ie RUBYLIB and GEM_HOME are not set).   This resulted 
> >>>>>> in my tool running but it couldn't find my gem.
> >>>>>> 
> >>>>>> So I tried adding ruby explicitly as a tool dependency for my 
> >>>>>> downstream tool (this seems wrong though ... since it is required by 
> >>>>>> protk ... and if I include protk I should get it automatically 
> >>>>>> right?).  After doing this though I was getting an error on installing 
> >>>>>> protk about "List index out of range". 
> >>>>>> 
> >>>>>> Just to summarize, I can't see how to setup my dependencies properly 
> >>>>>> so that the executables installed by protk get run with the correct 
> >>>>>> environment. 
> >>>>>> 
> >>>>>> The repository I'm trying to install is
> >>>>>> 
> >>>>>> http://testtoolshed.g2.bx.psu.edu/view/iracooke/omssa
> >>>>>> 
> >>>>>> I'm sure I've just got muddled somewhere ... but it feels like I'm 
> >>>>>> just messing around and getting it wrong.  I'd rather do it in the way 
> >>>>>> you envisioned.
> >>>>>> 
> >>>>>> If you could give me some pointers on what I've done wrong it would 
> >>>>>> help alot
> >>>>>> 
> >>>>>> Thanks
> >>>>>> Ira
> >>>>>> 
> >>>>>> 
> >>>>>> 
> >>>>>> 
> >>>>>> On 29/10/2013, at 8:14 PM, Bjoern Gruening <bjoern.gruen...@gmail.com> 
> >>>>>> wrote:
> >>>>>> 
> >>>>>>> 
> >>>>>>>> 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
> >>>>>>>>> 
> >>>>>>>>> 
> >>>>>>>>> 
> >>>>>>> 
> >>>>>>> 
> >>>>>>> 
> >>>>>> 
> >>>>> 
> >>>> 
> >>>> 
> >>>> <add_more_env_vars_to_ruby_install_environment.patch>
> >>> 
> >> 
> >> 
> >> 
> > 
> 



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