Hi Bjoern, 

I'll test, 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 :)!!

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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