New subject: Working with setup_ruby_environment tag

31 Oct 2013


      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?
Hope you can clarify.
Thanks
Ira
On 31/10/2013, at 6:06 AM, Ira Cooke mudflatsoftware@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.gruening@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...
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.gruening@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_dependencie...
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/77d58fdd1c2e0dfde37427620927...
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 iracooke@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.gruening@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.gruening@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%22%3E
>>>                   <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.gruening@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/0ef8d86cc3dcec4ee3a9a83edf2... )
>>>>>> 
>>>>>> 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>

Re: [galaxy-dev] Working with setup_ruby_environment tag