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> > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. 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