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
> >>>>
> >>>>
> >>>>
> >>
> >>
> >>
> >
>
diff -r 9b2268629fa4 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py Tue Oct 29 12:23:14 2013 -0400
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py Wed Oct 30 14:29:12 2013 +0100
@@ -231,14 +231,16 @@
log.debug( 'Invalid file %s specified, ignoring %s action.', env_shell_file_path, action_type )
return cmds
- def environment_dict(self, action_type='template_command'):
+ def environment_dict( self ):
env_vars = dict()
for env_shell_file_path in self.env_shell_file_paths:
if os.path.exists( env_shell_file_path ):
for env_setting in open( env_shell_file_path ):
env_string = env_setting.split( ';' )[ 0 ]
env_name, env_path = env_string.split( '=' )
- env_vars[ env_name ] = env_path
+ for token in env_path.split( ':' ):
+ if not token.strip().startswith('$'):
+ env_vars[ env_name ] = token
else:
log.debug( 'Invalid file %s specified, ignoring template_command action.', env_shell_file_path )
return env_vars
@@ -427,6 +429,25 @@
if return_code:
return
+ installed_env_dict = install_environment.environment_dict()
+ rubylib_path = installed_env_dict.get('RUBYLIB', False)
+ rubyhome_path = installed_env_dict.get('RUBY_HOME', False)
+
+ if not rubylib_path or not rubyhome_path:
+ log.warning( 'Missing RRUBYLIB or/and RUBY_HOME environment variable. Please check if your specified Ruby installation is valid.' )
+
+ modify_env_command_dict = dict( name="RUBYLIB", action="set_to", value=rubylib_path )
+ env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, modify_env_command_dict )
+ return_code = file_append( env_entry, env_file, skip_if_contained=True, make_executable=True )
+ if return_code:
+ return
+
+ modify_env_command_dict = dict( name="RUBYHOME", action="set_to", value=rubyhome_path )
+ env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, modify_env_command_dict )
+ return_code = file_append( env_entry, env_file, skip_if_contained=True, make_executable=True )
+ if return_code:
+ return
+
# Ruby libraries are installed to $INSTALL_DIR (install_dir), we now set the GEM_PATH path to that directory
# TODO: That code is used a lot for the different environments and should be refactored, once the environments are integrated
modify_env_command_dict = dict( name="GEM_PATH", action="prepend_to", value=install_dir )
@@ -435,7 +456,13 @@
if return_code:
return
- modify_env_command_dict = dict( name="PATH", action="prepend_to", value=os.path.join(install_dir, 'bin') )
+ modify_env_command_dict = dict( name="PATH", action="prepend_to", value=os.path.join( install_dir, 'bin' ) )
+ env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, modify_env_command_dict )
+ return_code = file_append( env_entry, env_file, skip_if_contained=True, make_executable=True )
+ if return_code:
+ return
+
+ modify_env_command_dict = dict( name="PATH", action="prepend_to", value=os.path.join( rubyhome_path, 'bin' ) )
env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, modify_env_command_dict )
return_code = file_append( env_entry, env_file, skip_if_contained=True, make_executable=True )
if return_code:
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