subject:"\[galaxy\-dev\] Working with setup_ruby

Re: [galaxy-dev] Working with setup_ruby_environment tag

2013-11-01 Thread Björn Grüning

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_ROOTFROMPATH/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

Re: [galaxy-dev] Working with setup_ruby_environment tag

2013-10-30 Thread Ira Cooke

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
 packageprotk=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

Re: [galaxy-dev] Working with setup_ruby_environment tag

2013-10-30 Thread Bjoern Gruening

Hi Ira,

that is strange, because PATH and GEM_HOME should be set automatically
for you.

That definition results on my test environment in:

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?

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

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

Re: [galaxy-dev] Working with setup_ruby_environment tag

2013-10-30 Thread Björn Grüning

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

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.

That definition results on my test environment in:

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?

With that new patch you will end up with

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

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.

Re: [galaxy-dev] Working with setup_ruby_environment tag

2013-10-30 Thread Ira Cooke

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.

That definition results on my test environment in:

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?

With that new patch you will end up with

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

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.

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,

Re: [galaxy-dev] Working with setup_ruby_environment tag

2013-10-30 Thread Ira Cooke

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

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

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 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

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.

That definition results on my test environment in:

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?

With that new patch you will end up with

Thanks very much for your feedback. I do not have any ruby repository so
I really appropriate

[galaxy-dev] Working with setup_ruby_environment tag

2013-10-29 Thread Ira Cooke

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
  packageprotk=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

Re: [galaxy-dev] Working with setup_ruby_environment tag

Re: [galaxy-dev] Working with setup_ruby_environment tag

Re: [galaxy-dev] Working with setup_ruby_environment tag

Re: [galaxy-dev] Working with setup_ruby_environment tag

Re: [galaxy-dev] Working with setup_ruby_environment tag

Re: [galaxy-dev] Working with setup_ruby_environment tag

[galaxy-dev] Working with setup_ruby_environment tag

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