Hi Dave,

> We're thinking that the following approach makes the most sense:
> 
> <action type="setup_perl_environment"> OR <action 
> type="setup_r_environment"> OR <action type="setup_ruby_environment"> OR 
> <action type="setup_virtualenv">
>      <repository changeset_revision="978287122b91" 
> name="package_perl_5_18" owner="iuc" 
> toolshed="http://testtoolshed.g2.bx.psu.edu";>
>          <package name="perl" version="5.18.1" />
>      </repository>
>      <repository changeset_revision="8fc96166cddd" 
> name="package_expat_2_1" owner="iuc" 
> toolshed="http://testtoolshed.g2.bx.psu.edu";>
>          <package name="expat" version="2.1" />
>      </repository>
> </action>
> 
> For all <repository> tag sets contained within these setup_* tags, the 
> repository's env.sh would be pulled in for the setup of the specified 
> environment without requiring a set_environment_for_install action type.
> 
> Would this work for your use cases?

Yes, the first one. But its a little bit to verbose or? Include the perl
repository in a setup_perl environment should be implicit or? We can
assume that this need to be present.
Do you have example why sourcing every <repository> by default can be
harmful? It would make such an installation so much easier and less
complex.

Also that did not solve the second use case. If have two <packages> one
that is installing perl libraries and the second a binary that is
checking or that needs these perl libs.

> If so, can you confirm that this should be done for all four currently 
> supported setup_* action types?

I think it will solve my current issues.

> Based on your response, Greg or I will implement this as soon as possible.

Thanks!
Bjoern

>     --Dave B.
> 
> On 11/06/2013 03:05 AM, Björn Grüning wrote:
> > Hi John,
> >
> >> Perl complicates things, TPP complicates things greatly.
> >
> > So true, so true ...
> >
> >> Bjoern, can I ask you if this hypothetical exhibits the same problem
> >> and can be used to reason about these things more easily and drive a
> >> test implementation.
> >
> > Yes to both questions :)
> >
> >> So right now, Galaxy has setup_virtualenv which will build and install
> >> Python packages in a virtual environment. However, some Python
> >> packages have C library dependencies that could prevent them from
> >> being installed.
> >>
> >> As a specific example - take PyTables (install via "pip install
> >> tables") - which is a package for managing hierarchical datasets. If
> >> you try to install this with pip the way Galaxy will - it will fail if
> >> you do not have libhdf5 installed. So at a high-level, it would be
> >> nice if the tool shed had a libhdf5 definition and the dependencies
> >> file had some mechanism for declaring libhdf5 should be installed
> >> before a setup_virtualenv containing "tables" and its environment
> >> configured properly so the pip install succeeds (maybe just
> >> LD_LIBRARY_PATH needs to be set).
> >
> > Indeed, same problem. I think we have this problem in every high-level
> > install methodm because <set_environment_for_install> is not allowed as
> > first action tag.
> >
> > Can you think of any case where ENV vars can conflict with each other,
> > besides set_to, and assuming that we source every env.sh file by default
> > for every specified <package>.
> >
> > Cheers,
> > Bjoern
> >
> >> -John
> >>
> >>
> >> On Tue, Nov 5, 2013 at 3:35 PM, Björn Grüning
> >> <bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:
> >>> Hi Greg,
> >>>
> >>>
> >>> Hello Bjoern,
> >>>
> >>>
> >>> On Nov 5, 2013, at 12:13 PM, Bjoern Gruening <bjoern.gruen...@gmail.com>
> >>> wrote:
> >>>
> >>>> Hi Greg,
> >>>>
> >>>> I'm right now in implementing a setup_perl_environment and stumbled about
> >>>> a tricky problem (that is not only related to perl but also for ruby, 
> >>>> python
> >>>> and R).
> >>>>
> >>>> The Problem:
> >>>> Lets assume a perl package (A) requires a xml parser written in C/C++ 
> >>>> (Z).
> >>>> (Z) is a dependency that I can import but as far as I can see there is no
> >>>> way to call set_environment_for_install before setup_perl_environment,
> >>>> because setup_perl_environment defines an installation type.
> >>>
> >>>
> >>> The above is fairly difficult to understand - can you provide an actual 
> >>> xml
> >>> recipe that provides some context?
> >>>
> >>> Attached, please see a detailed explanation at the bottom.
> >>>
> >>>
> >>>
> >>>>
> >>>> I would like to discuss that issue to get a few ideas. I can think about
> >>>> these solutions:
> >>>>
> >>>> - hackish solution:
> >>>> I can call install_environment.add_env_shell_file_paths( action_dict[
> >>>> 'env_shell_file_paths' ] ) inside of the setup_*_environment path and 
> >>>> remove
> >>>> it from action type afterwards
> >>>
> >>> Again, it's difficult to provide good feedback on the above approach 
> >>> without
> >>> an example recipe.  However, your "hackish solution" term probably means 
> >>> it
> >>> is not ideal.  ;)
> >>>
> >>> :)
> >>>
> >>>>
> >>>> - import all env.sh variables from every (package) definition. Regardless
> >>>> if set_environment_for_install is set or not.
> >>>
> >>>
> >>> I don't think the above approach would be ideal.  It seems that it could
> >>> fairly easily create conflicting environment variables within a single
> >>> installation,
> >>> so the latest value for an environment variable may not be what is 
> >>> expected.
> >>>
> >>> What means conflicting ENV vars, I only can imagine multiple set_to that
> >>> overwrite each other. append_to and prepend_to should be save or?
> >>>
> >>>
> >>>
> >>>> I must admit, I do not understand why set_environment_for_install is
> >>>> actually needed. I think we can assume that if I specify a
> >>>>
> >>>>      <package name="R_3_0_1" version="3.0.1">
> >>>>          <repository name="package_r_3_0_1" owner="iuc"
> >>>> prior_installation_required="True" />
> >>>>      </package>
> >>>>
> >>>> I want the ENV vars sourced.
> >>>
> >>> Hmmm…so you are saying that you want the be able to define the above
> >>> <package> tag set inside of an <actions> tag set and have everything work?
> >>>
> >>>
> >>> Oh no, I mean just have it as package like it is but source the env.sh 
> >>> file
> >>> for every other <package> set automatically. So you do not need
> >>> <set_environment_for_install>.
> >>>
> >>> In the attached example:
> >>>      <package name="expat" version="2.1.0">
> >>>          <repository changeset_revision="8fc96166cddd"
> >>> name="package_expat_2_1" owner="iuc" prior_installation_required="True"
> >>> toolshed="http://testtoolshed.g2.bx.psu.edu"; />
> >>>      </package>
> >>>
> >>> Is not imported with <set_environment_for_install> so its actually useless
> >>> (now). But the env.sh needs to be sourced during the
> >>> "setup_perl_environment" part.
> >>>
> >>> I think this may cause problems because  I believe the
> >>> <set_environment_for_install> tag set restricts activity to only the time
> >>> when a dependent
> >>> repository will be using the defined environment from the required
> >>> repository in order to compile one or more of it's dependencies.
> >>> Eliminating this restriction may cause problems after compilation.  
> >>> ALthough
> >>> I cannot state this as a definite fact.
> >>>
> >>>> Furthermore, that can solve an other issue: Namely, the need of ENV vars
> >>>> from a package definition in the same file. Lets imagine package P has
> >>>> dependency D and you want to download compile both in one
> >>>> tool_dependencies.xml file.
> >>>> You can either do it in one <package> definition or you need to split 
> >>>> them
> >>>> up in 2 tool_dependencies.xml files, rigth?
> >>>> Maybe we can just assume a strict order in a tool_dependencies.xml file,
> >>>> where every ENV vars are sourced for the following one? Does that make
> >>>> sense?
> >>>
> >>> It may make sense, but without an example it's diffiecult to answer this 
> >>> for
> >>> sure.  Can you provide some xml recipes that use your different proposals?
> >>>
> >>>
> >>> Sure, attached.
> >>> Its quite complicated.
> >>>
> >>> - TPP needs libgd to compile C-Code (no problem).
> >>> - TPP needs some perl libs and perl -> "setup_perl_environment" (at 
> >>> runtime)
> >>>     - no problem until one of these perl packages (here XML-Parser) needs 
> >>> a C
> >>> library (expat)
> >>>    - I don't see how to source expat during "setup_perl_environment"
> >>> - TPP needs perl (at compile time) ... It would be more readable or 
> >>> logical
> >>> to separate this recipe into two parts: TPP and Perl libraries
> >>>
> >>> Something like that:
> >>>      <package name="trans_proteomic_pipeline_perl_libs" version="4.6.3">
> >>>          .....
> >>>          set PERL5LIBS
> >>>     </package>
> >>>      <package name="trans_proteomic_pipeline" version="4.6.3">
> >>>          ....
> >>>          Here I need the PERL5LIBS
> >>>      </package>
> >>>
> >>> - I don't see any way to get the PERL5LIBS from the perl libraries into a
> >>> separate <package> section which tries to compile TPP.
> >>>
> >>>> Any other ideas?
> >>>
> >>> Not yet, but possibly after your next response.  ;)
> >>>
> >>> :) Here we go!
> >>> Thanks Greg!
> >>> Bjoern
> >>>
> >>>
> >>>
> >>>> Thanks,
> >>>> Bjoern
> >>>
> >>> Thanks!
> >>>
> >>> Greg Von Kuster
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> ___________________________________________________________
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> >
> >
> >
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