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

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"; />

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
   - 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 name="trans_proteomic_pipeline" version="4.6.3">
        Here I need the PERL5LIBS

 - 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!

> > Thanks,
> > Bjoern
> Thanks!
> Greg Von Kuster

Attachment: tool_dependencies.xml
Description: XML document

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