Thanks Björn,

We'll have to digest this a bit and we'll get back to you.

Greg Von Kuster

On Nov 5, 2013, at 4:35 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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