On Thu, Nov 7, 2013 at 1:46 AM, Björn Grüning
<bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:
> Am Donnerstag, den 07.11.2013, 00:25 -0600 schrieb John Chilton:
>
> My two cents below.
>
> On Wed, Nov 6, 2013 at 4:20 PM, Björn Grüning
> <bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:
>> 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.
>
> I am not sure I understand this paragraph - I have a vague sense I
> agree but is there any chance you could rephrase this or elaborate?
>
> My first use case will be addressed by this suggestion. I had hoped that we
> can create a less verbose syntax.
> If we I specify a package at the top of my xml file:
>
>
>     <package name="expat" version="2.1.0">
>         <repository name="package_expat_2_1" owner="iuc"
> prior_installation_required="True" />
>     </package>
>
> I need to repeat it either in a <action type="set_environment_for_install">
> or in a <action type="setup_perl_environment">.
> My hope was to get rid of these. Once a package definition is
> specified/build, every ENV var is available in any downstream <package>.
> But if there is any downsides or pitfalls this more verbose and explicit
> syntax will work for my usecase.
>

I see, this makes perfect sense to me now, thanks! I certainly agree
that it should have to be spelled out twice unless there is a good
reason. I guess my preference would be to just see it inside of the
setup_perl_environment tag - why should it need to be at the top-level
as well? There could be many implementation details that make this
difficult though, so obviously I delegate to Greg/Dave on this.

>>
>> 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.
>
> We have discussed off list in another thread. Just to summarize my
> thoughts there - I think we should delay this or not make it a
> priority if there are marginally acceptable workarounds that can be
> found for the time being. Getting these four actions to work well as
> sort of terminal endpoints and allow specification as tersely as
> possible should be the primary goal for the time being. You will see
> Perl or Python packages depend on C libraries 10 times more frequently
> than you will find makefiles and C programs depend on complex perl or
> python environments (correct me if I am wrong). Given that there is
> already years worth of tool shed development outlined in existing
> Trello cards - this is just how I would prioritize things (happy to be
> overruled).
>
> Ok point taken. Lets focus on real issue. That use case is just a
> simplification / more structured way to write tool depdendecies,
> its not strictly needed to get my packages done.
> John just to make that use case clearer:
> - You have a package (A) with dependency (B)
> - B is not worth to put it in a extra repository (extra
> tool_dependencies.xml file)
>
> Currently, you are forced to define both in one <package> tag, because if
> you define it in two <package> tags A will not see B.
> The perl and python was a bad example you have that problem with every
> dependency that are not worth to put it in a separate repository.
>
>
> To summarize:
> I'm fine with that approach. It will address my current use case and it
> would be great to have it as proposed by Dave!
>
> Thanks a lot!
> Bjoern
>
>
>>
>>> If so, can you confirm that this should be done for all four currently
>>> supported setup_* action types?
>
> I think it would be best to tackle setup_r_environment and
> setup_ruby_environment first. setup_virtualenv cannot have nested
> elements at this time - it is just assumed to be a bunch of text
> (either a file containing the dependencies or a list of the
> dependencies).
>
> So setup_r_environment and setup_ruby_environment have the same structure:
>
> <setup_ruby_environment>
>   <repository .. />
>   <package .. />
>   <package .. />
> </setup_ruby_environment>
>
> ... but setup_virtualenv is just
>
> <setup_virtualenv>requests=1.20
> pycurl==1.3</setup_virtualenv>
>
> I have created a Trello card for this: https://trello.com/c/NsLJv9la
> (and some other related stuff).
>
> Once that is tackled though, it will make sense to allow
> setup_virtualenv to utilize the same functionality.
>
> Thanks all,
> -John
>
>>
>> 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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>>
>>
>>
>
>
>

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