Lets wait until this potential problem materializes before we address
it with a sourcing attribute. Dependencies should be appending or
prepending to common paths or otherwise they should be setting up
environment variables that are just required for that individual
package or tool, so there should not be conflicts and if there are
they probably should be corrected at the level of the tool dependency
file.

I will try to find some time to work on this, but if someone else
beats me to it that would be fine too :).

-John

On Thu, Nov 7, 2013 at 6:26 PM, Björn Grüning
<bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:
>
>
>> The potential problem I see here is that environment variables are not
>> name spaced in any way, so if all env.sh files are sourced no matter
>> what, there is the potential for a certain environment variable to get
>> set to a certain dependency version, and then later during the
>> installation (assuming a hierarchy of repository dependencies), the
>> same environment variable gets set to a different version of the same
>> dependency.  I'm not sure how often (if ever) this couls occur, but if
>> it did, it the installation would not be as expected.
>
>
> Mh possible, but really a rare corner case, I think. We could offer a
> 'do-not-source-automatically' tag, to prevent such corner cases.
>
> <repository name="package_expat_2_1" owner="iuc" sourcing="manual|auto">
>
>> > 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.
>
>>
>> Just so I'm clear on this, is this what you want implemented as an
>> enhancement to the setup_* tag sets?
>>
>>
>> <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.
>
> Yes, that would solve John's and my use case.
>
> Thanks Greg!
> Bjoern
>
>
>> >
>> > > >
>> > > > 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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