On Tue, Sep 17, 2013 at 3:03 AM, Bjoern Gruening
<bjoern.gruen...@gmail.com> wrote:
> Hi all,
>
> that is now implemented in:
>
> https://bitbucket.org/galaxy/galaxy-central/pull-request/219/implementation-of-the-a-r_environment-to/diff
>
> Any comments are much appreciated.

Fantastic work, I like this a lot.

> Is it still to complicated?
>
> Greg and Dave can we refactor the set_env_var functionality so we can
> set this automatically for the r-environment or even the
> python-environment?

Greg and/or Dave's comments on this point would be great. But, just to
clarify this point the Python version does set its environment
automatically:

https://bitbucket.org/galaxy/galaxy-central/src/48fad71361b3075c85c7d365dd52c106cabad73a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py?at=default#cl-342

My vote is that you just add a similar command for R - even if the
code for doing so is sort of verbose for right now - and then once the
R/Ruby/Python (Perl?) stuff is added we revisit and refactor to remove
duplicated code. Again, Greg or Dave should weigh in though :).

Thanks Bjoern, great stuff!

-John

>
> If that patch will be merged my plan is to write a short wiki page with
> a 'best practice for R package development'. Furthermore, I will try to
> create a small script that will obtain the dependency tree of all the
> required tarballs.
>
> Speaking of tarballs, currently I just download them and host them in a
> separate github repository. That is not ideal and I will start a new
> discussion in one of my next mails about one central place.
>
> Thanks!
> Bjoern
>
>
>
>> Cool work. I was thinking something like this would be needed
>> (https://github.com/viking/Renv), but I like your approach better.
>>
>> The one think I would say is that, like Python with setup_venv, if
>> this is best practices Galaxy should provide some high level support
>> for this. I was thinking your package install could look something
>> like this:
>>
>> <package name="deseq2" version="1.0.17">
>>   <install version="1.0">
>>     <actions>
>>         <action type="setup_r_environment">
>>           <base_r changeset_revision="bae5c9880b71"
>> name="package_r_3_0_1" owner="bgruening"
>> toolshed="http://testtoolshed.g2.bx.psu.edu"; />
>>           
>> <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGenerics_0.6.0.tar.gz</r_package>
>>           
>> <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/IRanges_1.18.2.tar.gz</r_package>
>>           
>> <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/GenomicRanges_1.12.4.tar.gz</r_package>
>>           
>> <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/Rcpp_0.10.4.tar.gz</r_package>
>>           
>> <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/RcppArmadillo_0.3.900.0.tar.gz</r_package>
>>           
>> <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/locfit_1.5-9.1.tar.gz</r_package>
>>           
>> <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/Biobase_2.20.1.tar.gz</r_package>
>>           
>> <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/DBI_0.2-7.tar.gz</r_package>
>>           
>> <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/RSQLite_0.11.4.tar.gz</r_package>
>>           
>> <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/AnnotationDbi_1.22.6.tar.gz</r_package>
>>           
>> <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/xtable_1.7-1.tar.gz</r_package>
>>           
>> <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/XML_3.98-1.1.tar.gz</r_package>
>>           
>> <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/annotate_1.38.0.tar.gz</r_package>
>>           
>> <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/genefilter_1.42.0.tar.gz</r_package>
>>           
>> <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/RColorBrewer_1.0-5.tar.gz</r_package>
>>           
>> <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/DESeq2_1.0.18.tar.gz</r_package>
>>         </action>
>>         <!-- Galxay provides plumbing for making package directory,
>> settings PATH and R_LIBS and running install.packages via Rscript -->
>>     </actions>
>>   </install>
>> </package>
>>
>> Obviously, someone would need to implement the action type
>> "setup_r_environment", but frankly I believe you have already done
>> most (or at least a large amount) of the work in demonstrating how it
>> should be implemented and that it is feasible.
>>
>> -John
>>
>> On Mon, Aug 5, 2013 at 11:10 AM, Bjoern Gruening
>> <bjoern.gruen...@gmail.com> wrote:
>> > Dear Commissioners,
>> >
>> > I have spent some time in prototyping an R wrapper for DESeq2 and RPy2.
>> > In the end I will skip RPy2 as dependency, because I will include a pure
>> > R-script. Currently it's more or less a prototype. My main Aim was to
>> > make R and RPy2 a first class citizen in the Tool Shed and to make it
>> > easy to write tools in R in a reproducible way.
>> >
>> > The result looks really simple, imho:
>> > http://testtoolshed.g2.bx.psu.edu/view/bgruening/deseq2
>> >
>> > As Ross already investigated [1] ... to make the R and a R package
>> > really reproducible is really hard or not possible at all with the R
>> > package management system. What I did is to track the dependencies down
>> > and upload the tarballs to some webspace and manually install them via
>> > install.packages().
>> >
>> > http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_deseq2_1_0_17
>> >
>> > Steps to write a R-wrapper:
>> > - link to the package_r_3_0_1
>> > - (optionally link to package_rpy2_2_3_6)
>> > - upload all dependencies of your R package to github/bitbucket ...
>> > - write a wrapper that is fetching these packages and install them in
>> > the right order to your own R package repository, not the basic R
>> > installation
>> >
>> > What do you think, is that to complicated? If you agree witch such an
>> > approach I will write a "best practice" wiki page.
>> >
>> > As a side note, this is using my 'complicated' R orphan tool dependency
>> > with atlas dependency. But I tweaked it a little bit with the new tool
>> > shed features to fail silently and fallback to a non-atlas mode. So OSX
>> > users, should be able to install it, finally :)
>> >
>> > Thanks!
>> > Bjoern
>> >
>> > [1] Subject: "Re: [galaxy-iuc] [Bioc-devel] finding specific (outdated!)
>> > bioc package archives?"
>> >
>> > _______________________________________________
>> > galaxy-iuc mailing list
>> > galaxy-...@lists.bx.psu.edu
>> > http://lists.bx.psu.edu/listinfo/galaxy-iuc
>
>
>
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