Hi Geert,

Hi,

Is there a default notation to specify perl modules (threading modules) in a tool configuration or in a submission to the toolshed?

I've got some tools to share that make extensive use of these modules, and they are not default in a perl distribution. Hence, I'd like to inform the users that they need to install these modules (or that they get installed by the the toolshed using cpan ?)

I'm not a perl erxpert but I will shortly explain what I try to do with R packages and how it works with python modules.

For python we can install every package to a separate directory and add it to PYTHONPATH. Once it is in PYTHONPATH every script can import the module. Important is that we have control over the version of the python module (we can fetch an archived tarball or specify the version with pip).

https://github.com/bgruening/galaxytools/blob/master/orphan_tool_dependencie...

In R that is not so easy to do, because R assumes that the User always want to install the latest version. But in Galaxy we need to install every version at any time to enable reproducibility. What we did is to archive the R tarballs in a github repository and download them from there, install the tarballs manually and add it to R_LIBS. Once it is in R_LIBS we can import it in any scripts.

https://github.com/bgruening/galaxytools/blob/master/orphan_tool_dependencie...

You can probably do the same in Perl, also it does not seem as easy as in python. Please have a look here:

http://stackoverflow.com/questions/540640/how-can-i-install-a-cpan-module-in... http://learn.perl.org/faq/perlfaq8.html#How-do-I-keep-my-own-module-library-...

Once you have done that you can add the library to PERL5LIB any you should be done.

Please also consider to create an orphan tool dependency if the perl library is common and the chance is high that other developers are also interested to use that package. The two examples above are orphan tool dependencies and are used by other packages.

http://wiki.galaxyproject.org/DefiningRepositoryDependencies

Hope that helps a little bit! Bjoern

Best,

Geert

Hi,

that is just great! Good to see perl packages are working nicely for you!

Thanks! Bjoern

Hij Bjoern,

I finally got around to trying your suggestions. It worked out nicely, so thanks for that!

I've added the modules as an example to the toolshed, as I didn't find an example yet. Three modules (threads, threads::shared and Thread::Queue) are bundled in a dependency definition called package_perl_threading.

Best,

Geert ________________________________________ Van: Geert Vandeweyer [geert.vandeweyer2@ua.ac.be] Verzonden: donderdag 8 augustus 2013 9:17 Aan: galaxy-dev@lists.bx.psu.edu Onderwerp: shed tool dependencies

Hi,

Is there a default notation to specify perl modules (threading modules) in a tool configuration or in a submission to the toolshed?

I've got some tools to share that make extensive use of these modules, and they are not default in a perl distribution. Hence, I'd like to inform the users that they need to install these modules (or that they get installed by the the toolshed using cpan ?)

Best,

Geert

--

Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726