Say option 3 is the way to go, would you say every new version of an R
package should be wrapped in a new galaxy package (and give them names
like "matrixStats_0_10_0") or create one package ("matrixStats") and
update that one if a new version is worth an update. In the first way
there would be an enormous amount of packages ;)Also if you do need an external R script as you say, how would I construct my tool_dependencies.xml to execute R code? And last, if that approach doesn't work out for me, how can copy a file in the repository to the installation dir? (to execute it with Rscript) Many thanks, Stef ----- Original message ----- From: "Kandalaft, Iyad" <iyad.kandal...@agr.gc.ca> To: Stef van Lieshout <stefvanliesh...@fastmail.fm>, "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Subject: RE: [galaxy-dev] R bioconductor dependencies when creating toolshed installation Date: Mon, 16 Jun 2014 18:19:46 +0000 I would typically recommend Option 3 as it is the best practice. However, human resources limit this as a viable option even though this should be the "Gold Standard" that you aim for. This allows you to reuse the dependencies later for other tool wrappers AND you don't have to re-install dependencies every time you make a modification to your tool wrapper repository. While briefly looking at Bioconductor, it seems that they keep old version of packages (ex: http://www.bioconductor.org/packages/2.13/data/experiment/bin/windows/contrib/3.0/AmpAffyExample_1.2.13.zip), where using the URLs directly might be advantageous if their BiocLite doesn't allow you to define which version to install. You don't necessarily need to have an external R script for the installation because many of these commands can be done within the tool_dependencies.xml. Regards, Iyad Kandalaft Microbial Biodiversity Bioinformatics Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada 960 Carling Ave.| 960 Ave. Carling Ottawa, ON| Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel iyad.kandal...@agr.gc.ca Telephone | Téléphone 613-759-1228 Facsimile | Télécopieur 613-759-1701 Teletypewriter | Téléimprimeur 613-773-2600 Government of Canada | Gouvernement du Canada -----Original Message----- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Stef van Lieshout Sent: Monday, June 16, 2014 10:04 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] R bioconductor dependencies when creating toolshed installation Hi all, I'm running into some difficulties on how to setup the installation procedure for a galaxy tool which executes an R script and has certain dependencies (mainly bioconductor packages). R can deal with dependencies, packages can be installed with install.packages (has a "dependencies" argument) or biocLite() for bioconductor packages. Yet, now I want my tool to be available at toolsheds. To do this I see several options: 1) setting up tool_dependencies.xml with "R CMD INSTALL" for all packages. BUT: need to download all dependencies before install, and can older versions still be downloaded? Maybe need to upload them to toolshed too.. 2) setting up tool_dependencies.xml to call an installation script with Rscript (where I could use install.packages), BUT: Dependencies are taken care of. But how do I select specific (older) versions, because if I dont, installing at different time can give different version. 3) creating a repository for each package and have all of them as requirement in my galaxy tool. BUT: a lot of work for a lot of dependencies All have pros and cons, how do people deal with this? Stef ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
