Hi,

For me, three solutions : - You can find existing packages which will install your library (https://testtoolshed.g2.bx.psu.edu/view/jeltje/package_dnacopy_1_40_0/118417... https://testtoolshed.g2.bx.psu.edu/view/jeltje/package_dnacopy_1_40_0/118417199f06). So you will just need to link a requirement (https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Crequirements... https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Crequirements.3E_tag_set) and a tool_dependencies.xml file - If not, you can write your own package. But thanks to Ross Lazarus, to deal with dependencies of dependencies of dependencies, there is a tool for that https://testtoolshed.g2.bx.psu.edu/view/fubar/biocdepgen_r_3_1_2/faafc60f3d6... https://testtoolshed.g2.bx.psu.edu/view/fubar/biocdepgen_r_3_1_2/faafc60f3d6a - If you lack of time, you install R and needed libraries on your serveur.

Unfortunately, I can’t explain you why you couldn’t install your library through your script because R use to allow installing in the user home.

Gildas

----------------------------------------------------------------- Gildas Le Corguillé - Bioinformatician/Bioanalyste Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424 Place Georges Teissier 29680 Roscoff FRANCE tel: +33 2 98 29 23 81 http://abims.sb-roscoff.fr ------------------------------------------------------------------

Le 26 févr. 2016 à 09:03, Xianrong Wong wongxr@gmail.com a écrit :

Hi, I am trying to package an R script (that requires certain R packages) into a galaxy tool. Any advice would be deeply appreciated!

I have tested it on planemo and it works. When I tried the version I uploaded onto the toolshed, I got an error saying that the R packages do not exist. I next added the following lines to the R script:

source("https://bioconductor.org/biocLite.R https://bioconductor.org/biocLite.R")

biocLite()

biocLite(c("DNAcopy", "preprocessCore"))

and I got the following error when running the installed tool on galaxy:

Installing package(s) ‘DNAcopy’, ‘preprocessCore’ Warning in install.packages(pkgs = doing, lib = lib, ...) : 'lib = "/usr/local/lib/R/site-library"' is not writable Error in install.packages(pkgs = doing, lib = lib, ...) : unable to install packages Calls: biocLite ... .biocLiteInstall -> .reposInstall -> install.packages Execution halted ___________________________________________________________ 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: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

I will update this post with more informations as needed:

https://biostar.usegalaxy.org/p/16259/

Thanks, Bjoern

Am 26.02.2016 um 09:37 schrieb Gildas Le Corguillé:

Hi,

For me, three solutions :

• You can find existing packages which will install your library

(https://testtoolshed.g2.bx.psu.edu/view/jeltje/package_dnacopy_1_40_0/118417...). So you will just need to link a requirement (https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Crequirements...) and a tool_dependencies.xml file

• If not, you can write your own package. But thanks to Ross Lazarus,

to deal with dependencies of dependencies of dependencies, there is a tool for that https://testtoolshed.g2.bx.psu.edu/view/fubar/biocdepgen_r_3_1_2/faafc60f3d6...

• If you lack of time, you install R and needed libraries on your serveur.

Unfortunately, I can’t explain you why you couldn’t install your library through your script because R use to allow installing in the user home.

Gildas

---

Gildas Le Corguillé - Bioinformatician/Bioanalyste Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424 Place Georges Teissier 29680 Roscoff FRANCE tel: +33 2 98 29 23 81 http://abims.sb-roscoff.fr

---

...

Le 26 févr. 2016 à 09:03, Xianrong Wong <wongxr@gmail.com mailto:wongxr@gmail.com> a écrit :

Hi, I am trying to package an R script (that requires certain R packages) into a galaxy tool. Any advice would be deeply appreciated!

I have tested it on planemo and it works. When I tried the version I uploaded onto the toolshed, I got an error saying that the R packages do not exist. I next added the following lines to the R script:

source("https://bioconductor.org/biocLite.R")

biocLite()

biocLite(c("DNAcopy","preprocessCore"))

and I got the following error when running the installed tool on galaxy:

Installing package(s) ‘DNAcopy’, ‘preprocessCore’ Warning in install.packages(pkgs = doing, lib = lib, ...) : 'lib = "/usr/local/lib/R/site-library"' is not writable Error in install.packages(pkgs = doing, lib = lib, ...) : unable to install packages Calls: biocLite ... .biocLiteInstall -> .reposInstall -> install.packages Execution halted ___________________________________________________________ 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: https://lists.galaxyproject.org/

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: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/