Re: [galaxy-dev] packaging R scripts

[Björn Grüning]

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_0/118417199f06).
> So you will just need to link a requirement
> (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/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 > > 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/
> 
___
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/

Re: [galaxy-dev] packaging R scripts

[Björn Grüning]

Hi Xianrong and Gildas,

this method works, but is a little bit outdated.
Please use the setup_r_environment like used here:

https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_deseq2_1_8_2/tool_dependencies.xml

You can use this script with small modifications to create you such a
file from scratch:

https://github.com/bioarchive/aRchive_source_code/blob/master/get_galaxy_tool_dependencies.py

At least to get started.

An other possibility is to use conda dependencies. So if you R package
is already in conda/bioconda you don't need a tool_depenencies.xml file
at all. Just specify the requirement tag in your tool with the conda
package name and version and activate conda in Galaxy. This will do the
trick. -> Only available in 16.01.

Ciao,
Bjoern


> 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_0/118417199f06).
> So you will just need to link a requirement
> (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/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 > > 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/
> 
___
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/

Re: [galaxy-dev] packaging R scripts

[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_0/118417199f06
 
).
 So you will just need to link a requirement 
(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/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  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/

[galaxy-dev] packaging R scripts

[Xianrong Wong]

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/