[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
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Re: [galaxy-dev] correctly installing to toolshed

[Xianrong Wong]

Thank you!

On Thu, Feb 25, 2016 at 7:50 PM, Karen Reddy <kred...@jhmi.edu> wrote:

> Thanks!
>
> Sent from Nine <http://www.9folders.com/>
>
> *From:* Gildas Le Corguillé <lecorgui...@sb-roscoff.fr>
> *Sent:* Feb 25, 2016 3:17 PM
> *To:* Karen Reddy
> *Cc:* Xianrong; Björn Grüning; Xianrong Wong; galaxy-...@lists.bx.psu.edu
> *Subject:* Re: [galaxy-dev] correctly installing to toolshed
>
> Hi all,
>
> You will found in attachment the modification, I proposed in my first
> email.
>
> As I said when your script is near your xml, you just need to use the
> interpreter attribute in 
>
>
>
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Re: [galaxy-dev] correctly installing to toolshed

[Xianrong Wong]

Hi Bjoern, it's stored in the same folder as the .xml

Hi Gildas, that is the tool.

Thanks!

On Tue, Feb 23, 2016 at 12:43 PM, Gildas Le Corguillé <
lecorgui...@sb-roscoff.fr> wrote:

> Is it this tool :
> https://testtoolshed.g2.bx.psu.edu/view/xianrong/removing_consecutive_bins_with_same_score/c19a0a942e1b
>
> 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 23 févr. 2016 à 18:35, Björn Grüning <bjoern.gruen...@gmail.com> a
> écrit :
>
> Hi,
>
> is the script rm_consecutive_sameScore.pl part of your TS repo and next
> to your tool XML file or where is it stored?
>
> Thanks,
> Bjoern
>
> Am 23.02.2016 um 17:46 schrieb Xianrong Wong:
>
> Hi, I'm new to publishing tools/repository on the toolshed.  I have used
> planemo and lint and tests as well as serve all worked.  I was able to
> use the tool.  However, when I uploaded it onto the test tool shed and
> imported the tool on a cloud instance, I keep getting this error when
> running job:
>
> Fatal error: Exit code 2 () Can't open perl script
> "rm_consecutive_sameScore.pl": No such file or directory
>
>
>
> Please advise! I've been downloading and looking at what others did but
> I still can't figure this out.
>
>
>
> I've attached my .xml file and here are some of the commands I used to
> upload the tool.
>
> planemo shed_create --shed_target testtoolshed
>
>
>
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>
>
>
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[galaxy-dev] correctly installing to toolshed

[Xianrong Wong]

Hi, I'm new to publishing tools/repository on the toolshed.  I have used
planemo and lint and tests as well as serve all worked.  I was able to use
the tool.  However, when I uploaded it onto the test tool shed and imported
the tool on a cloud instance, I keep getting this error when running job:

Fatal error: Exit code 2 () Can't open perl script
"rm_consecutive_sameScore.pl": No such file or directory



Please advise! I've been downloading and looking at what others did but I
still can't figure this out.



I've attached my .xml file and here are some of the commands I used to
upload the tool.

planemo shed_create --shed_target testtoolshed






   .$__tool_directory__/rm_consecutive_sameScore.pl "$input1" "$output1"
   















@misc{renameTODO,
  author = {LastTODO, FirstTODO},
  year = {TODO},
  title = {TODO},
  url = {manuscript in preparation},
}


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