Question: Publishing a Tool. How automated should the installation be?
gravatar for bornea27
2.8 years ago by
United States
bornea2720 wrote:

My lab is currently working towards generating a new tool that uses R and several R packages but sort of depends on having R and the ability to install bioconductor packages. I have a code that automatically does it some linux distributions but not all. Should the install process include installation of R and the required packages or inform the user that R environment could not be found or that the bioconductor packages needed could not be installed?

On a similar note the way it is set up now when installed 3rd party software is extracted and compiled automatically. Should these be the case or should I just inform them that this third party software is needed?

galaxy • 685 views
ADD COMMENTlink modified 2.8 years ago by Jennifer Hillman Jackson25k • written 2.8 years ago by bornea2720
gravatar for Jennifer Hillman Jackson
2.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:


More scientific users will be able to use your tool if the option for installing managed dependencies is included. Maybe your tool could leverage the R tools/packages already included in the Tool Shed?

Best, Jen, Galaxy team

ADD COMMENTlink written 2.8 years ago by Jennifer Hillman Jackson25k

I have attempted to use the R package already provided in galaxy but it would not work on my operating system (CentOs 7). I eventually resolved to allow the user to use R package if it will work (it is included in my tool_dependencies file) but inform the user that it may require manual installation of R.

ADD REPLYlink written 2.5 years ago by bornea2720
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