Issue while installing DAPPLE on local genepattern server

[Mouncef El Ouardi]

Hello, I encoutered an error while installing DAPPLE on a local genepatter server, i get the same error even if I try to install it from zip or from the repository, here is the error:

"

DAPPLE.zip

Errors:1.DAPPLE: no substitution available for <run-with-env> in command line <run-with-env> -u Python-2.6 -u R-3.1 python /web/wwwprod/htdocs/mpg/dapple/NewCode/BuildNetwork_slowTMP.py <Input.File> keyword=<Keyword> permute=<Permute.Length> plot=<Plot> genome=<genome.build> nearestgene=<nearest.gene>.

"

Can you please help me to fix it, thank you.

[Barbara Hill]

Hello, 

Apologies for the delay in responding. I realized that you had gotten this from our GParc repository and that we were hosting an outdated version there. I have updated the latest version in GParc (v0.19) to use our current method of running modules in Docker containers. 

Please download and install the updated version and let me know if you have any difficulties.

Best

-Barbara

[Mouncef El Ouardi]

Hello,

Thank you for your answer, there is still a problem in this command "RUN /code/downloadData.sh" (the last command in dockerfile),  the URL where data should be downloaded is not working (https://personal.broadinstitute.org/hhorn/dappleData/).

[Barbara Hill]

Hello,

I'm not sure why you building a new image.

The published version of DAPPLE in our GParc repository (or available by exporting from our cloud server) - uses genepattern/dapple:v0.19-pre.4 - and that is automatically pulled when the module is run. So you shouldn't need to build the image.

Here is the nightly test which ran successfully last night on our cloud server: https://cloud.genepattern.org/gp/pages/index.jsf?jobid=423163&openNewWindow=false

Please let us know if we can provide any further assistance.

Best

-Barbara