search

broadinstitute / PANOPLY

Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)
Other
33 stars 15 forks source link

The source R files in R-utiliites #34

Closed wangshisheng closed 2 years ago

wangshisheng commented 2 years ago

Hi all,

Where could I find the source r files in the R-utiliites? For example,

Rutil.path <- switch (Sys.info()[['sysname']], Windows = {'//flynn-cifs/prot_proteomics/Projects/R-utilities'}, Darwin = {'/Volumes/prot_proteomics/Projects/R-utilities'}, Linux = {'/prot/proteomics/Projects/R-utilities'})

I use Windows and I can not find where is the path '//flynn-cifs/prot_proteomics/Projects/R-utilities'.

Could someone share these r files in this path? Thanks a lot really.

Shisheng

drmani commented 2 years ago

The dockers for each PANOPLY task contain the required code in the Linux path (/prot/proteomics/Projects/R-utilities). The Windows and MacOS (Darwin) paths are internal to the Broad Institute.

wangshisheng commented 2 years ago

Thanks a lot, I will try it~~

wangshisheng commented 2 years ago

The dockers for each PANOPLY task contain the required code in the Linux path (/prot/proteomics/Projects/R-utilities). The Windows and MacOS (Darwin) paths are internal to the Broad Institute.

Hi drmani,

I have installed docker and do not know how to run the dockers. There is no introduction either. Could you give one example about how to run the docker in PANOPLY? Thanks a lot~~

Bests.

drmani commented 2 years ago

A docker tutorial is beyond the scope of PANOPLY -- google is your best bet for instructions.

But, if you want to run a docker (say broadcptac/panoply_common:1_1) and inspect the R-utilities code, you can run: % docker run -ti broadcptac/panoply_common:1_1 /bin/bash This will put you in the docker, with a shell prompt and you can explore the files in the docker.