Where is runIchorCNA.R installed to when using R CMD INSTALL?

[callunity]

Hello,

I tried to install ichorCNA using the following:

git clone git@github.com:broadinstitute/ichorCNA.git
cd ichorCNA
<install R dependencies>
R CMD INSTALL ichorCHA

This resulted in the following error message: Warning: invalid pachage 'ichorCNA'. Error: ERROR: no packages specified.

I was able to bypass this error message by instead running:

cd ichorCNA
R CMD INSTALL .

The install completes, but the resulting R library installation doesn't contain the runIchorCNA.R script anywhere:

tree <R_install_dir>/lib/R/ichorCNA
├── DESCRIPTION
├── extdata
│   ├── cytoBand_hg38.txt
│   ├── (wig files)
├── help
│   ├── aliases.rds
│   ├── AnIndex
│   ├── ichorCNA.rdb
│   ├── ichorCNA.rdx
│   └── paths.rds
├── html
│   ├── 00Index.html
│   └── R.css
├── INDEX
├── LICENSE
├── Meta
│   ├── features.rds
│   ├── hsearch.rds
│   ├── links.rds
│   ├── nsInfo.rds
│   ├── package.rds
│   └── Rd.rds
├── NAMESPACE
└── R
    ├── ichorCNA
    ├── ichorCNA.rdb
    └── ichorCNA.rdx

(The R/ichorCNA file is not a copy of the runIchorCNA.R file)

Have I missed something for getting runIchorCNA.R installed?

Thank you, Heather

[gavinha]

Hi @callunity

The script and pipeline is contained in this repo. So if you cloned it, then you will have it.

Please refer to https://github.com/broadinstitute/ichorCNA/wiki/SnakeMake-pipeline-for-ichorCNA to see how to use the snakemake pipeline.

Best, Gavin

[callunity]

Hi @gavinha , thanks for the speedy reply!

We don't use snakemake, and so would like to be able to install the runIchorCNA.R script for general use -- ideally as an R library. I had thought that R CMD INSTALL ichorCNA would allow us to do this, but it sounds like that's not the case. Can you recommend another option?

Thanks, Heather

[gavinha]

Hi @callunity

ichorCNA R package can be installed and used as a library. The runIchorCNA.R is a script that makes use of the ichorCNA library/package. Not sure if this answers your question.

Best, Gavin

[callunity]

Hi @gavinha ,

It does, thanks!

Cheers, Heather