Welcome to HCBC Platform¶
Welcome to our Platform guidelines web-page. Here analysts and developers will find guidelines on how to work with our most common environments.
We are developing platforms for each analysis type we have experience with at HCBC. Currently we fully support:
Go to each analysis-type section to learn how to use our platform.
Set up the package¶
-
Using O2 open OnDemand:
- Remove
bcbio
from youPATH
by commenting the line in your.bashrc
if you have it - Start Rstudio with these modules on:
gcc/9.2.0 imageMagick/7.1.0 geos/3.10.2 cmake/3.22.2 R/4.3.1 fftw/3.3.10 gdal/3.1.4 udunits/2.2.28 boost/1.75.0
- Add
--exclude=compute-f-17-[09-25]
to the 'Slurm Custom Arguments' field - When the session is started, set you library path typing this command in your console Rstudio window:
.libPaths("/n/app/bcbio/R4.3.1_rnaseq")
- Remove
-
Load bcbioR with
library(bcbioR)
- Make sure the version is 0.1.3 with this command
packageVersion("bcbioR")
or re-install withdevtools::install_github("bcbio/bcbioR",build_manual = TRUE, build_vignettes = TRUE)
, if you are in your own environment
General Project¶
Use the hcbc app to set up projects names. This name will be used for O2/FAS/github and dropbox. They may be already defined in the Trello card.
This set up needs bcbioR and usethis packages.
Make sure the version is 0.1.3
with this command packageVersion("bcbioR")
or re-install with devtools::install_github("bcbio/bcbioR",build_manual = TRUE, build_vignettes = TRUE)
, if you are in your own environment
- Create an R Project located in your project folder:
usethis::proj_activate("/path/to/analysis/folder")
- Deploy folders/files compatible with any project:
bcbioR::bcbio_templates(type="base", outpath="/path/to/analysis/folder")
- Start a git repository:
usethis::use_git()
If you want to push this project to GitHub, follow these steps:
- Only once every 30 days, set up your github credentials:
usethis::gh_token_help()
- NOTE You may want to run this first to keep this token working in future sessions in O2/FAS:
git config --global credential.helper store
- Push repository to HBC github as private:
usethis::use_github(org="hbc",private=TRUE)
RNAseq¶
Use this common library path to perform your analysis: .libPaths("/n/app/bcbio/R4.3.1_rnaseq")
.
* Follow the previous step to set up the base project
* Follow this instruction https://bcbio.github.io/bcbioR/#set-rnaseq-report-folder to start your RNAseq analysis
scRNAseq¶
Please, change to this common library path to perform your analysis: .libPaths("/n/app/bcbio/R4.3.1_singlecell")
.
ChipSeq¶
Please, change to this common library path to perform your analysis: .libPaths("/n/app/bcbio/R4.3.1_chipseq")
.
bcbioR supported templates¶
We used bcbioR
to deploy folders and code to our project directories to improve robustness in our analysis.
You can install bcbioR
as indicated here: https://github.com/bcbio/bcbioR/tree/main
Note¶
These materials have been developed by members of the teaching and platform team at the Harvard Chan Bioinformatics Core (HBC) RRID:SCR_025373.