Skip to content

Commit

Permalink
adding some more doc
Browse files Browse the repository at this point in the history
  • Loading branch information
jkobject committed Aug 29, 2022
1 parent 0835a1c commit f3a8d65
Showing 1 changed file with 14 additions and 9 deletions.
23 changes: 14 additions & 9 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,9 @@ _tools that you do not need to use directly as they have binding functions in ge

`pip install broad-genepy`

and then use with `from genepy.utils/epigenetics/... import ...`
and then use with `from genepy.utils/epigenetics/... import ...`

Please see the next step to get access to all bindings and tools.

### dev mode

Expand All @@ -56,30 +58,33 @@ from genepy.epigenetics import chipseq

```

## data:

hg38 genome sizes: from https://github.com/igvteam/igv/blob/master/genomes/sizes/hg38.chrom.sizes


## installation: to get access to all bindings
## installation: to get access to all bindings and tools

Install the following tools:
- [gcloud](https://cloud.google.com/sdk/docs/install-sdk)
- [firecloud-dalmatian](https://github.com/getzlab/dalmatian)
- [gsheets](https://github.com/xflr6/gsheets)
- [htslib/samtools](http://www.htslib.org/)
- [bwa](https://github.com/lh3/bwa)
just used once:
- [bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)

Some of these packages like gsheets, gcloud, firecloud-dalmatian will require you to create google accounts, login on your machine or download oauth files.

Finaly you can install R packages (GSEABase, erccdashboard, GSVA, DESeq2):

```bash
R -e 'if(!requireNamespace("BiocManager", quietly = TRUE)){install.packages("BiocManager")};BiocManager::install(c("GSEABase", "erccdashboard", "GSVA", "DESeq2"));'
```

## data:

hg38 genome sizes: from https://github.com/igvteam/igv/blob/master/genomes/sizes/hg38.chrom.sizes

## About

please do contribute, we do not have time to fix all issues or work on feature requests

Jeremie Kalfon [email protected] [email protected] https://jkobject.com

Javad Noorbakhsh [email protected]

Apache license 2.0.

0 comments on commit f3a8d65

Please sign in to comment.