From f3a8d65551d726a92341b3cb96d756c349816514 Mon Sep 17 00:00:00 2001 From: jkobject Date: Mon, 29 Aug 2022 21:14:13 +0000 Subject: [PATCH] adding some more doc --- README.md | 23 ++++++++++++++--------- 1 file changed, 14 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 8898977..5696bcb 100644 --- a/README.md +++ b/README.md @@ -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 @@ -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 jkalfon@broadinstitute.org jkobject@gmail.com https://jkobject.com -Javad Noorbakhsh jnoorbak@broadinstitute.org - Apache license 2.0.