From c56a370cbfaef30e5687db37e9081ab31db07cd6 Mon Sep 17 00:00:00 2001
From: Tobias Marschall <tobias.marschall@0ohm.net>
Date: Tue, 16 Jan 2018 15:11:19 +0100
Subject: [PATCH] Explain Bioconda in README
---
README.md | 20 +++++++++++++++++---
1 file changed, 17 insertions(+), 3 deletions(-)
diff --git a/README.md b/README.md
index 8af551f..501bbca 100644
--- a/README.md
+++ b/README.md
@@ -4,20 +4,34 @@
Preliminary SV calling using Strand-seq data - summarized in a [Snakemake](https://bitbucket.org/snakemake/snakemake) pipeline.
+
+### Bioconda environment
+To install the correct environment, you can use Bioconda.
+
+ 1. **Install MiniConda:**
+ In case you do not have Conda yet, it is easiest to just install [MiniConda](https://conda.io/miniconda.html).
+
+ 2. **Create environment:**
+ ```
+ conda env create -n strandseqnation -f conda-environment.yml
+ source activate strandseqnation
+ ```
+ That's it, you are ready to go.
+
### How to use it
1. **Install required software:**
* Install [mosaicatcher](https://github.com/friendsofstrandseq/mosaicatcher) (*currently you will need the `develop` branch*)
* Get the R-scripts from [strandsequtils](https://github.com/friendsofstrandseq/strandsequtils)
- * Install BSgenome.Hsapiens.UCSC.hg38:
+ * Install BSgenome.Hsapiens.UCSC.hg38 (can be skipped of you use the Bioconda environment, see above):
```
source("https://bioconductor.org/biocLite.R")
biocLite('BSgenome.Hsapiens.UCSC.hg38')
```
* [Strand-Phaser](https://github.com/daewoooo/StrandPhaseR) is installed automatically
- 2. **Set up the configuration of the smakemake pipeline**
+ 2. **Set up the configuration of the snakemake pipeline**
* Open `Snake.config.json` and specify the path to the executatables
(such as Mosaicatcher) and to the R scripts.
@@ -37,7 +51,7 @@ Preliminary SV calling using Strand-seq data - summarized in a [Snakemake](https
--cluster-config Snake.cluster.json \
--cluster "???"
```
-
+
### SNV calls
The pipeline will run simple SNV calling using [samtools](https://github.com/samtools/samtools)
--
GitLab