From 3e8194bc71ac2ff78684566a4e9ca738028535d5 Mon Sep 17 00:00:00 2001
From: peguerin <pierre-edouard.guerin@cefe.cnrs.fr>
Date: Wed, 24 Oct 2018 12:15:22 +0200
Subject: [PATCH] Update README.md
---
README.md | 68 +++++++++++++++++++++++++++----------------------------
1 file changed, 34 insertions(+), 34 deletions(-)
diff --git a/README.md b/README.md
index eb5f68c..5a40922 100644
--- a/README.md
+++ b/README.md
@@ -36,43 +36,43 @@ You must install the following softwares and packages :
- [SNAKEMAKE 5.3.0](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html)
* Check version and if the program is correctly installed by typing :
-```
-snakemake --version
-## should give you the output
-5.3.0
-```
+ ```
+ snakemake --version
+ ## should give you the output
+ 5.3.0
+ ```
- [STACKS 2.0b](http://catchenlab.life.illinois.edu/stacks/)
* Check version and if programs are correctly installed by typing :
-```
-process_radtags --version
-clone_filter --version
-gstacks --version
-populations --version
-## should give you the output
-2.0b
-```
+ ```
+ process_radtags --version
+ clone_filter --version
+ gstacks --version
+ populations --version
+ ## should give you the output
+ 2.0b
+ ```
- [BWA 0.7.17](https://icb.med.cornell.edu/wiki/index.php/Elementolab/BWA_tutorial)
* Download `bwa` at: http://sourceforge.net/projects/bio-bwa/files/
-```
-tar -xvf bwa-x.x.x.tar.bz2
-cd bwa-x.x.x
-./configure --prefix=/where/to/install
-make
-make install
-```
+ ```
+ tar -xvf bwa-x.x.x.tar.bz2
+ cd bwa-x.x.x
+ ./configure --prefix=/where/to/install
+ make
+ make install
+ ```
* Check version and if programs are correctly installed by typing :
-```
-bwa
-## should give you the output
-Program: bwa (alignment via Burrows-Wheeler transformation)
-Version: 0.7.17-r1188
-...
-```
+ ```
+ bwa
+ ## should give you the output
+ Program: bwa (alignment via Burrows-Wheeler transformation)
+ Version: 0.7.17-r1188
+ ...
+ ```
- [SAMTOOLS 1.9 ](http://www.htslib.org/)
* Download `htslib` and `samtools` at : http://www.htslib.org/download/
* Building each desired package from source is very simple:
@@ -91,13 +91,13 @@ Version: 0.7.17-r1188
```
* Check version and if programs are correctly installed by typing :
-```
-samtools --version
-## should give you the output
-samtools 1.9
-Using htslib 1.9
-Copyright (C) 2018 Genome Research Ltd.
-```
+ ```
+ samtools --version
+ ## should give you the output
+ samtools 1.9
+ Using htslib 1.9
+ Copyright (C) 2018 Genome Research Ltd.
+ ```
## 2.2 Data Files
The included data files are :
--
GitLab