Commit 3e8194bc authored by peguerin's avatar peguerin
Browse files

Update README.md

parent 7a51b5c0
......@@ -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 :
......
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