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reservebenefit
snakemake_stacks2
Commits
3e8194bc
Commit
3e8194bc
authored
Oct 24, 2018
by
peguerin
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Update README.md
parent
7a51b5c0
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@@ -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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