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reservebenefit
snakemake_stacks2
Commits
5bbb4c97
Commit
5bbb4c97
authored
Oct 30, 2018
by
peguerin
Browse files
Merge branch 'master' of
http://gitlab.mbb.univ-montp2.fr/reservebenefit/snakemake_stacks2
parents
92a8ed7e
ce268069
Changes
1
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README.md
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5bbb4c97
...
...
@@ -12,14 +12,12 @@ This was designed to process RADseq data from [RESERVEBENEFIT](https://www.biodi
1.
[
Prerequisite
](
#21-prerequisite
)
2.
[
Data Files
](
#22-data-files
)
3.
[
Set up
](
#23-set-up
)
3.
[
Reporting bugs
](
#
4
-reporting-bugs
)
3.
[
Reporting bugs
](
#
3
-reporting-bugs
)
4.
[
Running the pipeline
](
#5-running-the-pipeline
)
1.
[
Filter raw data
](
#51-filter-raw-data
)
2.
[
Georeferenced sequences alignments by species
](
#52-data-files
)
3.
[
Species sequence pairwise comparison
](
#53-species-sequence-pairwise-comparison
)
4.
[
Genetic Diversity calculation
](
#54-genetic-diversity-calculation
)
5.
[
Statistical analysis
](
#55-statistical-analysis
)
1.
[
Initialisation
](
#41-initialisation
)
2.
[
Configuration
](
#42-configuration
)
3.
[
Run the pipeline into a single command
](
#43-run-the-pipeline-into-a-single-command
)
4.
[
Run the pipeline step by step
](
#44-run-the-pipeline-step-by-step
)
# 1. Introduction
...
...
@@ -34,64 +32,70 @@ blablabla
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
```
*
Check version and if the program is correctly installed by typing :
```
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
```
*
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
```
-
[
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
```
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
...
```
-
[
SAMTOOLS
](
http://www.htslib.org/
)
Download
`htslib`
and
`samtools`
at : http://www.htslib.org/download/
Building each desired package from source is very simple:
```
cd htslib-1.x
./configure --prefix=/where/to/install
make
make install
cd ..
## and similarly for samtools :
cd samtools-1.x
./configure --prefix=/where/to/install
make
make install
```
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.
```
*
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
```
* 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
...
```
-
[
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:
```
cd htslib-1.x
./configure --prefix=/where/to/install
make
make install
cd ..
## and similarly for samtools :
cd samtools-1.x
./configure --prefix=/where/to/install
make
make install
```
* 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.
```
## 2.2 Data Files
The included data files are :
...
...
@@ -105,24 +109,27 @@ The included data files are :
clone the project and switch to the main folder, it's your working directory
```
git clone
dzdzdzworldmap_fish_genetic_diversity
.git
git clone
http://gitlab.mbb.univ-montp2.fr/reservebenefit/snakemake_stacks2
.git
cd snakemake_stacks2
```
You will see the following folders :
#
4
. Reporting bugs
#
3
. Reporting bugs
If you're sure you've found a bug — e.g. if one of my programs crashes
with an obscur error message, or if the resulting file is missing part
of the original data, then by all means submit a bug report.
I use
[
GitLab's issue system
](
https://gitlab.com/reservebenefit/
worldmap_fish_genetic_diversity
/issues
)
I use
[
GitLab's issue system
](
https://gitlab.com/reservebenefit/
snakemake_stacks2
/issues
)
as my bug database. You can submit your bug reports there. Please be as
verbose as possible — e.g. include the command line, etc
# 4. Running the pipeline
Quickstart
## 4.1 Initialisation
*
open a shell
*
make a folder, name it yourself, I named it workdir
...
...
@@ -134,10 +141,27 @@ cd workdir
*
clone the project and switch to the main folder, it's your working directory
```
git clone
git clone
http://gitlab.mbb.univ-montp2.fr/reservebenefit/snakemake_stacks2.git
cd snakemake_stacks2
```
## 4.2 Configuration
WORK IN PROGRESS !!!!
## 4.3 Run the pipeline into a single command
Once you finished
[
Initialisation
](
#41-initialisation
)
and
[
Configuration
](
#42-configuration
)
steps. You can run the whole pipeline simply typing :
```
## number of CPU cores available for running the pipeline (for instance here 64 cores)
N_CORES=64
## run the pipeline into a single command
bash main.sh $N_CORES
```
## 4.4 Run the pipeline step by step
WORK IN PROGRESS !!!!
that's it ! The pipeline is running and crunching your data. Look for the log folder output folder after the pipeline is finished.
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