Armadillo_SNPs_WF_test

Files for a SNPs workflow with docker in Armadillo caps

Files came from https://bitbucket.org/snakemake/snakemake/
in directory Snakemake / docs / tutorial / workflow / data /

The Workflow is the equivalent of Snakemake Tutorial with few modifications
All applications except Load Files are running with docker. To test it, you can use an ubuntu 16.04 in a virtual machine \

Prepare your VM

Open a terminal.
From your home directory, steps are :
$ sudo apt-get update
$ sudo apt-get install docker.io git unzip ant
$ sudo usermod -aG docker $(whoami)
$ sudo reboot # logout/login is enougth
$ docker --version
You need a positive answer like
Docker version 17.05.0-ce, build 89658be

Add depots

$ git clone https://github.com/JeGoi/armadillo2.git
$ git clone https://github.com/JeGoi/Armadillo_SNPs_WF_test.git
$ cd Armadillo_SNPs_WF_test ; unzip inputs.zip

Compilation

A GUI way to install and compile source is with netbeans.
$ sudo apt-get purge openjdk*
$ sudo add-apt-repository ppa:webupd8team/java
$ sudo apt-get update
$ sudo apt-get install oracle-java8-installer
$ wget http://download.netbeans.org/netbeans/8.2/final/bundles/netbeans-8.2-linux.sh
$ chmod +x netbeans-8.2-linux.sh
$ ./netbeans-8.2-linux.sh
Follow the steps dont forget to mention the path to jdk during the process
"/usr/lib/jvm/java-8-oracle"
or add it later in the netbeans config file in ~/netbeans-8.1/etc/netbeans.conf
with :
netbeans_jdkhome="/usr/lib/jvm/java-8-oracle"

Run netbeans (icon on desktop), go to File/Open project Go to ~/ and select armadillo2
Then go to Run/Clean&BuildProject
Wait until it's done

OR \

A CLI way is with ant
$ cd ~/armadillo2
$ ant clean jar

Running after compile:

Open a terminal
$ cd ~/armadillo2 ; cp dist/Armadillo.jar Armadillo.jar ; java -jar Armadillo.jar

Armadillo will start.

Start the test:

Perpare the workflow

Go to File/New project \

• Create a new name \
• Save it
  Go to File/Import Workflow in project \
• Select your home directory (second icon on right of path) \
• Choose Armadillo_SNPs_WF_test/NGS_workflow_Sankemake_AB_Final_empty.txt \
• or Armadillo_SNPs_WF_test/NGS_workflow_Sankemake_ABC_Final_empty.txt

Save your workflow

Add files

On the left side of the workflow, loading boxes are waiting. Double clic on them and choose the right file according the name box.
Genome file is in inputs/genome.fa
A fastq is in inputs/samples/A.fastq
B fastq is in inputs/samples/B.fastq
C fastq is in inputs/samples/C.fastq

Save your workflow

Run it

You can run it on local or on Mammouth parallèle II.
https://wiki.calculquebec.ca/w/Mp2/en
It's not yet tested on other Calcul Québec Clusters.

You need a private / public key to use it this way:
https://wiki.calculquebec.ca/w/G%C3%A9n%C3%A9rer_des_cl%C3%A9s_SSH/en
More information here:
https://wiki.calculquebec.ca/w/Connexion_%C3%A0_l%27aide_des_cl%C3%A9s_publiques_et_priv%C3%A9es/en

Then chose cluster on the top right.
In the Cluster box (top left of workflow design), add needed information.
Update them and then clic on "Test and Save" to presaved your connexion

Enjoy.

Steps to test Snakemake Tutorial on the same machine.

$ mkdir SnakeMakeTuto
$ cd SnakeMakeTuto/
$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash Miniconda3-latest-Linux-x86_64.sh
$ conda install -c bioconda snakemake
$ wget https://bitbucket.org/snakemake/snakemake-tutorial/get/v3.11.0.tar.bz2
$ tar -xf v3.11.0.tar.bz2 --strip 1
$ conda env create --name snakemake-tutorial --file environment.yaml
$ mv ~/Armadillo_SNPs_WF_test/SnakeSource ~/SnakeMakeTuto
$ mv ~/Armadillo_SNPs_WF_test/SnakeArmadillo ~/SnakeMakeTuto
$ source activate snakemake-tutorial
~ To get Amadillo equivalent
$ snakemake -s SnakeArmadillo
~ To get Tutorial WorkFlow
$ snakemake -s SnakeSource
~ To remove everything and restart
$ rm -rf calls/ mapped_reads/ sorted_reads/ .snakemake/ report.html
~ To exit from Sankemake environment
$ source deactivate

Enjoy