Run Automatically Docker

#Automatically - Docker Cnidaria can be run completely automatically using the Make system.

create two files:

run.sh

#!/bin/bash

set -xeu

rm data/*/*.{jf,timming} || true
find data/ -type d -exec chmod 777 {} \;

rm -rf out    || true
mkdir out     || true
chmod 777 out

clean.sh

#!/bin/bash

set -xeu

docker run --rm -it --name cnidaria_running -v $PWD/data:/home/cnidaria/cnidaria/data/data -v $PWD/out:/home/cnidaria/cnidaria/data/out sauloal/cnidaria_full make -C data $@

-1- Create a data folder data

mkdir data

-2- Create one folder to each of your samples. The name of the sample will be the name of the folder. be wise.

mkdir data/sample1 && cp <YOUR ORIGINAL DATA FOLDER 1>/*.fastq.gz data/sample1/
mkdir data/sample2 && cp <YOUR ORIGINAL DATA FOLDER 2>/*.fastq.gz data/sample2/

• The extensions allowed are .fq.gz .fastq.gz .fastq .fasta.gz .fa.gz .fasta .fa

-3- run clean.sh to change folder permission and create output folder

bash clean.sh

-4- run ./run.sh to find which parameters can be set

bash run.sh

-5- run ./run.sh make print to find the files that will be created

bash run.sh make print

-6- run ./run.sh make -n to preview which commands will be run

bash run.sh make -n

-7- run ./run.sh make to analyse the data (Check Automatically for options)

bash run.sh make