add docker file

[Luke-ebbis]

Building the container locally

 docker build -t your-image-name .

test command

docker run --rm -it your-image-name  -g test_dataset/Calbicans_SRR13587609.fasta.gz -s Candida_albicans -o Calbicans_SRR13587609_ChroQueTas

Put some...

   ____ _                ___            _____          
  / ___| |__  _ __ ___  / _ \ _   _  __|_   _|_ _ ___  
 | |   | '_ \| '__/ _ \| | | | | | |/ _ \| |/ _` / __| 
 | |___| | | | | | (_) | |_| | |_| |  __/| | (_| \__ \ 
  \____|_| |_|_|  \___/ \__\__\__,_|\___||_|\__,_|___/   v1.0.0


                                                            ...IN YOUR LIFE!

Four steps and you are there!

The species Candida_albicans has 11 proteins associated with AMR

PLEASE NOTE: as -c/--trans_code has not been specified and Candida_albicans belongs to CTG clade, genetic code has been automatically set to alternative yeast code (12)

Running protein prediction and extraction (step 1/4)
Done! (step 1/4)
Calculating protein similarity with reference (step 2/4)
Done! (step 2/4)
Performing alignment with reference (step 3/4)
Done! (step 3/4)
Inspecting mutations potentially causing AMR (step 4/4)
Done! (step 4/4)

 -FungAMR mutations found: 2
 -New mutations found: 0

Thanks for using ChroQueTas!


PLEASE NOTE: the mutations reported by ChroQueTas must be considered according their confidence scores, where different combinations might exist.

See the main repositories for further details:
 -https://github.com/nmquijada/ChroQueTas
 -https://card.mcmaster.ca/fungamrhome

Pushing the container

USER="sibbe2000"
REPOSITORY="test"
TAG=$(git rev-parse --abbrev-ref HEAD)
echo "=============================================================="
echo 'pushing the ChroQueTas to the $REPOSITORY repo owned by $USER'
echo 'using $TAG'
echo "=============================================================="
docker build -t "$USER/$REPOSITORY" .
docker push "$USER/$REPOSITORY"

[Luke-ebbis]

@nmquijada when you merge this PR, you can update the README with the instructions for the Docker image.