Microbial Utility Toolbox And wrapper for data traNsmission and Transformation
java --version
)conda install -c conda-forge singularity
git clone --recurse-submodules https://github.com/Clinical-Genomics/MUTANT.git
cd MUTANT
source setup.sh D_mutant
source activate D_mutant
self-test
.source activate D_mutant
cd MUTANT
mutant analyse sarscov2 tests/testdata/fasta_files --profiles local,docker --config_artic mutant/config/local/default_config.json --config_mutant mutant/config/local/mutant.json --config_case tests/testdata/MIC3109_artic.json
./results/
Or install MUTANT under S_mutant and run cg workflow mutant start frankhusky
with results in /home/proj/stage/mutant/cases/frankhusky
MUTANTs versioning is bumped manually post PR merge, using semver standards on this variable.
Deploy new version in production:
bash mutant/standalone/deploy_hasta_update.sh production main
Containers are available on dockerhub. The containers can be built locally (not possible on hasta) using the instructions below.
cd mutant/externals/gms-artic/
docker build -f environments/illumina/Dockerfile -t artic-ncov2019-illumina:<version> .
The following script will push artic-ncov2019-illumina:<version>
to Dockerhub.
docker login --username=<>
bash mutant/standalone/push_docker_image.sh <version>
clinicalgenomics/artic-ncov2019-illumina
singularity pull <MUTANTDIR>/mutant/externals/gms-artic/artic-ncov2019-illumina.sif docker://clinicalgenomics/artic-ncov2019-illumina
docker pull clinicalgenomics/artic-ncov2019-illumina
Setup
.mutant toolbox create-images
/vagrant
in the vm.
export VM=sylabs/singularity-ce-3.8-ubuntu-bionic64
vagrant init $VM
vagrant up
vagrant ssh
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && bash Miniconda3-latest-Linux-x86_64.sh -b && miniconda3/bin/conda init bash && source ~/.bashrc
Basic vagrant commands:
Vagrantfile
ctrl + d
vagrant destroy
vagrant box --help