Installation on local devices and HPCs

$ "${SHELL}" <(curl -L https://raw.githubusercontent.com/vivaxgen/MicroHaps/main/install.sh)

Copy and paste command into the command line in the folder you want the install to be saved to (we recommend you create a specific tools or software folder). When prompted for "Pipeline base directory? [./vvg-MicroHaps]" press enter again for the install to proceed.

The installation requires ~ 20-45 minutes as most of R packages need to be recompiled during installation.

Once the installation finished, it will show the command to activate the pipeline, as such:

$ /path/to/vvg-MicroHaps/bin/activate

Warning

For Conda-based users!

Be sure you are not in a conda environment or in the (base) conda environment prior to installing. To deactivate your conda environment or (base) environment, enter:

$ conda deactivate

This activation command has to be executed before all commands of the pipeline can be run. When activated, the terminal will show the (µhaps) prompt.

The installation process also performs indexing of the reference files. However, in case that the indexing fails, please perform manual indexing using the command:

$ ngs-pl initialize --target wgs

To test your install, and read about programme specifications / options:

$ ngs-pl run-discovery-variant-caller --help

Updating the pipeline

To update the pipeline line, assuming that the environment has been activated, run the following command:

$ $VVG_BIN/update-pipeline.sh