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Using Scientific Tools with Mamba and Conda

This assumes that you have already followed the using mamba for the first time tutorial on this site.

Mamba environments manage dependencies and packages for you, and are the preferred way to install R packages.
Most R packages can be installed from mamba by prepending "r-" eg "r-tidyverse" etc. Only where the package does not exist is it recommended to use package.install in R.

Note - all of these installations assume you have logged on to an interactive session on Alma.

ensembl-vep

This is a package for variant effect prediction found on github.
It is most commonly installed from github with perl but can be installed with conda.

When installed with conda, the package is called ensembl-vep. The plugins are aliased as vep_install, below shows the creation of a conda environment and the installation of the human cache. 

mamba create --name bio-perl-vep -c conda-forge -c bioconda -c defaults perl-bioperl=1.7.8 ensembl-vep
mamba activate bio-perl-vep
vep -help
vep_install -help
Example usage:
vep_install -a cf -s homo_sapiens -y GRCh38 -c ./ —CONVERT

vep --cache --dir_cache "./" \
   -i "./C1D_filtered_SOPRANO.vcf" \
   -o "./vep_output.txt" \
   --offline
You must have the cache and dir-cache flags specified, and the human data needs to be in the dir-cache. There is no online access on Alma.

MRCIEU/TwoSampleMR

This is a package for Mendelian Randomization analysis found on github.

  • Create and activate a virtual environment
    mamba create --name mamba-TwoSampleMR -c bioconda samtools bcftools r-tidyverse r-remotes r-base=4.3
mamba create --name mamba-TwoSampleMR -c bioconda r-tidyverse r-remotes r-base=4.3
mamba activate mamba-TwoSampleMR
  • Manually install some packages in a dependency safe way
    mamba install r-meta
mamba install r-nloptr
mamba install r-lme4
  • Install custom package
    R -e 'remotes::install_github("MRCIEU/TwoSampleMR")'

Nextflow (latest version)

See further nextflow instructions here. 

mamba create --name mamba_nf -c bioconda nextflow
mamba activate mamba_nf
nextflow -v