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ChristopherBarrington / scamp

single cell analysis and more pipeline
https://christopherbarrington.github.io/scamp/
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containerisation #9

Open ChristopherBarrington opened 1 year ago

ChristopherBarrington commented 1 year ago

processes should have their own environments, not expect software to be available for them

ChristopherBarrington commented 1 year ago 
conda create --name scamp --no-channel-priority  nextflow python openjdk=20 r-base pkg-config
pip install pandas ruamel.yaml
install.packages("BiocManager")
BiocManager::install("biomaRt")
BiocManager::install("GenomicRanges")
Biocmanager::install("rtracklayer")

install.packages("Seurat")
install.packages("Signac")
install.packages('tidyverse')
install.packages('remotes')

install_github('ChristopherBarrington/scampr', auth_token=<PAT>')
ChristopherBarrington commented 1 year ago

https://medium.com/@chadlagore/conda-environments-with-docker-82cdc9d25754

FROM continuumio/miniconda3
RUN conda create -n env python=3.6
RUN echo "source activate env" > ~/.bashrc
ENV PATH /opt/conda/envs/env/bin:$PATH
ChristopherBarrington commented 1 year ago

https://github.com/seqeralabs/wave-showcase https://docs.seqera.io/wave/guide