add install and uninstall scripts

scripts/install.sh

@@ -0,0 +1,38 @@
+#!/bin/bash
+
+# Install the plague-phylogeography pipeline
+echo "Installing the plague-phylogeography nextflow pipeline."
+echo "nextflow pull ktmeaton/plague-phylogeography"
+nextflow pull ktmeaton/plague-phylogeography
+# Create the plague-phylogeography conda environment
+echo "Creating the plague-phylogeography conda environment."
+echo "conda env create -f  ~/.nextflow/assets/ktmeaton/plague-phylogeography/environment.yaml"
+conda env create -f  ~/.nextflow/assets/ktmeaton/plague-phylogeography/environment.yaml
+
+# Install the nfcore/eager pipeline
+echo "Installing the nf-core/eager nextflow pipeline."
+echo "nextflow pull nf-core/eager"
+nextflow pull nf-core/eager
+echo "nextflow pull nf-core/eager -r 7b51863957"
+nextflow pull nf-core/eager -r 7b51863957
+# Create the nf-core/eager conda environment
+echo "Creating the nf-core/eager conda environment."
+echo "conda env create -f ~/.nextflow/assets/nf-core/eager/environment.yml"
+conda env create -f ~/.nextflow/assets/nf-core/eager/environment.yml
+echo "Installing supplementary programs to the nf-core/eager environment."
+echo "conda install -n nf-core-eager-2.2.0dev -c bioconda nextflow==20.01.0"
+conda install -n nf-core-eager-2.2.0dev -c bioconda nextflow==20.01.0
+echo "conda install -n nf-core-eager-2.2.0dev -c anaconda graphviz"
+conda install -n nf-core-eager-2.2.0dev -c anaconda graphviz
+
+# Create the nextstrain conda environment
+echo "Creating the nextstrain conda environment."
+echo "conda env create -f  ~/.nextflow/assets/ktmeaton/plague-phylogeography/config/nextstrain.yaml"
+conda env create -f  ~/.nextflow/assets/ktmeaton/plague-phylogeography/config/nextstrain.yaml
+echo "Installing supplementary programs to the nextstrain environment."
+echo "conda activate nextstrain-8.0.0"
+conda activate nextstrain-8.0.0
+echo "npm install --global auspice@2.17.0"
+npm install --global auspice@2.17.0
+echo "conda deactivate"
+conda deactivate

scripts/uninstall.sh

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+#!/bin/bash
+
+EAGER_CONDA_ENV="nf-core-eager-2.2.0dev"
+EAGER_NF_REV="7b51863957"
+PHYLO_CONDA_ENV="plague-phylogeography-0.1.4dev"
+NEXTSTRAIN_CONDA_ENV="nextstrain-8.0.0"
+
+# Remove the plague-phylogeography pipeline
+echo "Removing the plague-phylogeography nextflow pipeline."
+echo "nextflow drop ktmeaton/plague-phylogeography"
+nextflow drop ktmeaton/plague-phylogeography
+# Remove the plague-phylogeography conda env
+echo "Removing the plague-phylogeography conda environment."
+echo "conda remove -n ${PHYLO_CONDA_ENV} --all"
+conda remove -n ${PHYLO_CONDA_ENV} --all
+
+# Remove the nfcore/eager pipeline
+echo "Removing the nf-core/eager nextflow pipeline."
+echo "nextflow drop nf-core/eager"
+nextflow drop nf-core/eager
+# Remove the nfcore/eager conda env
+echo "Removing the nf-core/eager conda environment."
+echo "conda remove -n ${EAGER_CONDA_ENV} --all"
+conda remove -n ${EAGER_CONDA_ENV} --all
+
+# Remove the nextstrain conda env
+echo "Removing the nextstrain conda environment."
+echo "conda remove -n ${NEXTSTRAIN_CONDA_ENV} --all"
+conda remove -n ${NEXTSTRAIN_CONDA_ENV} --all