add actual config scripts for jetstream instances (#11)

extra/jetstream/minto_install.ctb.sh

@@ -0,0 +1,71 @@
+#!/usr/bin/env bash
+set -e
+set -x
+
+cd $HOME
+
+. /opt/miniconda3/etc/profile.d/conda.sh
+
+# Get MIntO
+
+git clone --depth 1 https://github.com/microbiomix/MIntO.git
+
+# Create MIntO conda env
+
+conda config --set channel_priority strict
+conda create --yes -n MIntO mamba snakemake=7 -c conda-forge -c bioconda
+conda activate MIntO
+export MINTO_DIR="$HOME/MIntO"
+cd $MINTO_DIR
+
+# Create conda envs
+
+cat >> $MINTO_DIR/smk/precreate_envs.smk <<__EOM__
+import os
+my_envs = ['MIntO_base.yml', 'avamb.yml', 'mags.yml', 'checkm2.yml', 'gene_annotation.yml', 'r_pkgs.yml']
+rule make_all_envs:
+    input:
+        expand("created-{name}", name=my_envs)
+for env_file in my_envs:
+    rule:
+        output:
+            temp("created-%s" % env_file)
+        conda:
+            config["minto_dir"]+"/envs/%s" % env_file
+        shell:
+            "touch {output}"
+__EOM__
+
+snakemake --use-conda --conda-prefix $MINTO_DIR/conda_env --config minto_dir=$MINTO_DIR --cores 4 -s $MINTO_DIR/smk/precreate_envs.smk
+mamba clean --tarballs --yes
+
+# Patch assembly to avoid indexing contig files
+
+sed -i "s/\.len//" $MINTO_DIR/smk/assembly.smk
+
+# Set up minimal database downloads
+
+sed -i -e "s|minto_dir: /mypath/MIntO|minto_dir: $MINTO_DIR|" $MINTO_DIR/configuration/dependencies.yaml
+cat >> $MINTO_DIR/configuration/dependencies.yaml <<__EOM__
+enable_GTDB: no
+enable_phylophlan: no
+enable_metaphlan: no
+enable_motus: no
+__EOM__
+
+# Download databases
+
+snakemake --use-conda --restart-times 1 --keep-going --latency-wait 60 --cores 14 --resources mem=50 --jobs 4 --shadow-prefix="./.snakemake" --conda-prefix $MINTO_DIR/conda_env --snakefile $MINTO_DIR/smk/dependencies.smk --configfile $MINTO_DIR/configuration/dependencies.yaml -U checkm2_db Kofam_db functional_db_descriptions KEGG_maps download_fetchMGs
+
+
+# Download Tutorial data
+
+mkdir -p $HOME/tutorial/metaG
+cd $HOME/tutorial/metaG
+
+# Get tarball, extract and delete tarball
+
+#wget --no-check-certificate https://arumugamlab.sund.ku.dk/tutorials/202404_MIntO/tutorial_data.tar.bz2
+#tar xfj tutorial_data.tar.bz2
+#rm tutorial_data.tar.bz2
+tar xfj /opt/shared/tutorial_data.tar.bz2

extra/jetstream/titus-configure.sh

@@ -0,0 +1,47 @@
+#! /bin/bash
+set -x
+set -e
+
+. /opt/miniconda3/etc/profile.d/conda.sh
+
+# add my ssh key
+#echo ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHAyNTYAAABBBHFz3WLVqV+0md4OkZi/S0a79cOO7Ax8S4Dledp832JhMQ0GJ0ZlmEnWZrIv83KnRexpAEi5w6H1aSackGjucgQ= [email protected] >> ~/.ssh/authorized_keys
+
+mkdir ~/data/
+
+cd ~/data/
+#curl -JLO http://farm.cse.ucdavis.edu/~ctbrown/transfer/IBD_tutorial_subset.tar.gz
+tar xzf /opt/shared/IBD_tutorial_subset.tar.gz
+#curl -JLO http://farm.cse.ucdavis.edu/~ctbrown/transfer/tutorial_other.tar.gz
+tar xzf /opt/shared/tutorial_other.tar.gz
+
+mkdir ~/databases/
+cd ~/databases/
+ln -fs /opt/shared/gtdb-rs214-k31.zip .
+ln -fs /opt/shared/gtdb-rs214.lineages.csv.gz .
+#curl -JLO https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs214/gtdb-rs214-k31.zip
+#curl -JLO https://farm.cse.ucdavis.edu/~ctbrown/sourmash-db/gtdb-rs214/gtdb-rs214.lineages.csv.gz
+
+cd ~/
+
+# fix up conda channels
+conda config --add channels defaults
+conda config --add channels bioconda
+conda config --add channels conda-forge
+conda config --set channel_priority strict
+
+## pre-download packages
+
+# single metagenome tutorial
+mamba create -n test.tax -y sourmash sourmash_plugin_branchwater
+conda activate test.tax
+pip install sourmash_plugin_abundhist sourmash_plugin_venn
+
+# comparison tutorial
+mamba create -n test.smash -y sourmash scikit-learn
+
+# AMRfinder tutorial
+mamba create -n test.amrfinder -y ncbi-amrfinderplus megahit prodigal csvtk
+
+## minto install
+bash /opt/shared/minto_install.ctb.sh

extra/jetstream/titus-get-ordinate.sh

@@ -0,0 +1,5 @@
+#! /bin/bash
+mkdir ~/scripts
+cd ~/scripts
+curl -JL -o ordinate.py https://raw.githubusercontent.com/ngs-docs/2024-pig-paradigm-workshop/main/scripts/ordinate.py
+chmod +x ordinate.py

extra/jetstream/titus-get-plot-amr.sh

@@ -0,0 +1,5 @@
+#! /bin/bash
+mkdir ~/scripts
+cd ~/scripts
+curl -JL -o plot_amr.py https://raw.githubusercontent.com/ngs-docs/2024-pig-paradigm-workshop/main/scripts/plot_amr.py
+chmod +x plot_amr.py

extra/jetstream/titus-init.sh

@@ -0,0 +1,7 @@
+#! /bin/bash
+set -x
+set -e
+
+# add my ssh key
+echo ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHAyNTYAAABBBHFz3WLVqV+0md4OkZi/S0a79cOO7Ax8S4Dledp832JhMQ0GJ0ZlmEnWZrIv83KnRexpAEi5w6H1aSackGjucgQ= [email protected] >> ~/.ssh/authorized_keys
+