CI
9a71302308
Build pipeline: openpipelines-bio.openpipeline-spatial.niche-compass-sxfbq
Source commit: 3edcea085b
Source message: merge edits
61 lines
2.0 KiB
Bash
Executable File
61 lines
2.0 KiB
Bash
Executable File
#!/bin/bash
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set -eo pipefail
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# get the root of the directory
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REPO_ROOT=$(git rev-parse --show-toplevel)
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# ensure that the command below is run from the root of the repository
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cd "$REPO_ROOT"
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DIR="resources_test/niche"
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ID="nichecompass"
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# create tempdir
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MY_TEMP="${VIASH_TEMP:-/tmp}"
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TMPDIR=$(mktemp -d "$MY_TEMP/$ID-XXXXXX")
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function clean_up {
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[[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
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}
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trap clean_up EXIT
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# Define file names
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orthologue_file="human_mouse_gene_orthologs.csv"
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enzymes_file="mouse_metabolite_enzymes.tsv"
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sensors_file="mouse_metabolite_sensors.tsv"
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if [ ! -d "$DIR" ]; then
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mkdir -p "$DIR"
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orthologue_url="https://raw.githubusercontent.com/Lotfollahi-lab/nichecompass/refs/tags/0.3.2/data/gene_annotations/human_mouse_gene_orthologs.csv"
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wget "$orthologue_url" -O "$DIR/$orthologue_file"
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enzymes_url="https://raw.githubusercontent.com/Lotfollahi-lab/nichecompass/refs/tags/0.3.2/data/gene_programs/metabolite_enzyme_sensor_gps/mouse_metabolite_enzymes.tsv"
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wget "$enzymes_url" -O "$DIR/$enzymes_file"
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sensors_url="https://raw.githubusercontent.com/Lotfollahi-lab/nichecompass/refs/tags/0.3.2/data/gene_programs/metabolite_enzyme_sensor_gps/mouse_metabolite_sensors.tsv"
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wget "$sensors_url" -O "$DIR/$sensors_file"
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fi
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# Generate omnipath and collectri network files for testing
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# These files are used to avoid API rate limits when running tests in parallel
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omnipath_file="omnipath_lr_network.csv"
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collectri_file="collectri_tf_network.csv"
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gp_mask="prior_knowledge_gp_mask.json"
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viash run src/nichecompass/gene_program_mask/config.vsh.yaml -- \
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--input_gene_orthologs_mapping_file "$DIR/$orthologue_file" \
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--input_metabolite_enzymes "$DIR/$enzymes_file" \
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--input_metabolite_sensors "$DIR/$sensors_file" \
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--output "${DIR}/${gp_mask}" \
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--output_omnipath_lr_network "${DIR}/${omnipath_file}" \
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--output_collectri_tf_network "${DIR}/${collectri_file}"
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# Sync to S3
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aws s3 sync \
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--profile di \
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"$DIR" \
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s3://openpipelines-bio/openpipeline_spatial/resources_test/niche \
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--delete \
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--dryrun
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