CI
cd0af18851
Build pipeline: vsh-ci-dev-k8tz4
Source commit: 2dbe3b7231
Source message: Fix pointers to test resources
51 lines
1.7 KiB
Bash
Executable File
51 lines
1.7 KiB
Bash
Executable File
#!/bin/bash
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set -eo pipefail
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# ensure that the command below is run from the root of the repository
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REPO_ROOT=$(git rev-parse --show-toplevel)
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cd "$REPO_ROOT"
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# settings
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mkdir -p "resources_test/remote_param_list/"
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OUT=resources_test/remote_param_list/test_param_list.yaml
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OUT_CSV=resources_test/remote_param_list/test_param_list.csv
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OUT_JSON=resources_test/remote_param_list/test_param_list.json
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cat > $OUT << HERE
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- id: "mouse"
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input: s3://openpipelines-data/concat_test_data/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix_subset_unique_obs.h5mu
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publish_dir: "foo_remote/"
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rna_min_counts: 2
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prot_min_counts: 3
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- id: "human"
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input: s3://openpipelines-data/concat_test_data/human_brain_3k_filtered_feature_bc_matrix_subset_unique_obs.h5mu
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publish_dir: "foo_remote/"
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rna_min_counts: 2
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prot_min_counts: 3
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HERE
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cat > $OUT_CSV << EOF
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"id","input","publish_dir","rna_min_counts","prot_min_counts"
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"mouse","s3://openpipelines-data/concat_test_data/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix_subset_unique_obs.h5mu","foo_remote/","2","3"
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"human","s3://openpipelines-data/concat_test_data/human_brain_3k_filtered_feature_bc_matrix_subset_unique_obs.h5mu","foo_remote/","2","3"
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EOF
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cat > $OUT_JSON << HERE
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[
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{
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"id": "mouse",
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"input": "s3://openpipelines-data/concat_test_data/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix_subset_unique_obs.h5mu",
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"publish_dir": "foo_remote/",
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"rna_min_counts": 2,
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"prot_min_counts": 3
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},
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{
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"id": "human",
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"input": "s3://openpipelines-data/concat_test_data/human_brain_3k_filtered_feature_bc_matrix_subset_unique_obs.h5mu",
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"publish_dir": "foo_remote/",
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"rna_min_counts": 2,
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"prot_min_counts": 3
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}
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]
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HERE |