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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,3 @@ | ||
| set -e | ||
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| aws s3 sync resources s3://data-intuitive-tmp/test-nextflow-wave-fusion/resources --delete |
54 changes: 54 additions & 0 deletions
54
scripts/run_batch-code_remote-input_s3-output_s3-work_s3.sh
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,54 @@ | ||
| #!/bin/bash | ||
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| set -e | ||
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| script_name=$(basename "$0") | ||
| TMPOUT=s3://data-intuitive-tmp/test-nextflow-wave-fusion/output/${script_name%.sh} | ||
| OUT=output/${script_name%.sh} | ||
| RES=s3://data-intuitive-tmp/test-nextflow-wave-fusion/resources | ||
| WORK=s3://data-intuitive-tmp/test-nextflow-wave-fusion/work/${script_name%.sh} | ||
| NXF_CONFIG=/tmp/${script_name%.sh}.config | ||
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| # clear output dir | ||
| echo "Clearing output directory" | ||
| aws s3 rm $TMPOUT --recursive | ||
| [ -d "$OUT" ] && rm -r "$OUT" | ||
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| # run component | ||
| echo "Running component" | ||
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| cat > $NXF_CONFIG <<EOF | ||
| process { | ||
| executor = 'awsbatch' | ||
| queue = 'di_compute' | ||
| container = 'bash:4.0' | ||
| } | ||
| aws { | ||
| region = 'eu-west-1' | ||
| batch { | ||
| cliPath = '/home/ec2-user/miniconda/bin/aws' | ||
| } | ||
| } | ||
| EOF | ||
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| NXF_VER=23.10.0 nextflow run \ | ||
| viash-io/test-nextflow-wave-fusion \ | ||
| -r main_build \ | ||
| -main-script target/nextflow/method/main.nf \ | ||
| -profile docker \ | ||
| -w $WORK \ | ||
| -c $NXF_CONFIG \ | ||
| -latest \ | ||
| --input $RES/input1.txt \ | ||
| --multiple_input "$RES/input1.txt;$RES/input2.txt" \ | ||
| --publish_dir "$TMPOUT" | ||
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| # sync output | ||
| echo "Syncing output" | ||
| aws s3 sync $TMPOUT $OUT | ||
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| # check if output is correct | ||
| echo "Checking output" | ||
| scripts/verify_output.sh "$OUT" |
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24 changes: 24 additions & 0 deletions
24
scripts/run_local-code_remote-input_s3-output_local-work_local.sh
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| #!/bin/bash | ||
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| set -e | ||
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| script_name=$(basename "$0") | ||
| OUT=output/${script_name%.sh} | ||
| RES=s3://data-intuitive-tmp/test-nextflow-wave-fusion/resources | ||
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| # clear output dir | ||
| [ -d "$OUT" ] && rm -r "$OUT" | ||
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| # run component | ||
| NXF_VER=23.10.0 nextflow run \ | ||
| viash-io/test-nextflow-wave-fusion \ | ||
| -r main_build \ | ||
| -main-script target/nextflow/method/main.nf \ | ||
| -profile docker \ | ||
| -latest \ | ||
| --input $RES/input1.txt \ | ||
| --multiple_input "$RES/input1.txt;$RES/input2.txt" \ | ||
| --publish_dir "$OUT" | ||
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| # check if output is correct | ||
| scripts/verify_output.sh "$OUT" |
33 changes: 33 additions & 0 deletions
33
scripts/run_local-code_remote-input_s3-output_s3-work_local.sh
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,33 @@ | ||
| #!/bin/bash | ||
|
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| set -e | ||
|
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| script_name=$(basename "$0") | ||
| TMPOUT=s3://data-intuitive-tmp/test-nextflow-wave-fusion/output/${script_name%.sh} | ||
| OUT=output/${script_name%.sh} | ||
| RES=s3://data-intuitive-tmp/test-nextflow-wave-fusion/resources | ||
|
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| # clear output dir | ||
| echo "Clearing output directory" | ||
| aws s3 rm $TMPOUT --recursive | ||
| [ -d "$OUT" ] && rm -r "$OUT" | ||
|
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| # run component | ||
| echo "Running component" | ||
| NXF_VER=23.10.0 nextflow run \ | ||
| viash-io/test-nextflow-wave-fusion \ | ||
| -r main_build \ | ||
| -main-script target/nextflow/method/main.nf \ | ||
| -profile docker \ | ||
| -latest \ | ||
| --input $RES/input1.txt \ | ||
| --multiple_input "$RES/input1.txt;$RES/input2.txt" \ | ||
| --publish_dir "$TMPOUT" | ||
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| # sync output | ||
| echo "Syncing output" | ||
| aws s3 sync $TMPOUT $OUT | ||
|
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| # check if output is correct | ||
| echo "Checking output" | ||
| scripts/verify_output.sh "$OUT" |
File renamed without changes.