diff --git a/test_data/createTestData.sh b/test_data/createTestData.sh index 0e49060250e12b7ca5766f3584867417316e8098..aec4e91bb71d5bb79d87cd76994f6253cfe63ea3 100644 --- a/test_data/createTestData.sh +++ b/test_data/createTestData.sh @@ -9,12 +9,12 @@ mkdir -p NEW_test_data ln -sfn `readlink -e ./test_data/auth/credential.json` ~/.deriva/credential.json -mkdir -p ./NEW_test_data/bagit +mkdir -p ./NEW_test_data/bag singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' deriva-download-cli dev.gudmap.org --catalog 2 ./workflow/conf/replicate_export_config.json . rid=Q-Y5F6 -cp Replicate_Q-Y5F6.zip ./NEW_test_data/bagit/Replicate_Q-Y5F6.zip +cp Replicate_Q-Y5F6.zip ./NEW_test_data/bag/Replicate_Q-Y5F6.zip mkdir -p ./NEW_test_data/fastq -unzip ./test_data/bagit/Replicate_Q-Y5F6.zip +unzip ./test_data/bag/Replicate_Q-Y5F6.zip singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' bash ./workflow/scripts/bdbagFetch.sh Replicate_Q-Y5F6 Replicate_Q-Y5F6 cp Replicate_Q-Y5F6.R1.fastq.gz ./NEW_test_data/fastq/Replicate_Q-Y5F6.R1.fastq.gz cp Replicate_Q-Y5F6.R2.fastq.gz ./NEW_test_data/fastq/Replicate_Q-Y5F6.R2.fastq.gz