d3b-center/cavatica-tools

Name: cavatica-tools

Owner: Center for Data Driven Discovery in Biomedicine

Description: null

Created: 2017-03-24 17:56:52.0

Updated: 2018-01-24 21:47:33.0

Pushed: 2018-01-09 18:52:20.0

Homepage: null

Size: 16516

Language: Perl

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README

cavatica-tools

cavatica-uploader

ad files to Cavatica

vatica-uploader/bin/cavatica-uploader.sh -t <token> -p <project_id>  <file_to_upload>

./cavatica-uploader/bin/cavatica-uploader.sh -h to see more usage

get file path ID on Cavatica

e: perl get_path_id.pl -t <token> -p <project_name>  <file>

ple: perl get_path_id.pl -t  ef6a1...das6 -p zhangb1/develop-project test.bam

post new volume

e: perl post_new_volume.pl -t <token> -b <bucket_name> -v <volume_name> -i <access_key_id> -k <secret_access_key>

ple: perl post_new_volume.pl -t  ef6a1...das6  -b test.cavatica -v task_test_volume -i AKIA...Q -k 8Z+mJ4...LG

improt file from S3 bucket to Cavatica

e: perl import_file_volume.pl -t <token> -p <project_name> -v <volume_name> <file_name_cavatica> <file_from_S3_bucket>

ple: perl import_file_volume.pl -t  ef6a1...das6 -p zhangb1/develop-project -v zhangb1/task_test_bucket2 test.bam test.bam

export file to S3 bucket

e: perl export_file_to_s3.pl -t <token> -p <project_name> -v <volume_name>  <file_name_cavatica>

 export_file_to_s3.pl -t ef...ec6 -p zhangb1/develop-project -v zhangb1/test_cavatica_wgs test.bam