v1.3.0

gcp-memory-retry currently doesn't work. It should be fixed on Cromwell's side. See this for details.

If upgrading from old Caper, then manually upgrade autouri to >=0.2.1 to fix the public bucket access issue.

$ pip install autouri --upgrade
$ autouri -v # check if version >= 0.2.1

Linear resource analysis for workflows run on Google Cloud.

• Can run this with any workflows run with Caper>=1.2.
• Usage: caper gcp_res_analsysis WORKFLOW_ID_OR_METADATA_JSON ... MORE_WORKFLOW_ID --plot-pdf result.pdf
• For each task, collect resource data from multiple workflows and do linear regression on
  • x: Input file sizes.
    • To simplify the problem to a single linear regression, all input file sizes are summed up by default. But users can use multiple linear regression without summation (scatter plot won't be available).
    • 2D scatter plot with a fitting line.
  • y: Resource taken
    • Max memory
    • Max disk usage
• Examples (ENCODE ATAC-Seq pipeline)
  • Plot: https://storage.googleapis.com/caper-data/gcp_resource_analysis/example_plot/atac.pdf
  • Input file variable definition JSON
    • Can be defined with --in-file-var-def-json.
    • If not defined, then analyze all tasks with all input variables.
    • https://storage.googleapis.com/caper-data/gcp_resource_analysis/in_file_vars_json/atac.json.

Change of default parameters for Python API.

• local_loc_dir: defaults to CWD/.caper_tmp.
• local_out_dir: defaults to CWD.

Bug fixes

• Cannot access to Google public buckets.
  • Updated localization module autouri>=0.2.1 to use Google's anonymous client for public buckets.
• caper init fails due to ~/ not expanded correctly.
• Server instance creation shell script fails when parsing startup script.
  • scripts/gcp_caper_server/create_instance.sh
• Misleading error messages
  • work_dir -> loc_dir.