ENCODE-DCC/croo: v0.4.0

• Important notice
  • UCSC browser web page no longer accepts long URL (where full track hub text is encoded in such URL). So instead, Croo makes another alternative link with a linked track hub txt file instead of a full track hub text. One issue is that this text file should be public. So this track hub txt file will be converted into public URL (according to parameters defined by users). e.g. being presigned on GCS.

We have replaced old localization module (Caper's CaperURI) with a new one (Autouri's AutoURI).

• Deprecated parameters

  • --http-user and --http-password: Autouri automatically uses ~/.netrc file for authentication of HTTP URLs. Use ~/.netrc file.
  • --use-gsutil-over-aws-s3: Old module used aws s3 CLI for S3 files and gsutil for GCS files. This parameter is no longer needed since new model uses Python interfaces instead of CLIs.

• Added parameters

  • --verbose (-V) and --debug (-D): Prints detailed logs. verbose >= INFO, debug >= DEBUG.
  • --use-gsutil-for-s3: This is different from the deprecated parameter --use-gsutil-over-aws-s3. Old loc module used gsutil CLI for file transfer between GCS (gs://) and any other. But new module optionally (controlled by this parameter) uses gsutil only for direct file transfer between GCS and S3 (s3://). If this flag is turned on gsutil will be used only for such direct file transfer.

• Bug fixes

  • --tmp_dir was not checked correctly (when it's on $CWD).
  • --no-graph: This has been removed, Croo will automatically check if dot executable exists on $PATH. This is a bit annoying since pip install graphviz does not install this important executable dot. Users can only get it with system-level installation command like sudo apt-get install graphviz.