Croo

Fix dependency problem.

- 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`.

Bug fixes
- Fix for `TypeError: 'NoneType' object is not iterable` error.

Added `--no-graph` to disable the task graph feature.
- Fix for issue 11

Added `graphviz` to pip package requirements.
- So that `graphviz` is automatically installed during `pip` installation
- However, `pip install graphviz` still doesn't install GraphViz's executable `dot`.
- Debian/Ubuntu: `sudo apt-get install graphviz`

Added a task graph.
- Pipeline developers: See [this doc](docs/OUT_DEF_JSON.md) how to update an output definition JSON file for your pipeline.

> **IMPORTANT**: Upgrade Caper to `>=0.5.0` first.

$ pip install caper==0.5.0


Deprecated parameters
- A flag `--use-rel-path-in-link`: we no longer need this since we can get a presigned/converted URL for both a file table and a UCSC browser track.

Presigning for cloud URIs (`gs://`, `s3://`)
- Use a flag `--use-presigned-url-gcs` and `--gcp-private-key [KEY_FILE]` to presign GCS URIs.
- Use a flag `--public-gcs` if your GCS bucket is public. Don't need presigning since it's already public.
- Use a flag `--use-presigned-url-s3` to presign S3 URIs.
- Use `--tsv-mapping-path-to-url [TSV_FILE]` to define mapping of local path prefix to a URL prefix. You may need to have a web server and organized outputs should be (symlinked) on there.

Added USCS genome browser tracks based on presigned/converted URLs
- Use `--ucsc-genome-db [GENOME]` to define genome DB for UCSC track (e.g. `hg38`)
- Use `--ucsc-genome-pos chr?:?????-??????` to define initial genome coord for tracks.