Caper

Hotfix for `MAPPING_PATH_TO_URL` issue (PR 25).

Can convert `gs://`, `s3://` URIs to presigned URLs.
- Also can convert local path into a URL.
- This is an update for Croo to be able to generate presigned URLs for UCSC genome browser tracks

Added delay (2 sec) between multiple cURL queries.
- To prevent the following cURL error.

curl: (35) OpenSSL SSL_connect: SSL_ERROR_SYSCALL in connection to **********

1) Deprecated old flags `--use-docker` and `--use-singularity`.
`--docker` and `--singularity` can work as flags too.
bash
$ caper run atac.wdl --docker this will use docker image defined in WDL
$ caper run atac.wdl --docker docker_image_location


2) `caper init`
Choose a platform and caper will auto-generate default configuration file (`~/.caper/default.conf`) with only required parameters for a chosen platform.
bash
$ caper init sherlock


3) Others
- A file DB is now compressed.
- Better error checking and troubleshooting.

* Bug fixes
- Deepcopied files still have unlocalized files (JSON/TSV/CSV) again.

* Bug fixes
- Deepcopied files still have unlocalized files (JSON/TSV/CSV).