Caper

* Added parameters
- `--java-heap-server`: Java heap size `java -Xmx` for `caper server` subcommand.
- `--java-heap-run`: Java heap size `java -Xmx` for `caper run` subcommand.

* Bug fixes
- `--docker` not correctly caught when it's already defined in WDL
- added warning when `--docker` is not defined for cloud backends

* Bug fix for `docker`
- Cromwell 42 defaults to use `delegated` flag for docker in mounting volumes but this flag was introduced in docker ce 17.04. Caper will not use this flag for backward compatibility (for docker ce < 17.04).

* final testing on AWS (since isolation issue for aliased tasks is fixed in cromwell-42)
- chip-seq-pipeline worked fine
* documentation for setting up cromwell server on AWS
* fixed bug in `file_exists()` for AWS
- `aws s3 ls` does not show exactly matched files. it also shows partially matched files.

* bug fix for locked copy (deadlock for URL to cloud URIs transfer)
* suppress gsutil/aws warnings (`no URLs matched one of the ...`)

* added `user` to `caper list` format
* users can filter workflows by submission datetime `--hide-result-before` ( or `hide-result-before` in your conf at `~/.caper/default.conf`)
- you can use the same (or shorter in terms of string length) datatime format shown in `caper list`.
- this is just about simple datetime string sorting

For example,

(base) leepc12kadru:/users/leepc12/code/test_wdl$ caper list
id status name str_label user submission
648d61d1-a6df-4d1d-8050-2b7fab0b1d7c On Hold None T5 leepc12 2019-06-13T11:12:25.661Z
afd8b507-928b-4ae9-9504-a584ce84442b On Hold None T4 leepc12 2019-06-13T11:12:21.917Z
05fd8f2b-da72-46c8-8e88-848bc4f0f5ea On Hold None T3 leepc12 2019-06-13T11:12:16.349Z
aa08ca19-0ac8-4ec6-995d-53bcfaaa1038 On Hold None T2 leepc12 2019-06-13T11:12:10.611Z
a6573ee9-5e08-432e-bf7f-5733069b7510 On Hold None T1 leepc12 2019-06-13T11:11:51.057Z
(base) leepc12kadru:/users/leepc12/code/test_wdl$ caper list --hide-result-before 2019-06-13T11:12:16
id status name str_label user submission
648d61d1-a6df-4d1d-8050-2b7fab0b1d7c On Hold None T5 leepc12 2019-06-13T11:12:25.661Z
afd8b507-928b-4ae9-9504-a584ce84442b On Hold None T4 leepc12 2019-06-13T11:12:21.917Z
05fd8f2b-da72-46c8-8e88-848bc4f0f5ea On Hold None T3 leepc12 2019-06-13T11:12:16.349Z
(base) leepc12kadru:/users/leepc12/code/test_wdl$ caper list --hide-result-before 2019-06-13
id status name str_label user submission
648d61d1-a6df-4d1d-8050-2b7fab0b1d7c On Hold None T5 leepc12 2019-06-13T11:12:25.661Z
afd8b507-928b-4ae9-9504-a584ce84442b On Hold None T4 leepc12 2019-06-13T11:12:21.917Z
05fd8f2b-da72-46c8-8e88-848bc4f0f5ea On Hold None T3 leepc12 2019-06-13T11:12:16.349Z
aa08ca19-0ac8-4ec6-995d-53bcfaaa1038 On Hold None T2 leepc12 2019-06-13T11:12:10.611Z
a6573ee9-5e08-432e-bf7f-5733069b7510 On Hold None T1 leepc12 2019-06-13T11:11:51.057Z
(base) leepc12kadru:/users/leepc12/code/test_wdl$ caper list --hide-result-before 2019-06-14
id status name str_label user submission

* Fix for SLURM Stanford Sherlock job failing issue even though Job is actually done successfully. `squeue` doesn't seem to work correctly.
- Job check-alive polling (`squeue -j {job_id}`) somtimes fail when server is busy
- Try `squeue` for every 20 second up to 3 times.
- increase interval for polling 180 sec -> 360 sec