Fix typo
Use traceback.format_exception_only to print error messages

Also, these errors are now printed on stderr rather than stdout.
PTFM-12607: adding bash helper variables

Summary:
1. Refactoring of code, so as to achieve sharing, between local and remote execution.
2. Adding several bash variables available to the application: filenames, prefixes, and paths.
3. Reducing the number of file uploads, to reduce runtime
4. Marking tests correctly, so as not to run jobs

Test Plan: application tests

Reviewers: klai

Reviewed By: klai

Differential Revision: https://phabricator.dnanexus.com/D140
PTFM-13510: Making the deepdirs test less fragile

Summary: Simplifying script a little, by avoiding pushd/popd. This seems to fix running on jenkins.

Test Plan: This is an existing test.

Reviewers: bagee

Reviewed By: bagee

Differential Revision: https://phabricator.dnanexus.com/D144
Remove experimental statement from dx-print-bash-vars
'dx cp' regression tests

Summary: Add regression tests for b4d0a74f as well as for other, pre-existing "dx cp" functionality.

Test Plan: This revision contains only test changes

Reviewers: psung

Reviewed By: psung

Subscribers: akislyuk

Differential Revision: https://phabricator.dnanexus.com/D137
PTFM-12428 Remove printing of stack trace for "dx run --ssh" when user's account not configured for SSH.

Summary: Additionally allow specifying DX_USER_CONF_DIR to override ~/.dnanexus_config (affects ../dxpy/scripts/dx.py: ssh_config and verify_ssh_config).

Test Plan: ./test_dxclient.py TestDXClientRun.test_dx_run_ssh_no_config

Reviewers: psung

Reviewed By: psung

Differential Revision: https://phabricator.dnanexus.com/D143
Changelog and version updates for v0.123.0
Minor test fixes

* Use dxpy instead of shelling out to "dx new project", "dx wait", etc.
  Considering that each setUp and tearDown used to invoke dx twice, this
  should save upwards of 300ms *per test*.
* Convert some print statements to test names.
* assertSubprocessFailure no longer prints out stderr unless the regexp
  assertion failed; it's likely that check_output already printed stderr
  out anyway, so such lines were duplicated.
Fixup bb71c96: use terminateJobs to reproduce original destroy call
Update exec_io.py

Updating to point to new reference genomes project (file based instead of gtable based) and also making sure that the bill-to for the project is org-dnanexus so outside users can't publish a project w/ the same name and have it discovered by dx in place of ours.
Moving options to import reads, mappings, and variants from visible options to hidden.  They're still available, but won't be advertised by the application.
Merge branch 'master' of https://github.com/dnanexus/dx-toolkit
Tweak help message
PTFM-12951 Move EE dependency installation code into dxpy