GitLab

peekJob.pl allows us to check which params a job has access to

add simulated output directories to the ascii.t exclude list so that we can keep our simulated lsid output identical to the expected output

* version/2.4:
  Check that LSF detection works as expected
  bugfix: keep the modified $PATH local to the test, otherwise it will bleed into the other tests
  Make sure this is a real LSF (or openlava) and exclude Slurm clusters that ship "lsid"
  Don't use the enhanced mode as it messes up most analysis names

* version/2.3:
  Don't use the enhanced mode as it messes up most analysis names

* version/2.2:
  Don't use the enhanced mode as it messes up most analysis names

In enhanced mode, the string "a_b" is displayed as "a" followed by "b"
in subscript. Most of our analyses use underscore, so the fix is to
disable the enhanced mode.

Bumps [junit](https://github.com/junit-team/junit4) from 4.12 to 4.13.1.
- [Release notes](https://github.com/junit-team/junit4/releases)
- [Changelog](https://github.com/junit-team/junit4/blob/main/doc/ReleaseNotes4.12.md)
- [Commits](https://github.com/junit-team/junit4/compare/r4.12...r4.13.1

)
Signed-off-by: dependabot[bot] <support@github.com>

This assumes apt-get update has been run

https://packages.ubuntu.com/bionic/libdbd-sqlite3-perl

* version/2.4:
  Add substitution example + one hash, to TestRunnable.py
  Comment not a question
  Allow a single hash in a string without substitution (in python wrapper)

* version/2.4:
  Don't attempt removing objects that haven't been stored
  Somehow, only 9.6 seconds seem to elapse on Travis when sleeping 10 seconds
  Simplified the Runnable: no need to check for the overhead, checking that it slept 10 seconds suffices

This happens quite often, so let's bake it in the test and make Travis
pass.

Simplified the Runnable: no need to check for the overhead, checking that it slept 10 seconds suffices

* version/2.4:
  bugfix: wrong number of arguments
  bugfix: autoflow is a property of the job, not the runnable

* version/2.4:
  Regenerated the scripts documentation using a recent toolchain
  Regenerated the Doxygen documentation with a recent Doxygen
  Regenerated the Doxygen documentation with a recent Doxygen
  Restored compatibility with recent versions of Doxygen
  Regenerated the Doxygen documentation with a recent Doxygen
  Regenerated the scripts documentation using a recent toolchain
  Regenerated the Doxygen documentation with a recent Doxygen
  Restored compatibility with recent versions of Doxygen
  Regenerated the scripts documentation using a recent toolchain
  Regenerated the Doxygen documentation with a recent Doxygen
  Restored compatibility with recent versions of Doxygen

* version/2.3:
  Regenerated the Doxygen documentation with a recent Doxygen
  Regenerated the scripts documentation using a recent toolchain
  Regenerated the Doxygen documentation with a recent Doxygen
  Restored compatibility with recent versions of Doxygen
  Regenerated the scripts documentation using a recent toolchain
  Regenerated the Doxygen documentation with a recent Doxygen
  Restored compatibility with recent versions of Doxygen

pm=C means that Doxygen will receive C-style annotations for *.pm files,
as ensembldoxygenfilter.pl returns. This option is only needed for Doxygen >1.8.7

* version/2.2:
  Regenerated the scripts documentation using a recent toolchain
  Regenerated the Doxygen documentation with a recent Doxygen
  Restored compatibility with recent versions of Doxygen

pm=C means that Doxygen will receive C-style annotations for *.pm files,
as ensembldoxygenfilter.pl returns. This option is only needed for Doxygen >1.8.7