Fix #46

[sebastian-luna-valero]

Hi @kevinrue

Thanks for reporting #46

We used to have "production" and "devel" environments but that's changed over time and the install script hasn't been updated accordingly.

Here is my suggested change. The code currently looks redundant but I would like to leave the if/then/else statement in place in case we think it is useful to go back to "production" and "devel" environments.

Please test and confirm whether it works for you.

Best regards, Sebastian

PS1: Also Travis has changed the default Ubuntu from Trusty to Xenial, which changed the way xvfb works, and I have updated the .travis.yml accordingly; https://docs.travis-ci.com/user/gui-and-headless-browsers/#using-xvfb-to-run-tests-that-require-a-gui

PS2: I had to add htslib as an explicit dependency to the cgat-apps.yml, to avoid errors like

/home/travis/build/cgat-developers/cgat-apps/conda-install/envs/cgat-a/compiler_compat/ld: cannot find -lhts

See example in: https://travis-ci.org/cgat-developers/cgat-apps/builds/574429702

[kevinrue]

Hi @sebastian-luna-valero The installation completed successfully now. Thanks a lot! I hope you're well. Best, Kevin

[Acribbs]

Hi @sebastian-luna-valero, these changes haven't inadvertently affected cgat-flow have they?

I accidentally committed to the master https://github.com/cgat-developers/cgat-flow/commit/73c29b35c6d6ccb11c966bbb93428acb21e3651a to change travis testing to reflect the xvfb changes you mentioned. However, the testing is failing https://travis-ci.org/cgat-developers/cgat-flow/builds/575047030

For the osx build I have no idea why there is a imp ValueError: Buffer for this type not yet supported, but the linux build seems to be failing due to over runs.

[sebastian-luna-valero]

Hi,

Please see https://github.com/cgat-developers/cgat-flow/pull/105

Best regards, Sebastian