search

nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
Other
382 stars 183 forks source link

FIX ice is now picked up globally and not locally #323

Closed NelleV closed 4 years ago

NelleV commented 4 years ago

The following lines caused a problem when the user upgraded iced outside of HiC-pro. HiC-pro was still using the ice script corresponding to an old version of the iced python package. The following change "just" rely on using the installed version of ice in the user's path rather than on a local version provided by HiC-pro. As a result the ice script used is always the one that is associated with the iced package installed.

NelleV commented 4 years ago

This PR is against master. Let me know if I should use devel instead.

nservant commented 4 years ago

Hi Nelle, Does it mean that I can remove the ice script from HiC-Pro scripts folder ?

NelleV commented 4 years ago

Yes : I'll update the installation procedure as well.

NelleV commented 4 years ago

Are tests being ran automatically? I thought a while back you had set up travis. If it's not the case, we should probably do that.

nservant commented 4 years ago

ok. Note that we will release a new version in the coming days (with python3 support) which does not install iced anymore but just ask it as a per-requisite

nservant commented 4 years ago

no continuous integration is not done so far ... but indeed it would be good

NelleV commented 4 years ago

That's awesome! That would solve the issue we have on our server!

nservant commented 4 years ago

ok. I will merge and include the change in the verison I just release to avoir confusion ... it's ok for you ?

NelleV commented 4 years ago

Sounds good to me!