Juicer Conda env with SLURM

638 views

Skip to first unread message

Xingbo Wu

unread,

Feb 24, 2021, 7:24:53 PM2/24/21

to 3D Genomics

Hi,

Is there a conda package for juicer?

I created a conda env for juicer, juicer with then launch several jobs. However, those submitted jobs seems not in conda env, thus could not run.

Does any one run juicer in SLURM with conda env?

Thanks.

Xingbo

Gaurav Agavekar

unread,

Mar 11, 2021, 10:51:38 AM3/11/21

to 3D Genomics

Hi Xingbo,

Kinda late reply, but hope it might help if necessary.

I struggled getting Juicer running on SLURM as well. I usually manage my other software using Conda, however, it seems like you don't need it for Juicer.

I used a script uploaded by David from Aiden Lab here: https://www.dropbox.com/s/hfwm7sjxtdi9hrd/juicer.tar.gz?dl=0 from this thread: https://groups.google.com/g/3d-genomics/c/tcoWAVoTS6A/m/MQcBCljcAwAJ

Our HPC has modules system and the necessary modules (bwa, java, etc.) were already installed. So I just changed the path to these modules in the script and partition names according to our cluster.