Category Archives: modules

Install pyEM on CentOS 7

After a week of silence, I’m back on track. I managed to integrate pyEM onto our systems, and this is my log about. We want it to export cryoSPARC data to relion. Since we don’t start from scratch, my first … Continue reading

Posted in bits, centos, linux, yum, python, EM, bash, modules, cryoSPARC | Leave a comment

Topaz install on CentOS 7

Yes I’m back to work. I should have logged it more, but I was busy with so many issues that the only thing I wanted to write was fiction. Anyway. Today we are going to install Topaz over our already … Continue reading

Posted in bits, centos, docker, EM, linux, modules, nvidia, python | Leave a comment

CCP-EM install on CentOS 7

The CCP-EM software suite is a package containing tools for cryo-EM. You can find it here. I want to install it together with the already existing software. The Brief instructions seem to work fine, provided you have the requirements. This … Continue reading

Posted in bash, bits, EM, modules, python | Leave a comment

crYOLO conda error: bad interpreter

Creating a new virtual environment for crYOLO, that implement You Only Look Once for particle picking, I stumbled upon this error. I saw it before, but here we don’t use python so much, I mean, we use it only for … Continue reading

Posted in bits, centos, EM, linux, modules, python, software, sphire | Leave a comment

A leginon docker on CentOS 7 Part II: centos7AutoInstallation.py

On the previous post, we prepared a basic LAMP docker to hold a leginon installation.  I assume now you downloaded the installer for CentOS 7 and copied it to the docker via ssh or shared folder. We can simply run … Continue reading

Posted in bits, centos, containers, docker, EM, filesystems, leginon, linux, modules, mysql, yum | 1 Comment

A MATLAB Runtime module

First we download the chosen package from the MATLAB site. Then we unzip it on a test folder and run the provided install script. The procedure is quite easy, no programming knowledge is needed. We choose the path to our … Continue reading

Posted in bits, linux, matlab, modules, slurm | Leave a comment

Add module path on CentOS 7

If you installed software modules on CentOS 7, you know that the module definitions are stored on /usr/share/Modules/modulefiles/ by default. We want to change that, so that we can store the modules on the place we want, or add different … Continue reading

Posted in bash, centos, modules, software | Leave a comment