Category Archives: EM

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

CryoSPARC 2 install on CentOS 7

There’s a new CryoSPARC available. We had a previous installation, but it can not be updated to this version. You need to ask for a new license. This is a boring post about how it is installed, plus the installation … Continue reading

Posted in bash, centos, cryoSPARC, EM, GPU, software, Uncategorized | 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

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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 leginon docker on CentOS 7 Part I: docker and database server install

Previously we we made a leginon CentOS 6 container on CentOS 7. Now the LXC containers are somehow more robust than a docker, but less popular and versatile. Therefore the need to make a docker instead. I start by cloning … Continue reading

Posted in bash, centos, containers, docker, EM, leginon, linux, python, yum | 2 Comments