Linux on Firas Sadiyah

Running PyEnsembl on CentOS HPC

Sun, 11 Feb 2024 12:00:00 +0000

Today, I am installing a Python package on one of the high-performance computing (HPC) systems that I work with. This CentOS 7 setup resembles a fortress, with its stringent security protocols, understandable due to hosting clinical data, but making it quite a challenge to install essential Python packages from public repositories.

The package I’m attempting to install is PyEnsembl, a handy tool for accessing Ensembl’s genetic information.

PyEnsembl Setup

I started by creating a new conda environment:

Ubuntu setup for data science

Sat, 16 Sep 2017 12:00:00 +0000

This posts shows how I setup a new Ubuntu for Data Science.

Update Ubuntu

1sudo apt update
2sudo apt upgrade

Configure apt

It’s always a good idea to check the baseline setup. So, let’s check the current apt keys.

1sudo apt-key list

Then, let’s check the sources.

1cat /etc/apt/sources.list
2cd /etc/apt/sources.list.d/

And finally, let’s check the users and group.

 1cut -d: -f1 /etc/passwd # will list all local users
 2cat /etc/passwd # will list all local users with groups and other properties
 3getent passwd # same as above
 4
 5cut -d: -f1 /etc/group # will list all local groups
 6cat /etc/group # will list all local groups
 7id -Gn
 8groups
 9
10getent group groupname # will list all members of groupaname
11id username # will list all the groups a particular username belongs to

Configure Unity

To get minimise window on clicking its icon:

Mounting remote drives locally using sshfs

Tue, 29 Aug 2017 12:00:00 +0000

To mount a network drive as a local one, you can use sshfs.

Generate SSH key

1$ mkdir ~/.ssh #if it does not already exist
2$ chmod 700 ~/.ssh
3$ cd ~/.ssh
4$ ssh-keygen -t rsa
5$ enter a keyname
6$ enter a passphrase
7$ ssh-copy-id -i [path to rsa file] USER@SERVER

Where -i indicates where the rsa file is located. The .pub key is the one needed to be copied.

[Optional] Start a SSH agent, and add the key to the SSH agent: