Followed the guide from https://mac.getutm.app/gallery/ubuntu-20-04, but importantly the 'Display' needs to be set to 'Console only' for the 18.04 iso from: http://old-releases.ubuntu.com/releases/bionic/ubuntu-18.04.4-server-arm64.iso
-
once ubuntu is installed the 'Display' can be reset to 'Full Graphics'
-
install a suitable desktop e.g. XFCE with
sudo apt install tasksel sudo tasksel install xubuntu-desktop sudo reboot
Once you've got an Ubuntu 18.04 up and running continue here.
Package Installation
sudo apt-get install mongodb python-pymongo python-flask
sudo apt-get install tabix libhts2 libhts-dev
sudo apt-get install python-pysam
sudo apt-get install python-pip # for installing flask_wtf
Packages not available via apt-get
- flask_wtf
-
installed v0.14.3 due to a werkzueg dependency conflict with older versions
-
need to install from source via pip
pip install -U https://github.com/wtforms/flask-wtf/archive/refs/tags/0.14.3.tar.gz
-
Config of GoDb codebase
This section will be obsolete as the codebase gets updated and is currently a working document.
- all the config files in /cfg need to be checked for valid paths
- in particular 'common.cfg', 'godb.cfg' and 'webapp.cfg'
- also affy.cfg, 'broad.cfg', 'exome.cfg' and 'illumina.cfg'
- strikes me that they should be rationalised and be more agnostic
- Now they all use the $GODBROOT environment variable instead
Mongo DB data loading
Firstly, mongod needs to be running. Currently this is on localhost:27017, but will need to be changed for production.
All the VCF data must be in this structure under $DATADIR (defined in cfg/common.cfg) which separates out each assay type:
$DATADIR/
-> affy/
-> broad/
-> exome/
-> illumina/
The vcf data should be bgzip compressed, tabix indexed and have two files per chromosome for all samples named:
chr1.vcf.gz .. chr22.vcf.gz
chr1.vcf.gz.tbi .. chr22.vcf.gz.tbi
The data are loaded via three shell scripts which call other perl/python scripts:
bash load/sh/load_variants_from_vcf_files.sh $GODBROOT/cfg/broad.cfg
bash load/sh/load_samples.sh $GODBROOT/cfg/broad.cfg
bash load/sh/load_filepaths.sh $GODBROOT/cfg/broad.cfg
Repeat for each of the four assay types replacing the cfg file name to suit.
Load the webapp via bash webapp/sh/run_server.sh
and the variants should be
queryable from the interface on localhost:8085.
Job done!
Followed this guide:
https://medium.com/@lizrice/linux-vms-on-an-m1-based-mac-with-vscode-and-utm-d73e7cb06133 https://mac.getutm.app/gallery/ubuntu-20-04
Start from Arm64 install of 20.04 Server
https://cdimage.ubuntu.com/releases/20.04/release/ubuntu-20.04.2-live-server-arm64.iso
After initial install of server
- Install Xubuntu GUI
sudo apt install tasksel
sudo tasksel install Xubuntu-desktop
sudo reboot
- Intall software packages
sudo apt-get install mongodb (v.3.6.8)
sudo apt-get install python (v2.7.18)
End no python-flask is available for python2 on 20.04. Dead end.