D I F F R N A : A RNA-Seq analysis pipeline
2021-11-29
Chapter 1 Prerequisites
1.1 Hardware and Operating System
The pipeline was developed and tested on Ubuntu 20.04.3 LTS
on top of the (GNU/Linux 5.4.0-88-generic x86_64)
kernel. The output of the commands uname
and neofetch
are provided to further detail our configuration.
$ uname -a
Linux machine329a7396-059f-41aa-94c7-4c41b4ec8290 5.4.0-88-generic #99-Ubuntu SMP Thu Sep 23 17:29:00 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
$ neofetch
.-/+oossssoo+/-. ubuntu@machine3f9ae3dc-6a4d-46b7-8131-04f00a1be146
`:+ssssssssssssssssss+:` --------------------------------------------------
-+ssssssssssssssssssyyssss+- OS: Ubuntu 20.04.3 LTS x86_64
.ossssssssssssssssssdMMMNysssso. Host: OpenStack Compute 18.2.1-1.el7
/ssssssssssshdmmNNmmyNMMMMhssssss/ Kernel: 5.4.0-88-generic
+ssssssssshmydMMMMMMMNddddyssssssss+ Uptime: 13 hours, 14 mins
/sssssssshNMMMyhhyyyyhmNMMMNhssssssss/ Packages: 719 (dpkg), 4 (snap)
.ssssssssdMMMNhsssssssssshNMMMdssssssss. Shell: bash 5.0.17
+sssshhhyNMMNyssssssssssssyNMMMysssssss+ Theme: Adwaita [GTK3]
ossyNMMMNyMMhsssssssssssssshmmmhssssssso Icons: Adwaita [GTK3]
ossyNMMMNyMMhsssssssssssssshmmmhssssssso Terminal: /dev/pts/0
+sssshhhyNMMNyssssssssssssyNMMMysssssss+ CPU: Intel (Haswell, no TSX, IBRS) (16) @ 2.294GHz
.ssssssssdMMMNhsssssssssshNMMMdssssssss. GPU: 00:02.0 Cirrus Logic GD 5446
/sssssssshNMMMyhhyyyyhdNMMMNhssssssss/ Memory: 635MiB / 64323MiB
+sssssssssdmydMMMMMMMMddddyssssssss+
/ssssssssssshdmNNNNmyNMMMMhssssss/
.ossssssssssssssssssdMMMNysssso.
-+sssssssssssssssssyyyssss+-
`:+ssssssssssssssssss+:`
.-/+oossssoo+/-.
This configuration was actually a virtual machine hosted on Biosphere’s RAINBio a cloud service maintained by the French Institue of Bioinformatics (Institut Français de Bioinformatique).
1.2 BioPipes: a Biosphere-commons app
The instance of the virtual machine we used is called BioPipes. It provides the most notable bioinformatics pipeline tools:
1.3 Main Tools
Their versions are specified to maximise reproducibility:
$ conda --version
conda 4.11.0
$ nextflow -v
nextflow version 21.10.0.5640
$ docker --version
Docker version 20.10.11, build dea9396
Detailed information about our development docker installation :
$ docker info
Client:
Context: default
Debug Mode: false
Plugins:
app: Docker App (Docker Inc., v0.9.1-beta3)
buildx: Build with BuildKit (Docker Inc., v0.6.3-docker)
scan: Docker Scan (Docker Inc., v0.9.0)
Server:
Containers: 0
Running: 0
Paused: 0
Stopped: 0
Images: 4
Server Version: 20.10.11
Storage Driver: overlay2
Backing Filesystem: xfs
Supports d_type: true
Native Overlay Diff: true
userxattr: false
Logging Driver: json-file
Cgroup Driver: cgroupfs
Cgroup Version: 1
Plugins:
Volume: local
Network: bridge host ipvlan macvlan null overlay
Log: awslogs fluentd gcplogs gelf journald json-file local logentries splunk syslog
Swarm: inactive
Runtimes: io.containerd.runc.v2 io.containerd.runtime.v1.linux runc
Default Runtime: runc
Init Binary: docker-init
containerd version: 7b11cfaabd73bb80907dd23182b9347b4245eb5d
runc version: v1.0.2-0-g52b36a2
init version: de40ad0
Security Options:
apparmor
seccomp
Profile: default
Kernel Version: 5.4.0-88-generic
Operating System: Ubuntu 20.04.3 LTS
OSType: linux
Architecture: x86_64
CPUs: 16
Total Memory: 62.82GiB
Name: machine3f9ae3dc-6a4d-46b7-8131-04f00a1be146
ID: XT4Y:2HUL:HXEA:CDXV:ERC7:Z7JZ:YYRU:WZBT:ERCU:6GGA:OBZ6:QLXE
Docker Root Dir: /mnt/docker-data
Debug Mode: false
Registry: https://index.docker.io/v1/
Labels:
Experimental: false
Insecure Registries:
127.0.0.0/8
Live Restore Enabled: false