basic machine setup cookbook
Prerequisite for vagrant
vagrant plugin install vagrant-chef-zero vagrant plugin install vagrant-omnibus
Our develop environment
vagrant version is
$ vagrant -v Vagrant 1.8.5
vagrant plugins version are
vagrant-chef-zero (2.0.0) vagrant-omnibus (1.4.1)
Setup using vagrant
berks vendor cookbooks vagrant up --provision
If you have some error message.
Sometimes it fails some reason(mostly network problem I think).
I'll hope to fix it and robust to finish the cookbooks.
I want to change recipe
apt-get -q -y --force-yes -o Dpkg::Options::='--force-confold' -o Dpkg::Options::='--force-all' install docker-engine=1.12.3-0~trusty
How long does it take to setup using vagrant
When I executed vagrant up , it tooks 1.5 hour. It does not need to any interaction. Just type command and wait.
I think most of time takes to download compressed(gzip) sailfish index (11G) and extract it.
I test it with the VM which is assigned 4 CPU and 8GB RAM. I write these assignment to Vagrantfile.
sailfish index create by execute sailfish command.
If you have enough resource, you can choose the method of create sailfish index via sailfish command.
Sometimes job is fail.
Answer. Maybe machine resource is not enought to execute.
Almost case is that RAM is not enough.
HISAT2 require some times 32GB.
You try to run some jobs parallel.
vagrant halt VBoxManage sharedfolder remove bayesvm_1.3.0 --name vagrant VBoxManage export bayesvm_1.3.0 -o bayesvm_1.3.0-dev.ova
How does Galaxy runs ?
- Galaxy run in docker
- Galaxy run with systemctl
- Galaxy starts on boot by default setting
- Galaxy using port 28080, 29002
I can't access .
Galaxy is available port 28080.
How to change Galaxy port 28080 to 80
- Check port 80 is used or not.
- If port 80 is used, stop the service.
- Change port 28080 to 80 by editing
Why Galaxy default port is 28080 ?
To avoid conflict with other application.
Port 80 is using by httpd server (Apache httpd , Nginx is famous )
sudo /etc/init.d/docker-galaxy start
sudo /etc/init.d/docker-galaxy stop
Where is setting files.
- Start script
- Stop script
Other directories and files structure.
Run Galaxy following directory
|In host||In docker container||File or Directory||Note|
|/usr/local/galaxy-bitwf/scripts/2790.diff||/galaxy-central/2790.diff||file||Galaxy pull 2790 diff|
|/usr/local/galaxy-bitwf/data||/data||directory||for share Readonly|
NFS and docker
If you using NFS for data persistent, you need to care about order of NFS mount and docker galaxy start.
NFS needs to mount before docker galaxy start.
To check mount is success
/data is on NFS
docker exec galaxy_bitwf_1.3.0 ls /data
If there is no data , it fail to start. To resolve problem
sudo /etc/init.d/docker-galaxy stop docker rm galaxy_bitwf_1.3.0 sudo /etc/init.d/docker-galaxy start
Not start docker-galaxy at boot time
If you want to start docker-galaxy , you need to disable automatic start on boot.
sysv-rc-conf docker-galaxy off
Create conda environment and install
conda create -n myenvironment bwa=0.7.12 source activate myenvironment bwa
list conda envrionment
conda info -e
list conda channels
conda config --get channels conda config --get channels --system
conda remove -n myenvironment bwa
Remove conda environment
conda env remove -n myenvironment
Relation Virtual Machine and Cookbook Version
|VirtualMachine||Cookbook Name||Cookbook Version|
|1.4.0||basicsetup||1.3.0 and upgrade by hand|
Next Release 1.5.0 cookbook name change is scheduled.
Copyright (c) [2015-2017] [Manabu ISHII] and RIKEN Bioinformatics Research Unit Released under the [Apache License Version 2.0]