bellerbrock

#Docker deployments are now even easier and handled via docker-compose

git clone https://github.com/solgenomics/breedbase_dockerfile.git
cd breedbase_dockerfile

# For development
./prepare.sh
mkdir archive
mv sgn_local.conf.template sgn_local.conf # Edit default and add web_usr password
sudo docker-compose up -d

bellerbrock

#breedbase
alias log='tail -f -n 100 /var/log/sgn/error.log'

#docker commands

alias drm='docker stop $(docker ps -qa) && docker rm $(docker ps -qa) && docker image rm $(docker images) && docker volume rm $(docker volume ls)' # && docker ps -a && docker images && docker volume ls'
alias dps='docker ps --format "table {{.Names}}\t{{.Status}}\t{{.Image}}"'
alias dpsa='docker ps -a'
alias dstart='docker start $(docker ps -qa)'
alias dstop='docker stop $(docker ps -qa)'

bellerbrock

Install Rstudio
Install Peek
Install VirtualBox
Install Android Studio

sudo apt install docker.io
sudo apt install htop

Setup .bash_aliases

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dbhost breedbase-db
dbname breedbase
dbuser postgres
dbpass postgres

rootpath /home/production/cxgn
basepath /home/production/cxgn/sgn

composable_cvs trait,toy
composable_cvs_allowed_combinations Time Series|trait+toy

bellerbrock

Step 1: Download and install Protege. 
Step 2: Git clone the ontology repository into local directory.
Step 3: run git checkout -c topic/your_new_topic.
Step 4: Run Protege (./run.sh on linux) and load the .obo file.
Step 5: go to File -> Preferences -> New Entities. Set Auto Generated ID to Numeric, and set Start to an id that will start filling in an unused sequence. 
Step 6: Go to entities tab and add new terms by selecting parent class and clicking add subclass.
Step 7: When finished with edits, go to file -> save as and save as obo file.
Step 8: Finally add to git with git add -u, git commit -m "your message here", and git push --set-upstream topic/your_new_topic.
Step 9: Repeat with futher commits as needed, then go to github.com and submit pull request.

bellerbrock

#here's how I was able to create temp user accounts en masse for spb workshops. Could prove useful for future workshops:
Step1: 

Manually create a dummy account through the test site's user interface. Give it username 'password_source' and the password that you want to use for all the temp user accounts.

Then, connect to the test database using psql and run:

begin;

insert into sgn_people.sp_person (first_name, last_name, username, password, private_email, user_type) (select 'test' as first_name, 'user' || i as last_name, 'testuser' || i as username, (select password from sgn_people.sp_person where username = 'password_source') as password, 'spbuser' || i || '@mailinator.com' as email, 'submitter' as user_type from generate_Series(0,50) as i);

bellerbrock

Make sure your VM is shut down!

1.  In your virtualbox folder, find the correct disk image. If it isn't already a vdi, convert it:
    `VBoxManage clonehd box-disk1.vmdk box-disk1.vdi --format vdi`
    
2.  Enlarge the vdi file. 
    The number you give as an argument is in MB, or GB times 1024. In this case 250GB * 1024 MB/GB = 256000:
    `VBoxManage modifyhd box-disk1.vdi --resize 256000`
    
3. Open VirtualBox manager and click on the New icon in the top left to create a new machine. After naming it and picking the amount of memory,

bellerbrock

commit and push, or pull all branches to be included in update into master branch. 

1. run tests, including unit, unit fixture, and selenium tests. 
- for unit tests: `perl t/test_fixture.pl --noserver t/unit`
- for unit_fixture tests: `perl t/test_fixture.pl t/unit_fixture
- for selenium tests: 
  run selenium2 server in seperate terminal with `java -jar selenium-server-standalone-2.53.0.jar`. This jar file should be in the vagrant home directory
  then run `perl t/test_fixture.pl t/selenium2/`
  
  if any tests fail, they can be run individually and troubleshot to make any necessary fixes to the code on the master branch, or to update the test itself

bellerbrock

sudo R
update.packages(ask=TRUE)
install.packages('devtools')
devtools::install_github('c5sire/brapi')
quit()

bellerbrock

ssh production@vm-04.sgn.cornell.edu
sudo xl list
sudo xl destroy hidap.sgn.cornell.edu
sudo xl create /etc/xen/hidap.sgn.cornell.edu.cfg
ssh production@hidap.sgn.cornell.edu
sudo systemctl restart shiny-server