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

#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

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

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

Install Rstudio
Install Peek
Install VirtualBox
Install Android Studio

sudo apt install docker.io
sudo apt install htop

Setup .bash_aliases

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

#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

1. Download the latest schemaspy release from https://github.com/schemaspy/schemaspy

2. Check your java installation, and if not installed already install the required version of java. In this case java 8

To check: 

java -version
update-alternatives --list java

To install:  (from https://www.vultr.com/docs/how-to-manually-install-java-8-on-ubuntu-16-04)

bellerbrock

# starting in the cxgn directory clone or pull the latest updates in the sgn and Chado repos

git clone https://github.com/solgenomics/sgn.git
git clone https://github.com/GMOD/Chado.git

# Load the ontology terms
# If you get a message about missing packages it may be necessary to add to Chado modules to perl5lib: export PERL5LIB=/home/production/cxgn/Chado/chado/lib:$PERL5LIB

perl Chado/chado/bin/gmod_load_cvterms.pl -H db4.sgn.cornell.edu -D sandbox_batatabase -s TIME -d Pg -r postgres -p <PASSWORD> -n cxgn_time_ontology -u -v sgn/ontology/cxgn_time.obo

bellerbrock

Notes about confirmation email troubleshooting.

Confirmation emails sent with the local hostname go to spam, and Mail::Sendmail does seem to support SMTP auth very well. I could not get Mail::Sendmail to work with smtp.gmail.com. I also had no luck with Email::Sender::Transport::SMTP which is already a dependency, or Email::Sender::Transport::SMTPS

The best soultion I've found is Email::Send::SMTP::Gmail which works well and has bonus features like support for file attachments. To use it, install it (cpanm Email::Send::SMTP::Gmail) and make sure the gmail account being used for login has the 'allow access for less secure apps' setting turned on.

Here's a test script for proof of concept: