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

bellerbrock

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

bellerbrock

# Start by cloning  or pulling the latest updates in the ibp-sweetpotato-traits and Chado repos
git clone https://github.com/Planteome/ibp-sweetpotato-traits.git
git clone https://github.com/GMOD/Chado.git

# Load the ontology terms, then update cvterm paths. 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 CO_331 -d Pg -r postgres -p <PASSWORD> -n SweetpotatoTrait -u -v ibp-sweetpotato-traits/sweetpotato_trait.obo
perl Chado/chado/bin/gmod_make_cvtermpath.pl -H db4.sgn.cornell.edu -D sandbox_batatabase -d Pg -u postgres -p <PASSWORD> -c SweetpotatoTrait


# Example for other ontologies

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

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

#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

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#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)'

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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

Install Rstudio
Install Peek
Install VirtualBox
Install Android Studio

sudo apt install docker.io
sudo apt install htop

Setup .bash_aliases