Mark's idiosyncratic setup

[turbomam]

pip cache purge
git clone git@github.com:cmungall/semantic-sql.git
cd semantic-sql/
sed -i.bak '1 s/sh$/bash/' ./utils/create-semsql-db.sh
wget https://dlcdn.apache.org/jena/binaries/apache-jena-4.2.0.tar.gz
tar xzvf apache-jena-4.2.0.tar.gz 
export JENA_HOME=apache-jena-4.2.0
export PATH=$PATH:$JENA_HOME/bin
make bin/relation-graph
cd bin/
rm relation-graph 
ln -s ../relation-graph/bin/relation-graph
cd ..
make bin/rdftab
export PATH="$PATH:./bin"
python3.9 -m venv venv
source venv/bin/activate
pip install wheel
pip install -r requirements.txt

ERROR: linkml-runtime 1.1.2 has requirement pyyaml~=5.1, but you'll have pyyaml 6.0 which is incompatible.

curl -L -s http://purl.obolibrary.org/obo/pato.owl > owl/pato.owl
make db/pato.db
npm install obographviz
export PATH=$PATH:./node_modules/obographviz/bin/
python -m semsql.subgraph -d db/pato.db -f obojson -m label size > pato_size.json
og2dot.js --outfile pato_size.png --to=png  pato_size.json

[turbomam]

• no apt-get install equivalent for brew install jena in Ubuntu 20 #13
• relation-graph symlink broken #23
• ./utils/create-semsql-db.sh requires /bin/bash in Ubuntu Linux 20 #24
• linkml-runtime vs pyyaml version conflict #25
• running subgraph wihtout conda? #26
• elaboration of python3 -m semsql.subgraph dependency on ./node_modules/obographviz/bin/og2dot.js #27