PubMed mining tools.
We shall provide this functionality:
- update local cache, a mongo document database, from a query to PubMed
- build mesh term networks from queries to mongodb, as networkX graphs, save them to python pickle files
- plot these networks using matplotlib
- plot these networks using d3
- convert these networks to CSV files
These functions shall have a command line interface and those scripts shall have PSU Galaxy wrappers.
We hope to share this tool online from our own Galaxy instance. In the meantime you can roll your own and add our packages.
Follow these instructions to setup your own galaxy.
After you have installed your own Galaxy instance, make a clone of our repo:
git clone https://github.com/LC3-INMEGEN/pubmed-mining.git
Move to the Galaxy Tools directory:
cd galaxy/tools/
Asuming you cloned our repo at the same level, create a symbolic link to the repo clone:
ln -s ../../pubmed-mining/ .
Move to the config directory:
cd ../config/
Create a symbolic link to the tool configuration file on the repo, this will let our tools to be available on your local Galaxy instance:
ln -s ../../pubmed-mining/pubmedmining_tools.xml .
Delete the original galaxy config file:
rm -Rf galaxy.ini
Create a symbolic link to the galaxy conifg file on the repo:
ln -s ../../pubmed-mining/galaxy.ini .
Now go back to the Galaxy directory:
cd ..
Create a virtual environment there:
virtualenv .venv
Activate it
source .venv/bin/activate
Install the biopython, networkx, numpy and pymongo packages:
pip install -r ~/pubmed-mining/requirements.txt
Our tools should be available now for you to run on your local Galaxy instance, you should probably restart it.
##Galaxy Docker Image