########## What is CART ?
CART is a software that retrieves biological annotations of chemical sets and computes which are enriched. In a nutshell, the input consists in a list of chemical names and the output is a table of enriched biological terms that are associated to these chemical names. CART consists of three modules: Name Matching, Enrichment, Visualization. 
########## How to use it ?
In order to retrieve the enriched biological terms of a list of chemical names, you can either: 

1-Run everything at once
2-Run it step by step

########## OPTIONAL : if you have installed cart using the automatic installer, then activate the cart python virtual environment:
source ~/cart-virtualenv/bin/activate/
########## 1- Run everything at once
cd ${CART_INSTALLATION_DIRECTORY}/run-all-at-once/
Open the file run-all-at-once.sh
Set the arguments of your choice.
NB : you need to specify at least your foreground (argument fn_fg)
The other parameters relative to each step are optional and can be set by the user.
The document tutorial.pdf contains the full list of these paremeters, including a description and values they can hold.
The document tutorial.pdf is available under ${CART_INSTALLATION_DIRECTORY} or online at http://det.embl.de/static/tutorial-command-line.docx

########## 2- Run step by step
cd ${CART_INSTALLATION_DIRECTORY}
${description_file}=${CART_INSTALLATION_DIRECTORY}/static/all-drug-description_ver2.txt
${header_js}=${CART_INSTALLATION_DIRECTORY}/static/header_js.js
${footer_js}=${CART_INSTALLATION_DIRECTORY}/static/footer_js.hs

### Match chemical names
python src/name_matching.py -n  test/cmap_foreground_codim2.tsv -o nm_out_foreground.tsv -a true -e true;
python src/name_matching.py -n  test/cmap_background.tsv -o nm_out_background.tsv -a true -e true -s true

### Retrieve biological annotations and compute enrichments
python src/enrichment_calculation.py -f nm_out_foreground.tsv -b nm_out_background.tsv -d  -o enr_out_enr.tsv -p enr_out_ann.tsv -a 0.01 -m Fisher -c FDR --verbose 2

### Visualize results
python src/result_annotator.py -i enr_out_enr.tsv -o viz_out_table.html;
python src/network_generator.py -a enr_out_ann.tsv -e enr_out_enr.tsv -d ${description_file} -k ${header_js} -f ${footer_js} -o viz_out_network.html

### Get synonyms
python src/name_matching.py -n  cmap_foreground_codim2.tsv -o nm_out_foreground_synonyms.tsv -a true -e true -s true;



########## Terminology
Foreground: The set of chemicals on which enrichments will be computed
Background: The set of chemicals used by the fisher-test during the enrichment computation
CID: A chemical ID as found in one of the chemical universe
Chemical universe: Set of chemical names associated to CIDs. We use two chemical universe : Stitch and Pubchem
Database: Database used during the enrichment step. Each database contains specific biological terms associated to different chemicals
${CART_INSTALLATION_DIRECTORY} : CART installation directory