araport-contrib

Data files (and scripts used to generate these files) for the AIP Intermine, JBrowse and GBrowse2 installations

Shell scripts used to generate data files rely on methods available at the following github repository: tanghaibao/jcvi.

Setting up the data area

### choose location to download all relevant data files from TAIR FTP
### for this project, the data root is $AIP=/usr/local/projects/AIP
$ AIP=/usr/local/projdata/0611/projects/AIP && cd $AIP
$ mkdir -p DataProviders/TAIR && cd DataProviders/TAIR

### clone the araport-contrib repo
$ git clone https:/Arabidopsis-Information-Portal/araport-contrib.git

### download all TAIR data
$ ./download_tair_data.sh > download_tair.log 2>&1

### run the wrapper script
./run.sh $AIP > run.log 2>&1

Once the above setup process is complete, follow instructions for installing and loading data into JBrowse and GBrowse2 from their respective repos.