This will generate manifest/project files for projects recently delivered in the LIMS
- Access to the LIMS restful service
- Access to the Create Manifest Sheet java application
In the main repo directory, add the following to a file named constants.sh and fill in the variables for your setup:
today=$(date +%Y_%m_%d)
#paths
draftsDir=""
createManifestDir=""
jaPath=""
pyPath=""
#today is here to fill out logFile filename (log${today}.txt)
logFile=""
cdir=$(dirname $0)
getIdsCmd="$cdir/restful/pullInformationFromLIMS.py"
#email address to send emails if there are errors
to=""
In the restful directory, create a file named Connect.txt with the first line of the file containing the LIMS restful service username and the second line containing the corresponding password.
Also in the restful directory create a file named constants.py with the lines that follow:
baseUrl= ''
archivePath = ''
baseUrl is the url to the restful service archivePath is our path to where the fastqs are stored
./automate_delivery.sh <number of time units> <time unit>
Time unit options are m, d, w, y (minute, day, week, year)
./automate_delivery.sh 1 d Will run create manifest sheet on all projects delivered in the last 1 day
./automate_delivery.sh 12 m Will run create manifest sheet on all projects delivered in the last 12 minutes
Output will go to draftsDir specified in constants.sh
Output of the create manifest sheet will be printed to logFile
Each project can only have one type of "pairedness" (single end or paired end). Otherwise an e-mail will be sent to the email provided in the constants.sh