Standalone scripts

Repository to store standalone scripts that do not belong to any bigger package or repository.

Contents

backup_gihtub.py

Performs a backup of all the repositories in user's GitHub account.

Dependencies

• logbook
• pygithub3

data_to_ftp.py

Used to transfer data to user's ftp server maintaing the directory tree structure. Main intention is to get the data to user outside Sweden.

db_sync.sh

Script used to mirror (completely) Clarity LIMS database from production to staging server

quota_log.py

DO NOT USE THIS SCRIPT! Use taca server_status uppmax instead!

Returns a summary of quota usage in Uppmax

Dependencies

• couchdb
• pprint

couchdb_replication.py

handles the replication of the couchdb instance

Dependencies

• couchdb
• logbook
• pycrypto
• yaml

ZenDesk Attachments Backup

Takes a ZenDesk XML dump backup file and searches for attachment URLs that match specified filename patterns. These are then downloaded to a local directory.

Dependencies

• argparse
• os
• urllib2
• re

repooler.py

Calculates a decent way to re-pool samples in the case that the amount of clusters from each sample doesn't reach the required threshold due to mismeasurements in concentration.

Depdendencies

• couchdb
• re
• math
• cpÃollectis
• unicodedata
• csv
• copy
• click
• time, datetime
• Genologics: lims, config, entities