Standalone scripts

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

project_status_extended.py

Collects information about specified project from the filesystem of irma. Without any arguments prints statistics for each sample, such as:

• Number of reads
• Coverage
• Duplication rate
• Mapping rate

Usage

python project_status_extended.py P4601

To remove headers from the output, use option --skip-header

The script can take additional arguments:

  --sequenced           List of all the sequenced samples
  --resequenced         List of samples that have been sequenced more than
                        once, and flowcells
  --organized           List of all the organized flowcells
  --to-organize         List of all the not-organized flowcells
  --analyzed            List of all the analysed samples
  --to-analyze          List of samples that are ready to be analyzed
  --analysis-failed     List of all the samples with failed analysis
  --under-analysis      List of the samples under analysis
  --under-qc            List of samples under qc. Use for projects
                        without BP
  --incoherent          Project-status but only for samples which have
                        incoherent number of sequenced/organized/analyzed
  --low-coverage        List of analyzed samples with coverage below 28.5X
  --undetermined        List of the samples which use undetermined  
  --low-mapping         List of all the samples with mapping below 97 percent
  --flowcells           List of flowcells where each sample has been sequenced

backup_github.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.

This script should be run manually on tools when the manual ZenDesk backup zip files are saved.

Usage

Run with a typical ZenDesk backup zip file (will look for tickets.xml inside the zip file):

zendesk_attachment_backup.py -i xml-export-yyyy-mm-dd-tttt-xml.zip

Alternatively, run directly on tickets.xml:

zendesk_attachment_backup.py -i ngisweden-yyyymmdd/tickets.xml

Usage

If you're using this on tools for the first time, you'll need to set up conda. tools only has v2.6 of Python installed by default, which is old and not compatible with this script

These instructions get a copy of Python 2.7 for you. You only need to do this once:

1. Download & install Miniconda

wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

2. Tell the installer to prepend itself to your .bashrc file
3. Log out and log in again, check that conda is in your path
4. Create an environment for Python 2.7

conda create --name tools_py2.7 python pip

5. Add it to your .bashrc file so it always loads

echo source activate tools_py2.7 >> .bashrc

Now Python 2.7 is installed, the zendesk attachment backup script should work. You can run it by going to the Zendesk backup directory and running it on any new downloads:

zendesk_attachment_backup.py <latest_backup>.zip

Dependencies

• argparse
• os
• urllib2
• re
• sys
• zipfile

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.

Dependencies

• couchdb
• click
• Genologics: lims, config, entities

set_bioinforesponsible.py

Calls up the genologics LIMS directly in order to more quickly set a bioinformatics responsible.

Dependencies

• Genologics: lims, config

get_sample_names.py

Prints a list of analyzed samples with user_id and ngi_id

Usage:

get_sample_names.py P1234