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Name: Science For Life Laboratory

Type: Organization

Bio: Science for Life Laboratory (SciLifeLab) is a national center for molecular biosciences with focus on health and environmental research

Location: Stockholm University

Blog: http://www.scilifelab.se

Scilifelab modules

Installation

Installation is as simple as

python setup.py install

If you are running several virtual environments, where one (e.g. devel) is used for development, you can install a development version by running

workon devel
python setup.py develop

Documentation

Docs are located in the doc directory. To install, cd to doc and run

make html

Documentation output is found in build.

Running the tests

The modules are shipped with a number of unit tests, located in the tests directory. To run a test, issue the command

python setup.py nosetests

or if you want to run individual tests, cd to tests and run (for example)

nosetests -v -s test_db.py

Science For Life Laboratory's Projects

ngi-rnaseq

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

ngi-smrnaseq

Nextflow Small RNA Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

ngs.test.data

Test data set generation for ngs

nougat

NouGAT is a pipeline that automates de novo assembly project tasks, generating a first draft assembly.

opensource.scilifelab-theme

WordPress theme for Open Source SciLifeLab website.

orderportal

A portal for orders (a.k.a. requests, project applications) to a SciLifeLab facility from its users.

percolator

Semi-supervised learning for peptide identification from shotgun proteomics datasets

portal

SciLifeLab Genomics Customer Portal

ratatosk

ratatosk.ext.scilife

Ratatosk extension for use at Science for Life Laboratory

sarek

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

sarek-data

Sarek test data and references

scilifelab

Misc code snippets for Science For Life Laboratory

scilifelab.github.io

Web portal for open source (research) projects at SciLifeLab

scilifelab_epps

A collection of Genologics Clarity LIMS EPPs used at Scilifelab.

scilifelab_parsers

Module for scilifelab parsers of metrics and other files

slog

simple lab logging system

software-development

General guidelines and style guide for software developed at SciLifeLab

specfiles

rpm specfiles used for building packages in use at SciLifeLab

standalone_scripts

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

standalone_scripts-1

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

statusdb

Python wrappers and methods to work with CouchDB's instance at NGI Stockholm

svdb

structural variant database software

taca

Tool for the Automation of Cleanup and Analyses: tools for projects and data management at NGI Stockholm

taca-ngi-pipeline

A TACA plugin adding functionality relevant for the ngi_pipeline

tiddit

TIDDIT - structural variant calling

umi-transfer

A Rust software to extract Unique Molecular Identifiers in FastQ files and embedd them into the ID of the corresponding reads.

scilifelab Goto Github PK

Scilifelab modules

Installation

Documentation

Running the tests

Science For Life Laboratory's Projects

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