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Installation: How to download and install CRISPRAnalyzeR

Jan Winter edited this page Mar 13, 2018 · 13 revisions

How to download the CRISPRAnalyzeR

You can also check our live demo, which you can also use to analyse your screening data.

CRISPRAnalyzeR can be downloaded as as source code and is also available for a platform-independent installation as pre-configured docker image.

Please have a look at the installation tutorials below, which will assist you with the installation

We encourage users to obtain the pre-configured application which is described below.

The idea of installing CRISPRAnalyzeR is to provide a single installation within a Lab/Institute, so that everyone can access it via the web browser.
However, you can also also install CRISPRAnalyzeR on your local machine.

Minimum System Requirements

CRISPRAnalyzeR is based on R Shiny and uses many different R packages and tools which are listed separately. For a source code installation, we recommend the use of Ubuntu.

Type Source Code Installation Docker Container Installation
Operating System Ubuntu Any supported OS by Docker
CPU Dual Core (Quad Core recommended) Dual Core (Quad Core recommended)
RAM 8 GB 8GB
HDD 512 GB (SSD recommended) 512 GB (SSD recommended)
Additional Software Packages See list below! All included in container

Licenses

CRISPRAnalyzeR is published under the GPL-2 license and is free for non-commercial use only.

While CRISPRAnalyzeR does not require an additional license for commercial use itself, some included tools strictly require additional licensing.
Please note that Highcharts, the COSMIC database and the Enrichr API access require additional licensing for commercial use.
The authors of this application are not responsible for licensing or license issues - please contact the corresponding companies directly..

Highcharts Licensing Options https://shop.highsoft.com/
Please also have a look here: https://github.com/jbkunst/highcharter/issues/254#issuecomment-277253126

COSMIC Licensing Options https://cancer.sanger.ac.uk/cosmic/license

ENRICHR Licensing Options http://www.ip.mountsinai.org/

It is your responsibility to obtain all required licenses in case of commercial usage!

Latest Version and Changelog

Version 1.50 (latest)
- many fixes with mouse libraries
- improoved speed
- added new sample data for cell fittnes screen

Version 1.40
- added new library interface for pre-selection of screens
- added pre-made library re-evaluation for addgene-provide libraries
- fixed smaller bugs
- speed increase for some functions
- improved essential genes information
- added Advanced Options to skip FASTQ Quality Report, create own regular expression, use bad-quality libraries

Version 1.20
- added new user interface for data upload
- fixed many sgRNA libraries
- added Addgene sgRNA libraries for easier use
- started with BETA feature for gene essentiality
- improved overall speed

Version 1.17
- fixed BAGEL issues
- added the possibility to download all data from the DATA REVIEW tab
- improved the performance ovberall
- replaced FASTQ handling by new FASTQ and SAM parser based oN RUST -> speed increase by 6x!
- improved report
- added Visualization of GenomeCRISPR data in Hit Confirmation -> Gene Overview
- added Essential / Non-essential gene Read count in Quality Control
- added Essential/non-essential Log2 FC in Hit Calling section -> you can compare the effect to any published CRISPR screened cell line in GenomeCRISPR

OLDER VERSIONS are not available anymore.

User-Interface based installation (recommended) on macOS and Windows

Installation Tutorial

CRISPRAnalyzeR: How to install it using Kitematic

This installation will use a tool called Kitematic to offer a user interface to start, stop or change settings of the CRISPRAnalyzeR.
In principal, you first install and start docker, then install and start kitematic and finally download CRISPRAnalyzeR.

Individual Steps

  1. Download the Docker Installer for your operating system from the Docker Website

  2. Install the downloaded file

  3. Start Docker on your machine (e.g. by double clicking on the Docker icon on windows or Mac). A small docker symbol in the taskbar will tell you that docker is ready.

  4. Download the Docker Community Edition from the docker website

  5. __Install the Docker Community Edition

  6. Start Kitematic, which comes with it

  7. Search for CRISPRAnalyzeR

    Search for CRISPRAnalyzeR

    ATTENTION In case you will see a red error message like Could not connect to xxxx, this is an indication that you are behind a proxy server which blocks the access!
    If this is the case, please use a network connection without a proxy OR follow the Installation Procedure for Advanced Users

  8. Select CREATE to install the latest stable version of CRISPRAnalyzeR to install CRISPRAnalyzeR

  9. OPTIONAL If required, you can adjust a couple of parameters, such as a proxy server.
    All parameters are described in more detail below
    To adjust these parameters, click on the Settings tab on the upper right corner:

    CA_overview

  10. Hit the START button to start CRISPRAnalyzeR

  11. Adjust the port :

    Before using CRISPRAnalyzeR, you need to adjust the ports by going to Settings -> Ports as illustrated below:

    CA_port1

    Then proceed by clicking on SAVE, which will update the software:

    CA_port2

  12. Copy http://localhost:8000/CRISPRAnalyzeR/ to the webbrowser to access CRISPRAnalyzeR.

  13. Now you successfully installed and started CRISPRAnalyzeR!

How to Start, Stop or Restart CRISPRAnalyzeR

Hit the start, stop or restart button.

CA_overview

How to adjust the CRISPRAnalyzeR settings

As mentioned below, CRISPRAnalyzeR can be adjusted with several parameters.
With the user-interface provided by Kitematic, you can easily adjust all parameters from the Settings section.

Open Kitematic and click on the CRISPRAnalyzeR image - you will see a SETTING button on the top right.

CA_Options

ATTENTION: For some genome-wide screens, the available "C Stack" memory might not be sufficient to render the report. In this case, please increase the stack limit as shown HERE.

Install specific version

  1. Search for CRISPRAnalyzeR in the Kitematic UI repository

  2. Click on the three dots for more options

    More options

  3. Click on "Selected version"

  4. Select the version you want

    Version

  5. Click on the X at the bottom right

  6. Click CREATE


Command Line Installation (advanced users)

Installation Tutorial macOS

CRISPRAnalyzeR: How to install command line version

  1. Download the Docker Installer for your operating system from the Docker Website

  2. Install the downloaded file

  3. Start Docker on your machine (e.g. by double clicking on the Docker icon on windows or Mac). A small docker symbol in the taskbar will tell you that docker is ready.

  4. Open a terminal or command line (macOS: Terminal; Windows: cmd.exe)

  5. Download and run the CRISPRAnalyzeR directly from the online repository (without additional settings)

    docker run --rm -p 8000:8000 boutroslab/crispranalyzer:latest
    

    It is important to keep the 8000:8000 as this tells the software how to access it via the browser.
    By default, CRISPRAnalyzeR can be accessed by the web-browser using http://localhost/CRISPRAnalyzeR.

    If you want to run a specific version, just replace the latest with the specific version number

    docker run --rm -p 8000:8000 boutroslab/crispranalyzer:1.40
    

    All pre-configured versions are listed at the Docker Hub.

    ATTENTION: For some genome-wide screens, the available "C Stack" memory might not be sufficient to render the report. In this case, please increase the stack limit as shown HERE.

  6. Familiarize with the parameters you can use to start the CRISPRanalyzeR - they offer proxy settings or additional databases and local sgRNA re-evaluation.

  7. Access CRISPRAnalyzeR using your web-browser - http://localhost/CRISPRAnalyzeR

ATTENTION: For some genome-wide screens, the available "C Stack" memory might not be sufficient to render the report. In this case, please increase the stack limit as shown HERE.

CRISPRAnalyzeR re-evaluates every sgRNA during the analysis process. Thus, it needs to map each sgRNA against the reference genome.
This can be performed locally (does not require a fast internet connection) or via e-crisp.org (requires fast internet connection >10 mbit).

By default, CRISPRAnalyzeR uses e-crisp.org to re-evaluate your sgRNAs. If you want to perform local sgRNA re-evaluation, please see below.

Update CRISPRAnalyzeR to the latest version

In case you would like to update CRISPRAnalyzer to the latest version, just type

  docker pull boutroslab/crispranalyzer:latest

to download the latest version and then run it as described above:

  docker run --rm -p 8000:8000 boutroslab/crispranalyzer:latest

How to Start and Restart the CRISPRAnalyzeR

You can start and stop the CRISPRanalyzeR using docker.


Available Paramaters to start CRISPRAnalyzeR

CRISPRAnalyzeR has been designed to be installed once on a machine and then accessed via a webbrowser. Therefore, you can adjust all parameters during the start of the CRISPRAnalyzeR.

Parameter Meaning Default Value Accepted Values
websockets_behind_proxy use Websocket protocol TRUE TRUE or FALSE
downloadlogs Allow the download of LOG files RTRUE TRUE or FALSE
verbose_logfiles output of log files TRUE TRUE or FALSE
COSMIC_database Filename of the COSMIC Mutant database (CosmicMutantExport.tsv) NULL CosmicMutantExport.tsv
EnrichR Whether to enable or disable the Enrichr API access TRUE TRUE or FALSE
EnrichR_URL URL to the Enrichr API http://amp.pharm.mssm.edu/Enrichr/ Any URL
max_upload Maximum size of uploaded files in Megabytes 4096 any number
bowtie_threads Number of bowtie2 threads for mapping 2 any number, must be equal or smaller the number of CPU cores
proxy_url URL to your Proxy server NULL URL or NULL to inactivate
proxy_port Proxy server Port NULL Port number of NULL to inactivate

How to use the parameters with the recommended Kitematic installation

In Kitematic, just go to the settings tab and adjust the options.
Be sure to hit the save button after you have adjusted the settings.

CA_Options

How to use the parameters with the command line

All parameters can be set during the start by the following:

docker run --rm -e PARAMETER1 -e PARAMETER2 -e PARAMETER3 -p 8000:8000 boutroslab/crispranalyzer:latest

this means you always need to add -e in front of the parameters, e.g.:

-e websockets_behind_proxy=TRUE -e verbose_logfiles=TRUE -e bowtie_threads=4

e.g.

docker run --rm -e bowtie_threads=4 -e proxy_url="http://thisismyproxy.com" -e proxy_port=80 -p 8000:8000 boutroslab/crispranalyzer:latest
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