Eagle

The exome analysis graphical environment (Eagle) is a webbased user interface for exonic data analysis.

Installation

by conda (Python 3)

Using the conda package manager is the easiest way to install Eagle. (If you need to install conda first, choose the 64-bit Python3 version for your operating system. Eagle does not support Python2!)

To create a new environment named eagle , install Eagle with all of its dependencies into it, and activate the environment:

conda create --name eagle -c bioconda -c conda-forge  python=3.6 eagle
conda activate eagle

If you already have a conda environment into which you want to install Eagle, activate this environment and run

conda install -c bioconda -c conda-forge  eagle

by pip

An alternative to conda is pip (this is not recommended, as it cannot resolve all dependencies!):

pip install gi-eagle

by setup.py

You can install Eagle by running setup.py from a cloned repository, but then you have to worry about the dependencies (this is certainly not recommended!):

git clone git@bitbucket.org:christopherschroeder/eagle.git
cd eagle
python setup.py install

Create the data files

Instead of a central database Eagle stores the genetic information in structured h5 files. These files are created from vcfs annotated by SnpEff and SnpSift. As an example we assume having a vcf files named example.vcf, based on hg38 and containing the two samples sampleA and sampleB. Furthermore we assume a dbSNP vcf file stored as 150.vcf.gz (download).

Step 1. Annotate the vcf file

snpeff -noStats -t hg38 example.vcf | snpsift annotate -tabix 150.vcf.gz - > example.annotated.vcf

Step 2. Use eagle to convert the vcf file

eagle convert --samples sampleA sampleB example.annotated.vcf data

This creates two sample specific data files data/sampleA.h5 and data/sampleB.h5.

Create the config

Eagle requires a configuration file to run, containing path information to the previously created data files and to corresponding bam files. The config syntax follows the python supported INI file structure with a pathes and a reference section. Example config file config.cfg

[pathes]
snp: /vol/home/me/data/h5
bam: /vol/home/me/data/bam
group: /vol/home/me/data/groups

[reference]
version: hg38

The snp key contains the path to the data files, bam key the path to the corresponding bam files and group the path to a directory where Eagle stores custom sample groups. Please note that Eagle requires identical file basenames to match bam and h5, e.g. sampleA.bam and sampleA.h5.

Running

Local

The interface is launched by

eagle interface --config config.cfg

with a given previously created cfg file. Per default the local webserver is running on port 8000 and is accessed under http://127.0.0.1:8000 or http://localhost:8000, if the system's defaults are not customized.

Intranet

The previous command allows local access of the web-interface. The public flag provides public access:

eagle interface --config config.cfg --public

Public

It is often necessary for production systems to simulataniously provide access to multiple independent server instances. A common practice is to apply proxies, which forward url requests to different intranet servers and instances running on different ports. Assuming we have two servers.

A server name gate.local provides external access, while a second server my_server.local runs an eagle instance on port 10001.

To use Eagle in such configuration, we suggest to apply nginx as a proxy on gate.local. The nginx configuration entry for our example

    location /eagle/myeagle {
        auth_basic            "Restricted";
        auth_basic_user_file  /vol/home/foo/eagle/.htpasswd;
        rewrite /eagle/rb_zelllinien/(.*) /$1 break;
        proxy_pass http://my_server.local:10001;
        proxy_set_header Host $host;
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        proxy_set_header X-Scheme $scheme;
        proxy_set_header X-Script-Name /eagle/myeagle;
        proxy_read_timeout 500;
    }

Please note that this configuration requires a htpasswd file stored in /vol/home/foo/eagle, which is required for restricted access and user/password authentication.

After authentication, the proxie will now internally tunnel any request for http://gate.local/eagle/myeagle to http://my_server.local:10001

Please also note that the public flag is required, if Eagle is not executed locally on gate.local.

Licence

Copyright (c) 2017 Christopher Schr�der christopher.schroeder@tu-dortmund.de

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Who do I talk to?

For detailled information about my person please go to https://christopherschroeder.bitbucket.io