We prepared a script "installation_demo.sh" in order to generate a demo example of installation of RNASeqExpressionBrowser. Otherwise, if actual project data should be used, this can be done by following the command "python installation.py installation_example.conf" and modifying the textfile "installation_example.conf"
It is necessary to install docker using e.g. yum in fedora.
The Dockerfile can be found in the current release but will need some time to have everything ready for use in Docker.
#!/usr/bin/bash
service docker stop
service docker start
cd abc2
docker build -t abc2 .
docker run -d -p 8082:80 abc2
The code was modified from [Apache-with-python]{https://github.com/eriston/Apache-with-python-cgi-Docker/blob/master/Dockerfile}. Great thanks to Michał T. Lorenc for the suggestion of using the tool in Docker and for providing this code. Before, installation and configuration was rather difficult, now with Docker much easier to configure the tool.
In my case, the tool can be then visualized using
http://localhost:8082/index.cgi
In order to run the tool, it needs to install goatools and needs to normally to have root permission (can also work if the root would permit writing permission to the /var/www/cgi-bin folder and /var/www/html).
- installation of mysql, good tutorial over here: https://www.wikihow.com/Install-MySQL-on-Fedora
When MySQL is installed, you need to give a user and password, so that someone can access the database where the data is stored:
CREATE USER 'newuser'@'localhost' IDENTIFIED BY 'password';
You can find a good tutorial over here: https://www.digitalocean.com/community/tutorials/how-to-create-a-new-user-and-grant-permissions-in-mysql also don't forget to grant permissions:
GRANT ALL PRIVILEGES ON * . * TO 'newuser'@'localhost';
python2-mysql might be needed eventually:
yum install python2-mysql
A) Goatools installation should work with
'pip install goatools'
B) GO tools obo file Can be obtained over here: http://www.geneontology.org/page/download-ontology or using the the default version under go
cd go
unzip gene_ontology.1_2.zip
B) Installation of the tool
python installation.py installation_example.conf
RNASeqExpressionBrowser--a web interface to browse and visualize high-throughput expression data. Nussbaumer T1, Kugler KG1, Bader KC1, Sharma S1, Seidel M1, Mayer KF1. RNASeqExpressionBrowser