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Last pushed: 3 months ago
Short Description
VCF-Miner: GUI-based application for mining variants and annotations stored in VCF files.
Full Description

Getting VCF-Miner started with Docker

Type this into your commandline

docker run -d -p 8888:8080 stevenhart/vcf-miner

Alternatively, if you want to use a GUI:

  1. Install and open Kitematic
  2. Search for stevenhart/vcf-miner
  3. Click Create

Relevant links:

More advanced usage

VCF-Miner installation using Docker

Build locally

In a terminal, clone the repository:

git clone https://github.com/Steven-N-Hart/vcf-miner.git
cd vcf-miner

Next, build the image (see the following section if you get an error)

docker build -t vcfminer . # Dont forget the '.'!

On a Mac, when running 'docker build', you may need to run these commands to start the Docker daemon if you get this error: "Cannot connect to the Docker daemon. Is the docker daemon running on this host?"

# See: https://stackoverflow.com/questions/21871479/docker-cant-connect-to-docker-daemon
# And run these commands:
$ docker-machine start # Start virtual machine for docker
$ docker-machine env   # It helps to get environment variables
$ eval "$(docker-machine env default)" # Set environment variables

Run the image

docker run -d  -p 8888:8080 vcfminer
# To activate LDAP use:
# docker run -e LDAP=1 -d  -p 8888:8080 vcfminer
# note you will need IT help integrating with your existing LDAP!

Determine your docker IP Address. (Note: You may need to run the commands under the "On a Mac" section to see the $DOCKER_HOST variable)

# For example, 
$ echo $DOCKER_HOST
tcp://192.168.99.100:2376
# In this case the IP address is: 192.168.99.100

Open a browser to http://your-ip:8888/vcf-miner/

Username: Admin
Password: temppass

Reminders:

  • Doesn’t work on Internet Explorer

############################################################

Installing on bare metal centos6 or Docker

USER=example_user

# Note you may need sudo access to install on bare metal
yum install -y java-1.7.0-openjdk.x86_64 java-1.7.0-openjdk-devel wget tar git
wget -O /home/${USER}/mongodb.tgz https://fastdl.mongodb.org/linux/mongodb-linux-x86_64-rhel62-3.0.3.tgz
tar -zxvf /home/${USER}/mongodb.tgz -C /home/${USER}
cp /home/${USER}/mongodb-linux-x86_64-rhel62-3.0.3/bin/* /bin

mkdir -p /data/db /data/mongo
chmod 775 -R /data/mongo /data/db 

#Get tomcat
wget http://archive.apache.org/dist/tomcat/tomcat-7/v7.0.62/bin/apache-tomcat-7.0.62.tar.gz
tar xvzf apache-tomcat-7.0.62.tar.gz
mv apache-tomcat-7.0.62 /usr/local
chmod 775 /usr/local/apache-tomcat-7.0.62/bin/*sh

#Delpoy VCF MINER war files
git clone https://github.com/Steven-N-Hart/vcf-miner.git
cd vcf-miner
cp *.war /usr/local/apache-tomcat-7.0.62/webapps/


#If you want to not use LDAP (cp securityuserapp-no-ldap.war /usr/local/apache-tomcat-7.0.62/webapps/securityuserapp.war)

echo -e '/usr/local/apache-tomcat-7.0.62/bin/catalina.sh &\nmongod --storageEngine wiredTiger' > start.sh
chmod 775 ./start.sh
./start.sh

Now open your browser to http://server_IP_address:8080/vcf-miner/ (but obviously using your IP address instead)

  • Username: Admin
  • Password: temppass

You are all set!

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stevenhart
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