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Installation on Docker¶

In order to install the program, you need to install Docker first.

Installing Docker¶

To install Docker follow the docker website instructions and post-install instructions.

For Ubuntu:

sudo apt-get update
sudo apt-get install curl
sudo curl -sSL https://get.docker.com/ | sh

For Windows: follow the steps as described here

For Mac: follow the steps as described here

For Debian: follow the steps as described here

Create docker group and add a user¶

You need to add a user to docker group in order to give docker run permission to the user

sudo groupadd docker                
sudo usermod -aG docker [username] # replace [username] with your user name

Installing and updating Muscle X program suite¶

You need to have the muscle.sh script available in order to update, and run a Muscle X program on docker. You can download muscle.sh by

wget https://raw.githubusercontent.com/biocatiit/musclex/master/musclex.sh && chmod +x musclex.sh

or by

curl https://raw.githubusercontent.com/biocatiit/musclex/master/musclex.sh -o musclex.sh
&& chmod +x musclex.sh

If you do not have wget or curl installed you can download the script directly at the following link and saving into a file. After saving the file make it executable (e.g. using: chmod +x musclex.sh).

Running a Muscle X program¶

Running the program by running musclex.sh following by a program shortcut

./musclex.sh [program shortcut]

For example, run this command to run Equator

./musclex.sh eq

If you are using ssh to log into a remote server to run musclex there use the following instead

./musclex.sh -s eq

To see previous versions

./musclex.sh -l

To run a specific version

./musclex.sh -v 1-14.11 eq

To update musclex

./musclex.sh -u

To see all options

./musclex.sh -h

Running a Muscle X program by building Docker image¶

Use this to build your own docker image and run musclex program on it. This would avoid any permission issues on the files created by the program. Download the following files and cd into the folder with these files.

musclex-uid.sh
dockerfile-uid

Run the following command to build the docker image,

./musclex-uid.sh -b

After successfully building the image, run musclex using the following command

./musclex-uid.sh [program shortcut]