diegozea/aspring repository overview

⁠🌼 ASPRING 🌼

REPO⁠

DOCS⁠

To ease the use and installation of ASPRING, we have created a Docker image that you can easily download and run. To run the aspring tool using the Docker image, you must have Docker installed on your system. You can download and install Docker from the official website⁠. Once Docker is installed, you can run aspring using the following command:

sudo docker run --mount type=bind,source=$(pwd),target=/data diegozea/aspring aspring --gene GENE_NAME

In this command, we use the docker run command to run aspring. We are mounting the current working directory using the --mount option, which is necessary for providing access to the data files required by aspring. The --mount option takes two parameters: type and source. type specifies the type of mount to use. In this case, we use a bind mount, which allows us to mount a directory from the host system to the container; that is a requirement to enable aspring to see the input files and to let it save the output files in your filesystem. source specifies the source directory to mount. In this case, we use $(pwd) to select the current working directory as the source. We are also specifying the target directory as /data in the container. This means that the files from the current working directory on the host system will be available in the /data directory in the container.

The aspring tool requires R and the HH-suite3, which are already installed in the Docker image. Therefore, there is no need to specify --path_hhsuite_scripts or --path_data; the last one is set to /data by default.

Finally, we specify the --gene option with GENE_NAME to run aspring on that gene.