SAMbA - SciPhy Reproducible Example

Running the SciPhy Workflow

This repository includes all the files you need to reproduce the example showed in our demonstration video (see below).

To execute this scientific workflow, you need a Docker container running in your current folder. If you don't have the SAMbA Docker image, you can pull it from here.

After saving the Docker image in the current folder, run the following command in your shell-like environment to start the SAMbA container:

docker run --cap-add mknod --cap-add sys_admin --device=/dev/fuse  \
       --privileged --rm -it -p 8000:8000 -p 9042:9042 \
       -v "$PWD/repository:/SAMbAFiles/SAMbA/gitblit/data/git" \
       -v "$PWD/database:/SAMbAFiles/apache-cassandra/data" \
       -v "$PWD:/home/samba/workspace" thaylongs/samba

After booting the container, clone this repo and then go to "SourceCode" directory to run the following commands:

cd $WORKSPACE
git clone https://github.com/UFFeScience/SambA-SciPhy.git
cd SourceCode
sh build.sh
sh submit.sh

If you want to change the inputs, you can change it in the submit.sh bash script changing the top of file entry with a command as:

echo "NAME;FASTA_FILE" > inputList.txt
echo "FILE_NAME;$WORKSPACE/inputs/FILE_NAME" >> inputList.txt

where FILE_NAME is the file name of the file that you want to add. We provided an additional input file sample name myExperiment2. If you wish to run the workflow with one second input example, just type:

echo "NAME;FASTA_FILE" > inputList.txt
echo "myExperiment2;$WORKSPACE/inputs/myExperiment2" >> inputList.txt

You can find all the original and reproducible inputs in the inputs/ folder. The web-based SAMbA-RaP dashboards will be available in your browser at https://localhost:8000.

A session recorded

The video below shows the sequence of commands you need to reproduce this workflow once the repository was already cloned.

Note: we renamed the Source Code directory to SourceCode (no space in between) to avoid possible conflicts of reserved characters.