This is a singularity container designed to be a portable and complete funannotate black box.

1. Download this repo:

git clone [email protected]:jdhayes/funbox.git

If you want additional licensed software (ie. SignalP, GeneMark, Phobius, etc...), then you will need to acquire those files on your own and copy them into the misc directory and also modify the Singularity recipe file by uncommenting out the corresponding lines in the %files section.

Here is a good resource describing how to get these files (you do not need docker): https://funannotate.readthedocs.io/en/latest/docker.html

2. Build container image:

cd funbox
sudo singularity build images/funbox.img Singularity # Root privileges are required

At this point you could transfer the funbox.img image and funannotate symlink to a remote machine if needed.

3. Add parent directory to PATH:

export PATH=/path/to/image/and/symlink/directory:$PATH

4. Setup database:

export SINGULARITY_BINDPATH=/path/to/needed/filesystem #optional
export FUNANNOTATE_DB=/path/to/funannotate_db
funannotate setup -i all -b all

5. Test (replace --cpus 1 as desired):

funannotate test -t all --cpus 1