Installation guide for SeMa-Trap:

In order to install SeMa-Trap, first install Anaconda3 described in their installation page.

Afterwards, clone the source code from bitbucket with below command. This will download all the necessary files for web-application and configurations.

git clone https://mehmetdirenc@bitbucket.org/mehmetdirenc/sematrap.git

Once you have downloaded the repository, find the "sematrap.yml" file which is located in the "static" folder of "sematrap" directory from the repository you cloned from bitbucket. It can also be downloaded from here.Then, create a conda environment and install all the dependencies used by SeMa-Trap (give the path of the ".yml" file if not in the same directory). Simplified code below assumes you have installed anaconda3 and downloaded the repository.

For Debian:
conda env create --file ./sematrap/sematrap/static/sematrap_debian.yml -n sematrap python=3.8.10
For Macos:
conda env create --file ./sematrap/sematrap/static/sematrap_macos.yml -n sematrap python=3.8.10
WARNING: If you are having dependency or download issues with the commands above, you can use the command below which is OS independent. Although this approach might take hours for conda to resolve such issues.
conda env create --file ./sematrap/sematrap/static/sematrap_from_history.yml -n sematrap python=3.8.10
----
conda activate sematrap
conda-develop ./sematrap
export EGGNOG_DATA_DIR=/your/eggnog/data/directory (example: export EGGNOG_DATA_DIR=/home/users/john/data)
mkdir /your/eggnog/data/directory
download_eggnog_data.py
wget https://arts.ziemertlab.com/static/zip_refsets/all_references.zip
unzip all_references.zip -d ./arts_references

Final step is to change the diamond version in your conda environments bin folder. If you're unsure where that is, you can easily find out by typing "which diamond" when you're inside the "sematrap" environment which you have activated few steps back. It will print out a path like "/home/john/anaconda3/envs/sematrap/bin/diamond"

For Debian:
cp ./sematrap/sematrap/static/diamond_debian /home/john/anaconda3/envs/sematrap/bin/diamond
For Macos:
cp ./sematrap/sematrap/static/diamond_macos /home/john/anaconda3/envs/sematrap/bin/diamond

For instructions on how to run it locally, please see the Readme page.