pommevilla / germs_blaster

GERMS BLASTER

Upload BLAST results to our database so that you can interact with them on the dashboard.

Getting started

Create your .env file

1. Get access to the MongoDB database (ask Paul for help)
2. Create an .env file by copying and renaming .env.example.
3. Fill in your MongoDB password and username in .env.
   • .env is under gitignore, so your private credentials won't be uploaded to git in the event you pushed to the repo.

Creating the conda environment

1. Install conda, the Python package manager. I actually recommend using mamba, but you can use whichever you like.
2. Create the environment by entering conda env create -f environment.yml. If you are using mamba, instead type mamba env create -f environment.yml. This will set up the virtual environment with all the required packages for the pipeline.

Uploading BLAST results

1. Edit config.yml:
   • If you are uploading a single file, change the blast_results_file path to point to your file.
   • If you are uploading a directory of BLAST results files, change the blast_results_directory path to point to your directory.
   • Change project_name to whatever project you'd like these results to be under. This is just metadata to help other people search for these results. Some example values might be LAMPS or CABBI or DNR_HABS
2. Activate the virtual environment by typing conda activate germs_blaster. You should see germs_blaster appear on your command line somewhere, indicating that you are in that environment now.
3. You're ready to upload.
   • To upload a single file, type snakemake -F upload_blast_results_file -c 1
   • To upload a directory, use snakemake -F upload_blast_results_directory

After the records are uploaded, you'll see a {file_name}_mongodb.res file in the outputs directory for each file you uploaded. This file contains some information about the run.

If there weren't any problems with the upload, the new data should be available on the dashboard right away.

Notes:

• This pipeline assumes your BLAST results are in outfmt 6 without any modification.
• Caution: When uploading a directory of results, ensure that blast_results_directory contains only BLAST results files. Otherwise, the pipeline will crash.

Planned features

For this backend helper:

• Submit fasta file for remote BLAST
• Upload BLAST results file
• Allow any column headers

For the dashboard:

• Best n hits per query sequence
• Look up annotation info in nt/nr
• Downloadable reports

Random notes

To drop all files in the blast_results collection using MongoDB Compass

1. Connect to the database using MongoDB Compass
2. In mongosh, to set all_blast_results as the working collection, type:
   • use blast_results
   • db.all_blast_results
3. Enter db.dropDatabase() to remove all of the entries in the all_blast_results database.