Magma via Conda Env

[foamy1881]

I'm new to this community and could use some help. How exactly does one execute Magma after installing it through Conda? I've followed the instructions and installed both magma-env-1 and magma-env-2. However, I'm at a loss regarding the next steps, specifically how to incorporate the sample sheet and execute the YAML file. Could anyone offer some guidance?

[abhi18av]

Hi @foamy1881 , thank you for your interest in the pipeline!

As this is not a feature/bug report, I am converting this into a discussion and will respond to these questions in a point-wise manner

Point-1

I've followed the instructions and installed both magma-env-1 and magma-env-2

This sounds good 👍

The next step here, I'd recommend you to do is to make sure that the WHO resistance catalog for tb-profiler has been loaded (I realized we didn't document this on Readme, I'll fix this).

NOTE: Basically the instructions, which are used to build the necessary docker containers.

⚠️ We do highly recommend usage of the containers wherever possible 🐳

1. Download magma_resistance_db_who_v1.zip and unzip it

wget https://github.com/TORCH-Consortium/MAGMA/files/14559680/resistance_db_who_v1.zip

unzip resistance_db_who

2. Activate magma-env-1, which has tb-profiler

conda activate magma-env-1

3. Move inside that folder and use tb-profiler load_library functionality to load the database

cd resistance_db_who

tb-profiler load_library ./resistance_db_who

Success, would look like this

Point-2

... how to incorporate the sample sheet ...

For this, we provide a dummy samplesheet, which you'd have to customize as per your samples and other metadata from the sequencer and sample.

Reference: Mentioned on the readme here.

Below is a formatted version of that sample CSV.

Study	Sample	Library	Attempt	R1	R2	Flowcell	Lane	Index Sequence
Study_Name	S0001	1	1	full_path_to_directory_of_fastq_files/S0001_01_R1.fastq.gz	full_path_to_directory_of_fastq_files/S0001_01_R1.fastq.gz	1	1	1
Study_Name	S0002	1	1	full_path_to_directory_of_fastq_files/S0002_01_R1.fastq.gz	full_path_to_directory_of_fastq_files/S0002_01_R2.fastq.gz	1	1	1
Study_Name	S0003	1	1	full_path_to_directory_of_fastq_files/S0003_01_R1.fastq.gz	full_path_to_directory_of_fastq_files/S0003_01_R2.fastq.gz	1	1	1
Study_Name	S0004	1	1	full_path_to_directory_of_fastq_files/S0004_01_R1.fastq.gz	full_path_to_directory_of_fastq_files/S0004_01_R2.fastq.gz	1	1	1

Point-3

... execute the YAML file

Actually the YAML is a condensed form of all inputs to the pipeline, therefore, you can pass/give it to the pipeline rather than execute in this case.

This information is covered here on Readme.