/assembly_UCE

This tutorial describes assembling a UCE with the Phyluce package in a SLURM (Simple Linux Utility for Resource Management) system.

Primary LanguageShell

Instructions for Executing Analyses To execute these analyses, you need Phyluce pre-installed and your raw data cleaned.

First Step: Initiate Anaconda or Miniconda Activate Anaconda or Miniconda by running one of the following commands:

bash Copy code source ~/anaconda3/bin/activate or

bash Copy code source ~/miniconda3/bin/activate

Second Step: Activate Your Version of Phyluce

Verify the available Conda environments using the command:

bash Copy code

conda env list

Activate your desired Phyluce environment with:

bash Copy code

conda activate phyluce-XXX

Here are some example environments:

phyluce-1.6.8 located at /home/tiagobelintani/miniconda3/envs/phyluce-1.6.8

phyluce-1.7.3 located at /home/tiagobelintani/miniconda3/envs/phyluce-1.7.3

phylyce-1.7.0 located at /home/tiagobelintani/miniconda3/envs/phylyce-1.7.0

Third Step: Verify Phyluce Installation Check the version of Phyluce to ensure it is correctly installed by running:

bash Copy code

phyluce_assembly_assemblo_spades --version

Fourth step: create jobs and execute. Access and edit job:

assembly_job.sh https://github.com/TiagoBelintani/assembly_UCE/blob/main/assembly_job.sh