Commit 0f139471 authored by peguerin's avatar peguerin
Browse files

readme update

parent 24c3ad80
......@@ -14,7 +14,8 @@ _________________________________
2. [Installation](#2-installation)
1. [Dependencies](#21-dependencies)
2. [Singularity containers](#22-singularity-containers)
3. [Reference database](#23-reference-database)
3. [Conda environment](#24-conda-environment)
4. [Reference database](#24-reference-database)
3. [Running the workflow](#3-running-the-workflow)
1. [Initialisation](#31-initialisation)
2. [Configuration](#32-configuration)
......@@ -66,8 +67,22 @@ singularity pull --name obitools.simg shub://Grelot/bioinfo_singularity_recipes:
You will get a file named `obitools.simg`. Snakemake will need it to run softwares it contains.
## 2.3 Conda environment
## 2.3 Reference database
The default conda solver is a bit slow and sometimes has issues with selecting the latest package releases. Therefore, we recommend to install Mamba as a drop-in replacement via
conda install -c conda-forge mamba
Then, you can install Snakemake, pandas, biopython and dependencies with
mamba create -n snakemake_only_obitools -c conda-forge -c bioconda snakemake biopython
from the conda-forge and bioconda channels. This will install all required software into an isolated software environment, that has to be activated with
conda activate snakemake_only_obitools
## 2.4 Reference database
In addition, you will need a "miseq" reference database for taxonomic assignment. You can build a reference database by following the instructions [here](
......@@ -171,8 +186,19 @@ bash $CORES
with `CORES` the number of available cores to apply parallelization on the workflow.
that's it ! The workflow is running and crunching your data. Look for the [04-final_tables](04-final_tables) and [99-log](99-log) folders after the workflow is finished. See [Results](#4-results) section.
Alternatively you can use `conda` instead of `singularity`
conda activate snakemake_only_obitools
bash $CORES
## 3.4 Run the workflow step by step
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