use preinstalled conda envs

README.md

@@ -1,28 +1,40 @@
-# unite-train
-
-A pipeline to build [Qiime2](https://qiime2.org/) taxonomy [classifiers](https://docs.qiime2.org/2021.11/data-resources/) for the [UNITE database](https://unite.ut.ee/repository.php).
-
-### [Download a pre-trained classifier here! 🎁](https://github.com/colinbrislawn/unite-train/releases)
-
-[![Issues](https://img.shields.io/github/issues/colinbrislawn/unite-train?style=for-the-badge)](https://github.com/colinbrislawn/unite-train/issues)
-[![release](https://img.shields.io/github/release-date-pre/colinbrislawn/unite-train?style=for-the-badge)](https://github.com/colinbrislawn/unite-train/releases)
-[![Downloads](https://img.shields.io/github/downloads/colinbrislawn/unite-train/total.svg?style=for-the-badge)](https://github.com/colinbrislawn/unite-train/releases)
-
-# Running Snakemake workflow
-
-Set up:
- - Install [mamba](https://mamba.readthedocs.io/en/latest/installation.html) and configure [Bioconda](https://bioconda.github.io/). Then install [Snakemake](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html) and activate the Snakemake environment.
-
-Run:
-```bash
-snakemake --cores 8 --use-conda --conda-create-envs-only
-# Connect to a worker node, if needed, then
-snakemake --cores 8 --use-conda --resources mem_mb=9000
-# This takes about 11 hours on my machine
-```
-
-Reports:
-```bash
-snakemake --report results/report.html
-snakemake --forceall --dag --dryrun | dot -Tpdf > results/dag.pdf
-```
+# unite-train
+
+A pipeline to build [Qiime2](https://qiime2.org/) taxonomy [classifiers](https://docs.qiime2.org/2021.11/data-resources/) for the [UNITE database](https://unite.ut.ee/repository.php).
+
+## [Download a pre-trained classifier here! 🎁](https://github.com/colinbrislawn/unite-train/releases)
+
+[![Issues](https://img.shields.io/github/issues/colinbrislawn/unite-train?style=for-the-badge)](https://github.com/colinbrislawn/unite-train/issues)
+[![release](https://img.shields.io/github/release-date-pre/colinbrislawn/unite-train?style=for-the-badge)](https://github.com/colinbrislawn/unite-train/releases)
+[![Downloads](https://img.shields.io/github/downloads/colinbrislawn/unite-train/total.svg?style=for-the-badge)](https://github.com/colinbrislawn/unite-train/releases)
+
+---
+
+## Running Snakemake workflow
+
+Set up:
+
+- Install [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge) and configure [Bioconda](https://bioconda.github.io/).
+- Install the version of [Qiime2](https://docs.qiime2.org/) you want using the recomended environment name.
+  (For a faster install, you can replace `conda` with `mamba`.)
+- Install [Snakemake](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html) into an environment, then activate that environment.
+
+Configure:
+
+- Open up `config/config.yaml` and configure it to your liking.
+  (For example, you may need to update the name of your Qiime2 environment.)
+
+Run:
+
+```bash
+snakemake --cores 8 --use-conda --resources mem_mb=10000
+```
+
+This takes about 15 hours on my machine
+
+Reports:
+
+```bash
+snakemake --report results/report.html
+snakemake --forceall --dag --dryrun | dot -Tpdf > results/dag.pdf
+```

config/config.yaml

@@ -1,7 +1,9 @@
 # Qiime2 version number
 q2v: "2023.2"
-# Qiime2 conda environment, copied from https://github.com/qiime2/environment-files
-q2env: "envs/qiime2-2023.2-py38-linux-conda.yml"
+# Qiime2 conda environment
+# Get full file from from https://github.com/qiime2/environment-files
+# Or specify name of already installed Qiime2 environment
+q2env: "qiime2-2023.2"
 
 # UNITE Major version listed in file names
 version: "ver9"