pixi

mrvollger · Nov 23, 2024 · 8e1d0a7 · 8e1d0a7
1 parent 38f8516
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diff --git a/README.md b/README.md
@@ -24,4 +24,12 @@ pixi install
 pixi run snakemake ...
 ```
 
+And if you want to run this Snakemake from another directory you can do so with:
+
+```bash
+pixi run --manifest-path /path/to/snakemake/pixi.toml snakemake ...
+```
+
+where you update `/path/to/snakemake/pixi.toml` to the path of the `pixi.toml` you cloned.
+
 And in place of `...` use all the normal Snakemake arguments for your workflow.
diff --git a/pixi.toml b/pixi.toml
@@ -12,7 +12,8 @@ test = { cmd = [
   "snakemake",
   # once established you can add more arguments with your test data here
 ] }
-snakemake = "snakemake"
+snakemake = { cmd = "cd $INIT_CWD && snakemake -s $PIXI_PROJECT_ROOT/workflow/Snakefile" }
+
 
 [dependencies]
 conda = "*"