fix

Author: uniqueg

1

@@ -0,0 +1,6 @@
+Requirement already satisfied: snakemake-executor-plugin-cluster-generic in /home/uniqueg/Software/miniforge3/envs/zarp-cli/lib/python3.11/site-packages (1.0.9)
+Requirement already satisfied: snakemake-interface-common<2.0.0,>=1.13.0 in /home/uniqueg/Software/miniforge3/envs/zarp-cli/lib/python3.11/site-packages (from snakemake-executor-plugin-cluster-generic) (1.17.4)
+Requirement already satisfied: snakemake-interface-executor-plugins<10.0.0,>=9.0.0 in /home/uniqueg/Software/miniforge3/envs/zarp-cli/lib/python3.11/site-packages (from snakemake-executor-plugin-cluster-generic) (9.3.5)
+Requirement already satisfied: ConfigArgParse<2.0,>=1.7 in /home/uniqueg/Software/miniforge3/envs/zarp-cli/lib/python3.11/site-packages (from snakemake-interface-common<2.0.0,>=1.13.0->snakemake-executor-plugin-cluster-generic) (1.7)
+Requirement already satisfied: argparse-dataclass<3.0.0,>=2.0.0 in /home/uniqueg/Software/miniforge3/envs/zarp-cli/lib/python3.11/site-packages (from snakemake-interface-common<2.0.0,>=1.13.0->snakemake-executor-plugin-cluster-generic) (2.0.0)
+Requirement already satisfied: throttler>=1.2.2 in /home/uniqueg/Software/miniforge3/envs/zarp-cli/lib/python3.11/site-packages (from snakemake-interface-executor-plugins<10.0.0,>=9.0.0->snakemake-executor-plugin-cluster-generic) (1.2.2)

docs/guides/installation.md

@@ -43,6 +43,10 @@ Installation requires the following:
     Snakemake execution [profiles][snakemake-profiles] to connect _ZARP_
     runs to your HPC cluster.
 
+    Note that _ZARP-cli_ installs the Snakemake 8+ plugin
+    `snakemake-executor-plugin-cluster-generic` required for HPC cluster
+    execution by default.
+
 ## Installation steps
 
 ### 1. Clone _ZARP_

docs/includes/references.md

@@ -9,7 +9,7 @@
 [ena]: <https://www.ebi.ac.uk/ena/browser/home>
 [genomepy]: <https://github.com/vanheeringen-lab/genomepy>
 [github-signup]: <https://github.com/signup>
-[htsinfer]: <https://github.com/zavolanlab/htsinfer> 
+[htsinfer]: <https://github.com/zavolanlab/htsinfer>
 [kallisto]: <https://github.com/pachterlab/kallisto>
 [salmon]: <https://github.com/COMBINE-lab/salmon>
 [snakemake]: <https://github.com/snakemake/snakemake>
@@ -22,6 +22,6 @@
 [zarp-docs]: <https://zavolanlab.github.io/zarp/>
 [zarp-issue-tracker]: <https://github.com/zavolanlab/zarp/issues>
 [zarp-qa]: <https://github.com/zavolanlab/zarp/discussions>
-[zarp-supplementary]: <https://zenodo.org/records/10797372.
+[zarp-supplementary]: <https://zenodo.org/records/10797372>
 [zavolab-gh]: <https://github.com/zavolanlab>
 [zenodo]: <https://zenodo.org/>

install/environment.dev.yml

@@ -27,5 +27,6 @@ dependencies:
   - snakemake >=8
   - types-pyyaml >=6.0.11
   - pip:
+    - snakemake-executor-plugin-cluster-generic >=1
     - -e ..
 

install/environment.yml

@@ -17,4 +17,5 @@ dependencies:
   - rich >=12.5.1
   - snakemake >=8
   - pip:
+    - snakemake-executor-plugin-cluster-generic >=1
     - -e ..

tests/snakemake/test_run.py

@@ -102,7 +102,10 @@ def test_compile_command_dep_embedding(self, dependency_embedding, tmpdir):
         run_config.dependency_embedding = dependency_embedding
         my_run = SnakemakeExecutor(run_config=run_config, exec_dir=tmpdir)
         cmd = my_run.compile_command(snakefile=snakefile)
-        my_param = f"--software-deployment-method {dependency_embedding.value.lower()}"
+        my_param = (
+            "--software-deployment-method"
+            f" {dependency_embedding.value.lower()}"
+        )
         assert my_param in cmd
 
     @pytest.mark.parametrize(