From f6fa4d33e03f88337772807b51e740c31059bef8 Mon Sep 17 00:00:00 2001 From: pdimens Date: Fri, 7 Jun 2024 10:28:42 -0400 Subject: [PATCH] simplify code, add fs text --- src/harpy/hpc.py | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/src/harpy/hpc.py b/src/harpy/hpc.py index 1629dfec8..ff47d514d 100644 --- a/src/harpy/hpc.py +++ b/src/harpy/hpc.py @@ -37,7 +37,7 @@ def generic(): Using a scheduler requires installing an additional Snakemake plugin. If you haven't already, install the `generic-cluster` plugin with: ```bash -mamba install -c bioconda -c conda-forge snakemake-executor-plugin-cluster-generic +mamba install bioconda::snakemake-executor-plugin-cluster-generic ``` """)) with open(outfile, "w", encoding = "utf-8") as yml: @@ -59,6 +59,7 @@ def generic(): yml.write("# [optional] command for sidecar process\n") yml.write("cluster-generic-sidecar-cmd VALUE\n") yml.write("\n# This section is for advanced copying into a scratch directory #\n") + yml.write("## requires snakemake-storage-plugin-fs, which can be installed via conda\n") yml.write("#default-storage-provider: fs\n") yml.write("#local-storage-prefix: /home2/$USER\n") yml.write("#shared-fs-usage:\n") @@ -78,7 +79,7 @@ def lsf(): Using a scheduler requires installing an additional Snakemake plugin. If you haven't already, install the `lsf` plugin with: ```bash -mamba install -c bioconda -c conda-forge snakemake-executor-plugin-lsf +mamba install bioconda::snakemake-executor-plugin-lsf ``` """)) with open(outfile, "w", encoding = "utf-8") as yml: @@ -94,6 +95,7 @@ def lsf(): yml.write("latency-wait: 60\n") yml.write("retries: 1\n") yml.write("\n# This section is for advanced copying into a scratch directory #\n") + yml.write("## requires snakemake-storage-plugin-fs, which can be installed via conda\n") yml.write("#default-storage-provider: fs\n") yml.write("#local-storage-prefix: /home2/$USER\n") yml.write("#shared-fs-usage:\n") @@ -113,7 +115,7 @@ def htcondor(): Using a scheduler requires installing an additional Snakemake plugin. If you haven't already, install the `htcondor` plugin with: ```bash -mamba install -c bioconda -c conda-forge snakemake-executor-plugin-htcondor +mamba install bioconda::snakemake-executor-plugin-htcondor ``` """)) with open(outfile, "w", encoding = "utf-8") as yml: @@ -128,6 +130,7 @@ def htcondor(): yml.write("latency-wait: 60\n") yml.write("retries: 1\n") yml.write("\n# This section is for advanced copying into a scratch directory #\n") + yml.write("## requires snakemake-storage-plugin-fs, which can be installed via conda\n") yml.write("#default-storage-provider: fs\n") yml.write("#local-storage-prefix: /home2/$USER\n") yml.write("#shared-fs-usage:\n") @@ -147,7 +150,7 @@ def slurm(): Using a scheduler requires installing an additional Snakemake plugin. If you haven't already, install the `slurm` plugin with: ```bash -mamba install -c bioconda -c conda-forge snakemake-executor-plugin-slurm +mamba install bioconda::snakemake-executor-plugin-slurm ``` """)) with open(outfile, "w", encoding = "utf-8") as yml: @@ -161,6 +164,7 @@ def slurm(): yml.write("latency-wait: 60\n") yml.write("retries: 1\n") yml.write("\n# This section is for advanced copying into a scratch directory #\n") + yml.write("## requires snakemake-storage-plugin-fs, which can be installed via conda\n") yml.write("#default-storage-provider: fs\n") yml.write("#local-storage-prefix: /home2/$USER\n") yml.write("#shared-fs-usage:\n") @@ -180,7 +184,7 @@ def googlebatch(): Using a scheduler requires installing an additional Snakemake plugin. If you haven't already, install the `googlebatch` plugin with: ```bash -mamba install -c bioconda -c conda-forge snakemake-executor-plugin-googlebatch +mamba install bioconda::snakemake-executor-plugin-googlebatch ``` """)) with open(outfile, "w", encoding = "utf-8") as yml: @@ -240,4 +244,4 @@ def googlebatch(): hpc.add_command(htcondor) hpc.add_command(lsf) hpc.add_command(generic) -hpc.add_command(googlebatch) \ No newline at end of file +hpc.add_command(googlebatch)