Move general instructions to WIKI

NBISweden · Jun 19, 2024 · f842973 · f842973
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diff --git a/config/slurm/README.md b/config/slurm/README.md
@@ -1,60 +1,6 @@
-# GenErode execution on SLURM clusters
+# GenErode execution on Dardel (PDC/KTH)
 
-With the switch to Snakemake version 8, GenErode can be run 
-the following on SLURM clusters:
-
-1) Create the GenErode conda environment or update an earlier 
-version. The latest conda environment contains the Snakemake 
-executor plugin for slurm:
-
-```
-conda create -f environment.yaml -n generode
-```
-
-2) Copy one of the example configuration files `config/slurm/profile/config_plugin_rackham.yaml` 
-or `config/slurm/profile/config_plugin_dardel.yaml` to 
-`slurm/config.yaml`. This file specifies compute resources 
-for each rule or group jobs. Any rule or group job that is 
-not listed under `set-threads` or `set-resources` uses 
-default resources specified under `default-resources`. If 
-any rule or group jobs fail due to too little memory or run 
-time, their compute resources can be updated in this file. 
-
-> Note that the current configuration files were adjusted to the 
-HPC clusters Rackham from UPPMAX and Dardel from PDC/KTH. Details 
-on how to configure and run GenErode on Dardel are provided below. 
-Memory requirements are specified three times in these configuration 
-files: 1) under `set-threads` (used by Snakemake to specify threads 
-in rules), 2) under `set-resources` and therein under `mem_mb`, 
-specifying the memory in Megabytes (multiplying the number of threads 
-with the available memory per thread), and 3) under `set-resources` 
-and therein under `cpus-per-task` (the same number as specified under 
-`set-threads`, required for correct memory assignment on Dardel). The 
-configuration file for Snakemake version 7 was kept for comparison, 
-which was also written for Rackham/UPPMAX. 
-
-3) Start GenErode the following:
-
-- Open a tmux or screen session
-- Activate the GenErode conda environment
-- Start the dry run:
-
-```
-snakemake --profile slurm -np &> YYMMDD_dry.out
-```
-
-- Start the main run:
-
-```
-snakemake --profile slurm &> YYMMDD_main.out
-```
-
-> Useful flags for running the pipeline: `--ri` to re-run 
-incomplete jobs and `-k` to keep going in case a job fails. 
-
-## Specific instructions for Dardel
-
-1) Load the following modules on Dardel:
+1) Load the following modules:
 
 ```
 module load PDC UPPMAX bioinfo-tools conda singularity tmux

diff --git a/utilities/mutational_load_snpeff/slurm/profile/README.md b/utilities/mutational_load_snpeff/slurm/profile/README.md
@@ -1,57 +1,6 @@
-# GenErode execution on SLURM clusters
+# GenErode execution on Dardel
 
-With the switch to Snakemake version 8, GenErode can be run 
-the following on SLURM clusters:
-
-1) Create the GenErode conda environment or update an earlier 
-version. The latest conda environment contains the Snakemake 
-executor plugin for slurm:
-
-```
-conda create -f environment.yaml -n generode
-```
-
-2) Copy the example configuration file `slurm/profile/config_plugin_dardel.yaml` 
-to `slurm/config.yaml`. This file specifies compute resources 
-for each rule or group jobs. Any rule or group job that is 
-not listed under `set-threads` or `set-resources` uses 
-default resources specified under `default-resources`. If 
-any rule or group jobs fail due to too little memory or run 
-time, their compute resources can be updated in this file. 
-
-> Note that the current configuration file was adjusted to the 
-HPC cluster Dardel from PDC/KTH. Details on how to configure and 
-run GenErode on Dardel are provided below. Memory requirements are 
-specified three times in the configuration file: 1) under 
-`set-threads` (used by Snakemake to specify threads in rules), 2) 
-under `set-resources` and therein under `mem_mb`, specifying the 
-memory in Megabytes (multiplying the number of threads with the 
-available memory per thread), and 3) under `set-resources` and 
-therein under `cpus-per-task` (the same number as specified under 
-`set-threads`, required for correct memory assignment on Dardel). 
-
-3) Start GenErode the following:
-
-- Open a tmux or screen session
-- Activate the GenErode conda environment
-- Start the dry run:
-
-```
-snakemake --profile slurm -n &> YYMMDD_dry.out
-```
-
-- Start the main run:
-
-```
-snakemake --profile slurm &> YYMMDD_main.out
-```
-
-> Useful flags for running the pipeline: `--ri` to re-run 
-incomplete jobs and `-k` to keep going in case a job fails. 
-
-## Specific instructions for Dardel
-
-1) Load the following modules on Dardel:
+1) Load the following modules:
 
 ```
 module load PDC UPPMAX bioinfo-tools conda singularity tmux