updated readme; configs: updated conda env path in all sbatch.sh files

README.md

@@ -30,4 +30,14 @@ snakemake -s workflow/Snakefile --configfile config/GDB/config.yaml --use-conda
 ./config/GDB/sbatch.sh
 # report
 snakemake -s workflow_report/Snakefile --configfile config/GDB/config.yaml --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline --cores 1 -rpn
+```
+
+### `conda` environment
+
+If the path specified above does not exists, you can create the environment from `requirements.yaml`
+and replace the env. path in `sbatch.sh` files by `"ONT_pilot"`.
+
+```bash
+# will create env. ONT_pilot
+conda env create -f requirements.yaml
 ```
\ No newline at end of file

config/GDB/sbatch.sh

@@ -10,7 +10,7 @@
 #SBATCH --qos=qos-batch
 
 # conda env name or path
-ONTP_ENV="ONT_pilot" # CHANGE as needed
+ONTP_ENV="/scratch/users/vgalata/miniconda3/ONT_pilot" # CHANGE as needed
 # config files
 ONTP_CONFIG="config/GDB/config.yaml"
 ONTP_SLURM="config/GDB/slurm.yaml"

config/GIS20/sbatch.sh

@@ -10,7 +10,7 @@
 #SBATCH --qos=qos-batch
 
 # conda env name or path
-ONTP_ENV="ONT_pilot" # CHANGE as needed
+ONTP_ENV="/scratch/users/vgalata/miniconda3/ONT_pilot" # CHANGE as needed
 # config files
 ONTP_CONFIG="config/GIS20/config.yaml"
 ONTP_SLURM="config/GIS20/slurm.yaml"

config/Zymo/sbatch.sh

@@ -10,7 +10,7 @@
 #SBATCH --qos=qos-batch
 
 # conda env name or path
-ONTP_ENV="ONT_pilot" # CHANGE as needed
+ONTP_ENV="/scratch/users/vgalata/miniconda3/ONT_pilot" # CHANGE as needed
 # config files
 ONTP_CONFIG="config/Zymo/config.yaml"
 ONTP_SLURM="config/Zymo/slurm.yaml"