Commit cf5125be authored by Valentina Galata's avatar Valentina Galata
Browse files

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

parent d6aef8eb
......@@ -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
......@@ -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"
......
......@@ -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"
......
......@@ -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"
......
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