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 ...@@ -30,4 +30,14 @@ snakemake -s workflow/Snakefile --configfile config/GDB/config.yaml --use-conda
./config/GDB/sbatch.sh ./config/GDB/sbatch.sh
# report # report
snakemake -s workflow_report/Snakefile --configfile config/GDB/config.yaml --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline --cores 1 -rpn 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 @@ ...@@ -10,7 +10,7 @@
#SBATCH --qos=qos-batch #SBATCH --qos=qos-batch
# conda env name or path # 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 # config files
ONTP_CONFIG="config/GDB/config.yaml" ONTP_CONFIG="config/GDB/config.yaml"
ONTP_SLURM="config/GDB/slurm.yaml" ONTP_SLURM="config/GDB/slurm.yaml"
......
...@@ -10,7 +10,7 @@ ...@@ -10,7 +10,7 @@
#SBATCH --qos=qos-batch #SBATCH --qos=qos-batch
# conda env name or path # 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 # config files
ONTP_CONFIG="config/GIS20/config.yaml" ONTP_CONFIG="config/GIS20/config.yaml"
ONTP_SLURM="config/GIS20/slurm.yaml" ONTP_SLURM="config/GIS20/slurm.yaml"
......
...@@ -10,7 +10,7 @@ ...@@ -10,7 +10,7 @@
#SBATCH --qos=qos-batch #SBATCH --qos=qos-batch
# conda env name or path # 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 # config files
ONTP_CONFIG="config/Zymo/config.yaml" ONTP_CONFIG="config/Zymo/config.yaml"
ONTP_SLURM="config/Zymo/slurm.yaml" ONTP_SLURM="config/Zymo/slurm.yaml"
......
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