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Commit 34ac0857 authored by Valentina Galata's avatar Valentina Galata
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configs: sbatch.sh: run snakemake only if conda env activation has worked

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config/GDB/sbatch.sh
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...@@ -10,15 +10,14 @@ ...@@ -10,15 +10,14 @@
#SBATCH --qos=qos-batch #SBATCH --qos=qos-batch
# conda env name or path # conda env name or path
ONTP_ENV="ONT_pilot" ONTP_ENV="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"
# slurm cluster call # slurm cluster call
ONTP_CLUSTER="sbatch -p {cluster.partition} -q {cluster.qos} {cluster.explicit} -N {cluster.nodes} -n {cluster.n} -c {threads} -t {cluster.time} --job-name={cluster.job-name}" ONTP_CLUSTER="sbatch -p {cluster.partition} -q {cluster.qos} {cluster.explicit} -N {cluster.nodes} -n {cluster.n} -c {threads} -t {cluster.time} --job-name={cluster.job-name}"
conda activate ${ONTP_ENV} conda activate ${ONTP_ENV} && \
snakemake -s workflow/Snakefile -rp --jobs 10 --local-cores 1 \ snakemake -s workflow/Snakefile -rp --jobs 10 --local-cores 1 \
--configfile ${ONTP_CONFIG} --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline \ --configfile ${ONTP_CONFIG} --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline \
--cluster-config ${ONTP_SLURM} --cluster "${ONTP_CLUSTER}" --cluster-config ${ONTP_SLURM} --cluster "${ONTP_CLUSTER}"
config/GIS20/sbatch.sh
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...@@ -10,15 +10,14 @@ ...@@ -10,15 +10,14 @@
#SBATCH --qos=qos-batch #SBATCH --qos=qos-batch
# conda env name or path # conda env name or path
ONTP_ENV="conda activate /scratch/users/vgalata/miniconda3/ONT_pilot" ONTP_ENV="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"
# slurm cluster call # slurm cluster call
ONTP_CLUSTER="sbatch -p {cluster.partition} -q {cluster.qos} {cluster.explicit} -N {cluster.nodes} -n {cluster.n} -c {threads} -t {cluster.time} --job-name={cluster.job-name}" ONTP_CLUSTER="sbatch -p {cluster.partition} -q {cluster.qos} {cluster.explicit} -N {cluster.nodes} -n {cluster.n} -c {threads} -t {cluster.time} --job-name={cluster.job-name}"
conda activate ${ONTP_ENV} conda activate ${ONTP_ENV} && \
snakemake -s workflow/Snakefile -rp --jobs 10 --local-cores 1 \ snakemake -s workflow/Snakefile -rp --jobs 10 --local-cores 1 \
--configfile ${ONTP_CONFIG} --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline \ --configfile ${ONTP_CONFIG} --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline \
--cluster-config ${ONTP_SLURM} --cluster "${ONTP_CLUSTER}" --cluster-config ${ONTP_SLURM} --cluster "${ONTP_CLUSTER}"
config/Zymo/sbatch.sh
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...@@ -10,15 +10,14 @@ ...@@ -10,15 +10,14 @@
#SBATCH --qos=qos-batch #SBATCH --qos=qos-batch
# conda env name or path # conda env name or path
ONTP_ENV="conda activate /scratch/users/vgalata/miniconda3/ONT_pilot" # CHANGE as needed ONTP_ENV="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"
# slurm cluster call # slurm cluster call
ONTP_CLUSTER="sbatch -p {cluster.partition} -q {cluster.qos} {cluster.explicit} -N {cluster.nodes} -n {cluster.n} -c {threads} -t {cluster.time} --job-name={cluster.job-name}" ONTP_CLUSTER="sbatch -p {cluster.partition} -q {cluster.qos} {cluster.explicit} -N {cluster.nodes} -n {cluster.n} -c {threads} -t {cluster.time} --job-name={cluster.job-name}"
conda activate ${ONTP_ENV} conda activate ${ONTP_ENV} && \
snakemake -s workflow/Snakefile -rp --jobs 10 --local-cores 1 \ snakemake -s workflow/Snakefile -rp --jobs 10 --local-cores 1 \
--configfile ${ONTP_CONFIG} --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline \ --configfile ${ONTP_CONFIG} --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline \
--cluster-config ${ONTP_SLURM} --cluster "${ONTP_CLUSTER}" --cluster-config ${ONTP_SLURM} --cluster "${ONTP_CLUSTER}"
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