Commit cdfe3e7e authored by Valentina Galata's avatar Valentina Galata
Browse files

config: unified sbatch scripts, snakemake's conda env path as arg

parent 9b637e54
...@@ -10,7 +10,9 @@ ...@@ -10,7 +10,9 @@
# conda env name or path # conda env name or path
SMK_ENV="/scratch/users/vgalata/miniconda3/ONT_pilot" # CHANGE as needed SMK_ENV=$1
# where to create snakemake's conda env.s (path)
SMK_CONDA=$2
# config files # config files
SMK_CONFIG="config/aquifer/config.fast5.yaml" SMK_CONFIG="config/aquifer/config.fast5.yaml"
SMK_SLURM="config/aquifer/slurm.fast5.yaml" SMK_SLURM="config/aquifer/slurm.fast5.yaml"
...@@ -20,5 +22,5 @@ SMK_CLUSTER="sbatch --partition {cluster.partition} {cluster.qos} {cluster.expli ...@@ -20,5 +22,5 @@ SMK_CLUSTER="sbatch --partition {cluster.partition} {cluster.qos} {cluster.expli
conda activate ${SMK_ENV} && \ conda activate ${SMK_ENV} && \
snakemake -s workflow_fast5/Snakefile -rp --jobs 5 --local-cores 1 \ snakemake -s workflow_fast5/Snakefile -rp --jobs 5 --local-cores 1 \
--configfile ${SMK_CONFIG} --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline \ --configfile ${SMK_CONFIG} --use-conda --conda-prefix ${SMK_CONDA} \
--cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}" --cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}"
\ No newline at end of file
...@@ -11,7 +11,8 @@ ...@@ -11,7 +11,8 @@
# conda env name or path # conda env name or path
SMK_ENV=$1 SMK_ENV=$1
SMK_CONDA="/scratch/users/vgalata/miniconda3/ONT_pilot" # CHANGE as needed # where to create snakemake's conda env.s (path)
SMK_CONDA=$2
# config files # config files
SMK_CONFIG="config/aquifer/config.yaml" SMK_CONFIG="config/aquifer/config.yaml"
SMK_SLURM="config/aquifer/slurm.yaml" SMK_SLURM="config/aquifer/slurm.yaml"
...@@ -20,6 +21,6 @@ SMK_CLUSTER="sbatch --partition {cluster.partition} {cluster.qos} {cluster.expli ...@@ -20,6 +21,6 @@ SMK_CLUSTER="sbatch --partition {cluster.partition} {cluster.qos} {cluster.expli
--ntasks {cluster.ntasks} --cpus-per-task {threads} --time {cluster.time} --job-name={cluster.job-name}" --ntasks {cluster.ntasks} --cpus-per-task {threads} --time {cluster.time} --job-name={cluster.job-name}"
conda activate ${SMK_ENV} && \ conda activate ${SMK_ENV} && \
snakemake -s workflow/Snakefile -rp --jobs 1 --local-cores 1 --rerun-incomplete \ snakemake -s workflow/Snakefile -rp --jobs 7 --local-cores 1 \
--configfile ${SMK_CONFIG} --use-conda --conda-prefix ${SMK_CONDA} \ --configfile ${SMK_CONFIG} --use-conda --conda-prefix ${SMK_CONDA} \
--cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}" --cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}"
...@@ -11,7 +11,8 @@ ...@@ -11,7 +11,8 @@
# conda env name or path # conda env name or path
SMK_ENV=$1 SMK_ENV=$1
SMK_CONDA="/scratch/users/vgalata/miniconda3/ONT_pilot" # CHANGE as needed # where to create snakemake's conda env.s (path)
SMK_CONDA=$2
# config files # config files
SMK_CONFIG="config/gdb/config.fast5.yaml" SMK_CONFIG="config/gdb/config.fast5.yaml"
SMK_SLURM="config/gdb/slurm.fast5.yaml" SMK_SLURM="config/gdb/slurm.fast5.yaml"
......
...@@ -11,7 +11,8 @@ ...@@ -11,7 +11,8 @@
# conda env name or path # conda env name or path
SMK_ENV=$1 SMK_ENV=$1
SMK_CONDA="/scratch/users/vgalata/miniconda3/ONT_pilot" # CHANGE as needed # where to create snakemake's conda env.s (path)
SMK_CONDA=$2
# config files # config files
SMK_CONFIG="config/gdb/config.yaml" SMK_CONFIG="config/gdb/config.yaml"
SMK_SLURM="config/gdb/slurm.yaml" SMK_SLURM="config/gdb/slurm.yaml"
...@@ -20,6 +21,6 @@ SMK_CLUSTER="sbatch --partition {cluster.partition} {cluster.qos} {cluster.expli ...@@ -20,6 +21,6 @@ SMK_CLUSTER="sbatch --partition {cluster.partition} {cluster.qos} {cluster.expli
--ntasks {cluster.ntasks} --cpus-per-task {threads} --time {cluster.time} --job-name={cluster.job-name}" --ntasks {cluster.ntasks} --cpus-per-task {threads} --time {cluster.time} --job-name={cluster.job-name}"
conda activate ${SMK_ENV} && \ conda activate ${SMK_ENV} && \
snakemake -s workflow/Snakefile -rp --jobs 1 --local-cores 1 \ snakemake -s workflow/Snakefile -rp --jobs 7 --local-cores 1 \
--configfile ${SMK_CONFIG} --use-conda --conda-prefix ${SMK_CONDA} \ --configfile ${SMK_CONFIG} --use-conda --conda-prefix ${SMK_CONDA} \
--cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}" --cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}"
...@@ -11,7 +11,8 @@ ...@@ -11,7 +11,8 @@
# conda env name or path # conda env name or path
SMK_ENV=$1 SMK_ENV=$1
SMK_CONDA="/scratch/users/vgalata/miniconda3/ONT_pilot" # CHANGE as needed # where to create snakemake's conda env.s (path)
SMK_CONDA=$2
# config files # config files
SMK_CONFIG="config/nwc/config.yaml" SMK_CONFIG="config/nwc/config.yaml"
SMK_SLURM="config/nwc/slurm.yaml" SMK_SLURM="config/nwc/slurm.yaml"
...@@ -20,6 +21,6 @@ SMK_CLUSTER="sbatch --partition {cluster.partition} {cluster.qos} {cluster.expli ...@@ -20,6 +21,6 @@ SMK_CLUSTER="sbatch --partition {cluster.partition} {cluster.qos} {cluster.expli
--ntasks {cluster.ntasks} --cpus-per-task {threads} --time {cluster.time} --job-name={cluster.job-name}" --ntasks {cluster.ntasks} --cpus-per-task {threads} --time {cluster.time} --job-name={cluster.job-name}"
conda activate ${SMK_ENV} && \ conda activate ${SMK_ENV} && \
snakemake -s workflow/Snakefile -rp --jobs 10 --local-cores 1 \ snakemake -s workflow/Snakefile -rp --jobs 7 --local-cores 1 \
--configfile ${SMK_CONFIG} --use-conda --conda-prefix ${SMK_CONDA} \ --configfile ${SMK_CONFIG} --use-conda --conda-prefix ${SMK_CONDA} \
--cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}" --cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}"
...@@ -7,10 +7,12 @@ ...@@ -7,10 +7,12 @@
#SBATCH -c 1 #SBATCH -c 1
#SBATCH --time=2-00:00:00 #SBATCH --time=2-00:00:00
#SBATCH -p batch #SBATCH -p batch
#SBATCH -q normal
# conda env name or path # conda env name or path
SMK_ENV="/scratch/users/vgalata/miniconda3/ONT_pilot" # CHANGE as needed SMK_ENV=$1
# where to create snakemake's conda env.s (path)
SMK_CONDA=$2
# config files # config files
SMK_CONFIG="config/rawdata/config.yaml" SMK_CONFIG="config/rawdata/config.yaml"
SMK_SLURM="config/rawdata/slurm.yaml" SMK_SLURM="config/rawdata/slurm.yaml"
...@@ -20,5 +22,5 @@ SMK_CLUSTER="sbatch --partition {cluster.partition} {cluster.qos} {cluster.expli ...@@ -20,5 +22,5 @@ SMK_CLUSTER="sbatch --partition {cluster.partition} {cluster.qos} {cluster.expli
conda activate ${SMK_ENV} && \ conda activate ${SMK_ENV} && \
snakemake -s workflow_rawdata/Snakefile -rp --jobs 5 --local-cores 1 \ snakemake -s workflow_rawdata/Snakefile -rp --jobs 5 --local-cores 1 \
--configfile ${SMK_CONFIG} --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline \ --configfile ${SMK_CONFIG} --use-conda --conda-prefix ${SMK_CONDA} \
--cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}" --cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}"
\ No newline at end of file
...@@ -10,7 +10,9 @@ ...@@ -10,7 +10,9 @@
# conda env name or path # conda env name or path
SMK_ENV="/scratch/users/vgalata/miniconda3/ONT_pilot" # CHANGE as needed SMK_ENV=$1
# where to create snakemake's conda env.s (path)
SMK_CONDA=$2
# config files # config files
SMK_CONFIG="config/rumen/config.fast5.yaml" SMK_CONFIG="config/rumen/config.fast5.yaml"
SMK_SLURM="config/rumen/slurm.fast5.yaml" SMK_SLURM="config/rumen/slurm.fast5.yaml"
...@@ -20,5 +22,5 @@ SMK_CLUSTER="sbatch --partition {cluster.partition} {cluster.qos} {cluster.expli ...@@ -20,5 +22,5 @@ SMK_CLUSTER="sbatch --partition {cluster.partition} {cluster.qos} {cluster.expli
conda activate ${SMK_ENV} && \ conda activate ${SMK_ENV} && \
snakemake -s workflow_fast5/Snakefile -rp --jobs 5 --local-cores 1 \ snakemake -s workflow_fast5/Snakefile -rp --jobs 5 --local-cores 1 \
--configfile ${SMK_CONFIG} --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline \ --configfile ${SMK_CONFIG} --use-conda --conda-prefix ${SMK_CONDA} \
--cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}" --cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}"
\ No newline at end of file
...@@ -11,7 +11,8 @@ ...@@ -11,7 +11,8 @@
# conda env name or path # conda env name or path
SMK_ENV=$1 SMK_ENV=$1
SMK_CONDA="/scratch/users/vgalata/miniconda3/ONT_pilot" # CHANGE as needed # where to create snakemake's conda env.s (path)
SMK_CONDA=$2
# config files # config files
SMK_CONFIG="config/rumen/config.yaml" SMK_CONFIG="config/rumen/config.yaml"
SMK_SLURM="config/rumen/slurm.yaml" SMK_SLURM="config/rumen/slurm.yaml"
...@@ -20,6 +21,6 @@ SMK_CLUSTER="sbatch --partition {cluster.partition} {cluster.qos} {cluster.expli ...@@ -20,6 +21,6 @@ SMK_CLUSTER="sbatch --partition {cluster.partition} {cluster.qos} {cluster.expli
--ntasks {cluster.ntasks} --cpus-per-task {threads} --time {cluster.time} --job-name={cluster.job-name}" --ntasks {cluster.ntasks} --cpus-per-task {threads} --time {cluster.time} --job-name={cluster.job-name}"
conda activate ${SMK_ENV} && \ conda activate ${SMK_ENV} && \
snakemake -s workflow/Snakefile -rp --jobs 5 --local-cores 1 --rerun-incomplete \ snakemake -s workflow/Snakefile -rp --jobs 7 --local-cores 1 \
--configfile ${SMK_CONFIG} --use-conda --conda-prefix ${SMK_CONDA} \ --configfile ${SMK_CONFIG} --use-conda --conda-prefix ${SMK_CONDA} \
--cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}" --cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}"
...@@ -11,7 +11,8 @@ ...@@ -11,7 +11,8 @@
# conda env name or path # conda env name or path
SMK_ENV=$1 SMK_ENV=$1
SMK_CONDA="/scratch/users/vgalata/miniconda3/ONT_pilot" # CHANGE as needed # where to create snakemake's conda env.s (path)
SMK_CONDA=$2
# config files # config files
SMK_CONFIG="config/zymo/config.fast5.yaml" SMK_CONFIG="config/zymo/config.fast5.yaml"
SMK_SLURM="config/zymo/slurm.fast5.yaml" SMK_SLURM="config/zymo/slurm.fast5.yaml"
...@@ -20,6 +21,6 @@ SMK_CLUSTER="sbatch --partition {cluster.partition} {cluster.qos} {cluster.expli ...@@ -20,6 +21,6 @@ SMK_CLUSTER="sbatch --partition {cluster.partition} {cluster.qos} {cluster.expli
--ntasks {cluster.ntasks} --cpus-per-task {threads} --time {cluster.time} --job-name={cluster.job-name}" --ntasks {cluster.ntasks} --cpus-per-task {threads} --time {cluster.time} --job-name={cluster.job-name}"
conda activate ${SMK_ENV} && \ conda activate ${SMK_ENV} && \
snakemake -s workflow_fast5/Snakefile -rp --jobs 10 --local-cores 1 \ snakemake -s workflow_fast5/Snakefile -rp --jobs 5 --local-cores 1 \
--configfile ${SMK_CONFIG} --use-conda --conda-prefix ${SMK_CONDA} \ --configfile ${SMK_CONFIG} --use-conda --conda-prefix ${SMK_CONDA} \
--cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}" --cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}"
\ No newline at end of file
...@@ -11,7 +11,8 @@ ...@@ -11,7 +11,8 @@
# conda env name or path # conda env name or path
SMK_ENV=$1 SMK_ENV=$1
SMK_CONDA="/scratch/users/vgalata/miniconda3/ONT_pilot" # CHANGE as needed # where to create snakemake's conda env.s (path)
SMK_CONDA=$2
# config files # config files
SMK_CONFIG="config/zymo/config.yaml" SMK_CONFIG="config/zymo/config.yaml"
SMK_SLURM="config/zymo/slurm.yaml" SMK_SLURM="config/zymo/slurm.yaml"
...@@ -20,6 +21,6 @@ SMK_CLUSTER="sbatch --partition {cluster.partition} {cluster.qos} {cluster.expli ...@@ -20,6 +21,6 @@ SMK_CLUSTER="sbatch --partition {cluster.partition} {cluster.qos} {cluster.expli
--ntasks {cluster.ntasks} --cpus-per-task {threads} --time {cluster.time} --job-name={cluster.job-name}" --ntasks {cluster.ntasks} --cpus-per-task {threads} --time {cluster.time} --job-name={cluster.job-name}"
conda activate ${SMK_ENV} && \ conda activate ${SMK_ENV} && \
snakemake -s workflow/Snakefile -rp --jobs 1 --local-cores 1 \ snakemake -s workflow/Snakefile -rp --jobs 7 --local-cores 1 \
--configfile ${SMK_CONFIG} --use-conda --conda-prefix ${SMK_CONDA} \ --configfile ${SMK_CONFIG} --use-conda --conda-prefix ${SMK_CONDA} \
--cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}" --cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}"
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