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

config/aquifer/sbatch.fast5.sh

@@ -10,7 +10,9 @@
 
 
 # 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
 SMK_CONFIG="config/aquifer/config.fast5.yaml"
 SMK_SLURM="config/aquifer/slurm.fast5.yaml"
@@ -20,5 +22,5 @@ SMK_CLUSTER="sbatch --partition {cluster.partition} {cluster.qos} {cluster.expli
 
 conda activate ${SMK_ENV} && \
 snakemake -s workflow_fast5/Snakefile -rp --jobs 5 --local-cores 1 \
---configfile ${SMK_CONFIG} --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline \
---cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}"
\ No newline at end of file
+--configfile ${SMK_CONFIG} --use-conda --conda-prefix ${SMK_CONDA} \
+--cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}"

config/aquifer/sbatch.sh

@@ -11,7 +11,8 @@
 
 # conda env name or path
 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
 SMK_CONFIG="config/aquifer/config.yaml"
 SMK_SLURM="config/aquifer/slurm.yaml"
@@ -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}"
 
 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} \
 --cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}"

config/gdb/sbatch.fast5.sh

@@ -11,7 +11,8 @@
 
 # conda env name or path
 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
 SMK_CONFIG="config/gdb/config.fast5.yaml"
 SMK_SLURM="config/gdb/slurm.fast5.yaml"

config/gdb/sbatch.sh

@@ -11,7 +11,8 @@
 
 # conda env name or path
 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
 SMK_CONFIG="config/gdb/config.yaml"
 SMK_SLURM="config/gdb/slurm.yaml"
@@ -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}"
 
 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} \
 --cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}"

config/nwc/sbatch.sh

@@ -11,7 +11,8 @@
 
 # conda env name or path
 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
 SMK_CONFIG="config/nwc/config.yaml"
 SMK_SLURM="config/nwc/slurm.yaml"
@@ -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}"
 
 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} \
 --cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}"

config/rawdata/sbatch.sh

@@ -7,10 +7,12 @@
 #SBATCH -c 1
 #SBATCH --time=2-00:00:00
 #SBATCH -p batch
-
+#SBATCH -q normal
 
 # 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
 SMK_CONFIG="config/rawdata/config.yaml"
 SMK_SLURM="config/rawdata/slurm.yaml"
@@ -20,5 +22,5 @@ SMK_CLUSTER="sbatch --partition {cluster.partition} {cluster.qos} {cluster.expli
 
 conda activate ${SMK_ENV} && \
 snakemake -s workflow_rawdata/Snakefile -rp --jobs 5 --local-cores 1 \
---configfile ${SMK_CONFIG} --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline \
---cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}"
\ No newline at end of file
+--configfile ${SMK_CONFIG} --use-conda --conda-prefix ${SMK_CONDA} \
+--cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}"

config/rumen/sbatch.fast5.sh

@@ -10,7 +10,9 @@
 
 
 # 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
 SMK_CONFIG="config/rumen/config.fast5.yaml"
 SMK_SLURM="config/rumen/slurm.fast5.yaml"
@@ -20,5 +22,5 @@ SMK_CLUSTER="sbatch --partition {cluster.partition} {cluster.qos} {cluster.expli
 
 conda activate ${SMK_ENV} && \
 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}"
\ No newline at end of file

config/rumen/sbatch.sh

@@ -11,7 +11,8 @@
 
 # conda env name or path
 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
 SMK_CONFIG="config/rumen/config.yaml"
 SMK_SLURM="config/rumen/slurm.yaml"
@@ -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}"
 
 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} \
 --cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}"

config/zymo/sbatch.fast5.sh

@@ -11,7 +11,8 @@
 
 # conda env name or path
 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
 SMK_CONFIG="config/zymo/config.fast5.yaml"
 SMK_SLURM="config/zymo/slurm.fast5.yaml"
@@ -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}"
 
 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} \
---cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}"
\ No newline at end of file
+--cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}"

config/zymo/sbatch.sh

@@ -11,7 +11,8 @@
 
 # conda env name or path
 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
 SMK_CONFIG="config/zymo/config.yaml"
 SMK_SLURM="config/zymo/slurm.yaml"
@@ -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}"
 
 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} \
 --cluster-config ${SMK_SLURM} --cluster "${SMK_CLUSTER}"