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ONT_pilot_gitlab
Commits
cdfe3e7e
Commit
cdfe3e7e
authored
Mar 10, 2021
by
Valentina Galata
Browse files
config: unified sbatch scripts, snakemake's conda env path as arg
parent
9b637e54
Changes
10
Hide whitespace changes
Inline
Side-by-side
config/aquifer/sbatch.fast5.sh
View file @
cdfe3e7e
...
...
@@ -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
View file @
cdfe3e7e
...
...
@@ -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
View file @
cdfe3e7e
...
...
@@ -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
View file @
cdfe3e7e
...
...
@@ -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
View file @
cdfe3e7e
...
...
@@ -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
View file @
cdfe3e7e
...
...
@@ -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
View file @
cdfe3e7e
...
...
@@ -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
View file @
cdfe3e7e
...
...
@@ -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
View file @
cdfe3e7e
...
...
@@ -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
View file @
cdfe3e7e
...
...
@@ -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
}
"
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