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ONT_pilot_gitlab
Commits
34ac0857
Commit
34ac0857
authored
4 years ago
by
Valentina Galata
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configs: sbatch.sh: run snakemake only if conda env activation has worked
parent
1b257f12
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3 changed files
config/GDB/sbatch.sh
+2
-3
2 additions, 3 deletions
config/GDB/sbatch.sh
config/GIS20/sbatch.sh
+2
-3
2 additions, 3 deletions
config/GIS20/sbatch.sh
config/Zymo/sbatch.sh
+2
-3
2 additions, 3 deletions
config/Zymo/sbatch.sh
with
6 additions
and
9 deletions
config/GDB/sbatch.sh
+
2
−
3
View file @
34ac0857
...
@@ -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
}
"
This diff is collapsed.
Click to expand it.
config/GIS20/sbatch.sh
+
2
−
3
View file @
34ac0857
...
@@ -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
}
"
This diff is collapsed.
Click to expand it.
config/Zymo/sbatch.sh
+
2
−
3
View file @
34ac0857
...
@@ -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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