Commit 73793776 authored by peguerin's avatar peguerin
Browse files

command using conda

parent a0ed35eb
......@@ -23,6 +23,7 @@ CONFIGFILE=$2
##
CORES=16
CONFIGFILE="config/config_marbec_rapdirun_test.yaml"
#CONFIGFILE="config/config_marbec_rapdirun_test_sdx.yaml"
#CONFIGFILE="01_infos/config_test.yaml"
#CONFIGFILE="01_infos/config_laperouse_alsace.yaml"
......@@ -34,15 +35,18 @@ snakemake --configfile "../"$CONFIGFILE -s readwrite_rapidrun_demultiplexing.py
cd ..
## assemble
cd 02_assembly
snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
#snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-conda --latency-wait 20
cd ..
## demultiplex
cd 03_demultiplex
snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
#snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-conda --latency-wait 20
cd ..
## filter samples
cd 04_filter_samples
snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
#snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-conda --latency-wait 20
cd ..
## concatenate samples into run
for projet in `ls results/04_filter_samples/04_filtered/`;
......@@ -59,7 +63,8 @@ do
done
## assignment
cd 05_assignment
snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
#snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-conda --latency-wait 20
cd ..
###############################################################################
......@@ -67,6 +72,6 @@ cd ..
# bash rename.sh 06_assignment
## clean
#snakemake --configfile "../"$CONFIGFILE -s Snakefile --delete-all-output --dry-run
#snakemake --configfile "../"$CONFIGFILE -s Snakefile --delete-all-output --rerun-incomplete
#snakemake --configfile "../"$CONFIGFILE -s Snakefile --delete-all-output --rerun-incomplete --cores 8
#nohup snakemake --configfile "../"$CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20 &
#snakemake --configfile "../"$CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20 --dry-run
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment