command using conda

main.sh

@@ -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