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Commit 17eeea19 authored by Veronique Legrand's avatar Veronique Legrand
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fixed 1 broken nrt test and added non regression tests for the multi cpu mode

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from common import check_class
ret=check_class("nrt.txt","UNKNOWN")
exit(ret)
\ No newline at end of file
ret=check_class("nrt.txt","-")
exit(ret)
#/bin/bash
DATA_PATH=./data
echo "running PhageTerm on HK97 genome and a dataset with a minimum 50x coverage"
python ../PhageTerm.py -c 4 -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r $DATA_PATH/HK97_assembly.fasta --nrt
python check_HK97_class.py
#/bin/bash
DATA_PATH=./data
echo "running PhageTerm on Lamda genome and a dataset with a minimum 50x coverage"
python ../PhageTerm.py -c 4 -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r $DATA_PATH/Lambda_assembly.fasta --nrt
python check_Lamda_class.py
#/bin/bash
DATA_PATH=./data
echo "running PhageTerm on P1 genome and a dataset with a minimum 50x coverage"
python ../PhageTerm.py -c 4 -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r $DATA_PATH/P1_assembly.fasta --nrt
python check_P1_class.py
#/bin/bash
DATA_PATH=./data
echo "running PhageTerm on Staph1N genome and a dataset with a minimum 50x coverage"
python ../PhageTerm.py -c 4 --nrt -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r $DATA_PATH/Staph1N_assembly.fasta
python check_Staph1N_class.py
#/bin/bash
DATA_PATH=./data
echo "running PhageTerm on T4 genome and a dataset with a minimum 50x coverage"
python ../PhageTerm.py -c 4 -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r $DATA_PATH/T4_assembly.fasta --nrt
python check_T4_class.py
#/bin/bash
DATA_PATH=./data
echo "running PhageTerm on T7 genome and a dataset with a minimum 50x coverage"
python ../PhageTerm.py -c 4 -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r $DATA_PATH/T7_assembly.fasta --nrt
python check_T7_class.py
......@@ -2,8 +2,8 @@
## VL: decided to write the checking of results in python scripts rather than shel script for portability.
echo "running non regression tests (short version)"
./run_HK97_long.sh || exit 1
./run_lamda_long.sh || exit 1
./run_N1_long.sh || exit 1
./run_Lamda_long.sh || exit 1
./run_StaphN1_long.sh || exit 1
./run_P1_long.sh || exit 1
./run_T4_long.sh || exit 1
./run_T7_long.sh || exit 1
#/bin/bash
## VL: decided to write the checking of results in python scripts rather than shel script for portability.
echo "running non regression tests (short version)"
./run_HK97_long_multiproc.sh || exit 1
./run_Lamda_long_multiproc.sh || exit 1
./run_StaphN1_long_multiproc.sh || exit 1
./run_P1_long_multiproc.sh || exit 1
./run_T4_long_multiproc.sh || exit 1
./run_T7_long_multiproc.sh || exit 1
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