diff --git a/docker/Dockerfile b/docker/Dockerfile index 9fa161f..0a20d7c 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -1,6 +1,6 @@ FROM ubuntu:16.04 -ENV NEUSOMATIC_VERSION 0.1.2 +ENV NEUSOMATIC_VERSION 0.1.3 ENV ZLIB_VERSION 1.2.11 ENV NUMPY_VERSION 1.14.3 ENV SCIPY_VERSION 1.1.0 diff --git a/neusomatic/python/_version.py b/neusomatic/python/_version.py index b3f4756..ae73625 100755 --- a/neusomatic/python/_version.py +++ b/neusomatic/python/_version.py @@ -1 +1 @@ -__version__ = "0.1.2" +__version__ = "0.1.3" diff --git a/test/NeuSomatic_ensemble.vcf b/test/NeuSomatic_ensemble.vcf index e90a4a9..72ff1b7 100644 --- a/test/NeuSomatic_ensemble.vcf +++ b/test/NeuSomatic_ensemble.vcf @@ -1,5 +1,5 @@ ##fileformat=VCFv4.2 -##NeuSomatic Version=0.1.2 +##NeuSomatic Version=0.1.3 ##FORMAT= ##FILTER= ##FILTER= diff --git a/test/NeuSomatic_standalone.vcf b/test/NeuSomatic_standalone.vcf index 4ffadd0..3288f06 100644 --- a/test/NeuSomatic_standalone.vcf +++ b/test/NeuSomatic_standalone.vcf @@ -1,5 +1,5 @@ ##fileformat=VCFv4.2 -##NeuSomatic Version=0.1.2 +##NeuSomatic Version=0.1.3 ##FORMAT= ##FILTER= ##FILTER= diff --git a/test/docker_test.sh b/test/docker_test.sh index d0d3fc5..a493c94 100755 --- a/test/docker_test.sh +++ b/test/docker_test.sh @@ -10,16 +10,16 @@ if [ ! -f Homo_sapiens.GRCh37.75.dna.chromosome.22.fa ] then if [ ! -f Homo_sapiens.GRCh37.75.dna.chromosome.22.fa.gz ] then - docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.1.2 /bin/bash -c \ + docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.1.3 /bin/bash -c \ "cd /mnt/example/ && wget ftp://ftp.ensembl.org/pub/release-75//fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa.gz" fi - docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.1.2 /bin/bash -c \ + docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.1.3 /bin/bash -c \ "cd /mnt/example/ && gunzip -f Homo_sapiens.GRCh37.75.dna.chromosome.22.fa.gz" fi if [ ! -f Homo_sapiens.GRCh37.75.dna.chromosome.22.fa.fai ] then - docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.1.2 /bin/bash -c \ + docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.1.3 /bin/bash -c \ "samtools faidx /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa" fi rm -rf work_standalone @@ -27,7 +27,7 @@ rm -rf work_standalone #Stand-alone NeuSomatic test -docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.1.2 /bin/bash -c \ +docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.1.3 /bin/bash -c \ "python /opt/neusomatic/neusomatic/python/preprocess.py \ --mode call \ --reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \ @@ -45,7 +45,7 @@ docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.1.2 --num_threads 1 \ --scan_alignments_binary /opt/neusomatic/neusomatic/bin/scan_alignments" -docker run -v ${test_dir}:/mnt -u $UID --memory 30G --shm-size 8G msahraeian/neusomatic:0.1.2 /bin/bash -c \ +docker run -v ${test_dir}:/mnt -u $UID --memory 30G --shm-size 8G msahraeian/neusomatic:0.1.3 /bin/bash -c \ "CUDA_VISIBLE_DEVICES= python /opt/neusomatic/neusomatic/python/call.py \ --candidates_tsv /mnt/example/work_standalone/dataset/*/candidates*.tsv \ --reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \ @@ -54,7 +54,7 @@ docker run -v ${test_dir}:/mnt -u $UID --memory 30G --shm-size 8G msahraeian/neu --num_threads 1 \ --batch_size 100" -docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.1.2 /bin/bash -c \ +docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.1.3 /bin/bash -c \ "python /opt/neusomatic/neusomatic/python/postprocess.py \ --reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \ --tumor_bam /mnt/tumor.bam \ @@ -66,7 +66,7 @@ docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.1.2 rm -rf /mnt/example/work_ensemble #Ensemble NeuSomatic test -docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.1.2 /bin/bash -c \ +docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.1.3 /bin/bash -c \ "python /opt/neusomatic/neusomatic/python/preprocess.py \ --mode call \ --reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \ @@ -85,7 +85,7 @@ docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.1.2 --ensemble_tsv /mnt/ensemble.tsv \ --scan_alignments_binary /opt/neusomatic/neusomatic/bin/scan_alignments" -docker run -v ${test_dir}:/mnt -u $UID --memory 30G --shm-size 8G msahraeian/neusomatic:0.1.2 /bin/bash -c \ +docker run -v ${test_dir}:/mnt -u $UID --memory 30G --shm-size 8G msahraeian/neusomatic:0.1.3 /bin/bash -c \ "CUDA_VISIBLE_DEVICES= python /opt/neusomatic/neusomatic/python/call.py \ --candidates_tsv /mnt/example/work_ensemble/dataset/*/candidates*.tsv \ --reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \ @@ -95,7 +95,7 @@ docker run -v ${test_dir}:/mnt -u $UID --memory 30G --shm-size 8G msahraeian/neu --ensemble \ --batch_size 100" -docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.1.2 /bin/bash -c \ +docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.1.3 /bin/bash -c \ "python /opt/neusomatic/neusomatic/python/postprocess.py \ --reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \ --tumor_bam /mnt/tumor.bam \