diff --git a/Dockerfile b/Dockerfile index 6daa7346..b9545b0a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -8,9 +8,7 @@ MAINTAINER Samantha Zarate RUN apt-get update && apt-get install -y curl wget # Install miniconda to /miniconda -RUN curl -LO http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -RUN bash Miniconda-latest-Linux-x86_64.sh -p /miniconda -b -RUN rm Miniconda-latest-Linux-x86_64.sh +RUN curl -LO http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh && bash Miniconda-latest-Linux-x86_64.sh -p /miniconda -b && rm Miniconda-latest-Linux-x86_64.sh ENV PATH=/miniconda/bin:${PATH} # RUN conda update -y conda @@ -78,8 +76,6 @@ RUN conda update -y pyopenssl WORKDIR / ADD resources.tar.gz / -RUN cp -a /resources/* / -RUN rm -rf /resources/ RUN conda install -c defaults -y numpy RUN pip install https://github.com/bioinform/breakseq2/archive/2.2.tar.gz diff --git a/dx_app_code/parliament2/dxapp.json b/dx_app_code/parliament2/dxapp.json index c5a618dc..7b6a43af 100644 --- a/dx_app_code/parliament2/dxapp.json +++ b/dx_app_code/parliament2/dxapp.json @@ -271,18 +271,10 @@ "doi:10.1186/s12864-015-1479-3" ], "upstreamAuthor": "Baylor College of Medicine", - "whatsNew": "* 0.1.9: Add more logging functionality; resolved bug breaking SVVIZ; improved documentation; migrate to all regions; more sophisticated BAM storage management; other bug fixes.\n* 0.1.8: Add optional upload of log files; update SURVIVOR; add quality scores; improved error messaging; bug fixes.\n* 0.1.7: Update CNVnator, SVTyper; bug fixes.\n* 0.1.6: Bug fixes.\n* 0.1.5: Dockerized Parliament2.\n* 0.1.0: Adding Parliament2." + "whatsNew": "* 0.1.10: Resolved bug breaking SVTyper; added Singularity functionality; modify run on DNAnexus. * 0.1.9: Add more logging functionality; resolved bug breaking SVVIZ; improved documentation; migrate to all regions; more sophisticated BAM storage management; other bug fixes.\n* 0.1.8: Add optional upload of log files; update SURVIVOR; add quality scores; improved error messaging; bug fixes.\n* 0.1.7: Update CNVnator, SVTyper; bug fixes.\n* 0.1.6: Bug fixes.\n* 0.1.5: Dockerized Parliament2.\n* 0.1.0: Adding Parliament2." }, "regionalOptions": { "aws:us-east-1": { - "assetDepends": [ - { - "project": "project-B6JG897KGbkGb6Z7pQ9Q02jG", - "folder": "/parliament2/", - "name": "parliament2:0.1.9", - "version": "0.0.1" - } - ], "systemRequirements": { "*": { "instanceType": "mem1_ssd1_x16" @@ -290,14 +282,6 @@ } }, "aws:cn-north-1": { - "assetDepends": [ - { - "project": "project-F3vk1f02GyKbj2JF0q1kQfV3", - "folder": "/parliament2/", - "name": "parliament2:0.1.9", - "version": "0.0.1" - } - ], "systemRequirements": { "*": { "instanceType": "mem1_ssd1_x16" @@ -305,14 +289,6 @@ } }, "aws:ap-southeast-2": { - "assetDepends": [ - { - "project": "project-F4gVXbj5qkxXq3v038V7qjxq", - "folder": "/parliament2/", - "name": "parliament2:0.1.9", - "version": "0.0.1" - } - ], "systemRequirements": { "*": { "instanceType": "mem1_ssd1_x16" @@ -320,14 +296,6 @@ } }, "aws:eu-central-1": { - "assetDepends": [ - { - "project": "project-FPXF2x84qJf3P5Fx8qpBZk1y", - "folder": "/", - "name": "parliament2:0.1.9", - "version": "0.0.1" - } - ], "systemRequirements": { "*": { "instanceType": "mem1_ssd1_x16" @@ -335,14 +303,6 @@ } }, "azure:westus": { - "assetDepends": [ - { - "project": "project-F3vk1q09FX8Jxxp20pq6z8P9", - "folder": "/parliament2/", - "name": "parliament2:0.1.9", - "version": "0.0.1" - } - ], "systemRequirements": { "*": { "instanceType": "azure:mem2_ssd1_x16" diff --git a/dx_app_code/parliament2/parliament2.py b/dx_app_code/parliament2/parliament2.py index 29ae39da..f531680b 100644 --- a/dx_app_code/parliament2/parliament2.py +++ b/dx_app_code/parliament2/parliament2.py @@ -20,8 +20,8 @@ def main(**job_inputs): # Running Docker image subprocess.check_call(['mkdir', '-p', '/home/dnanexus/in', '/home/dnanexus/out']) - docker_load = ['docker', 'load', '-i', '/docker_image/parliament2.tar'] - subprocess.check_call(docker_load) + docker_pull = ['docker', 'pull', 'dnanexus/parliament2:v0.1.9-13-g37d63065'] + subprocess.check_call(docker_pull) print "Downloading input files" @@ -33,7 +33,7 @@ def main(**job_inputs): ref_name = "/home/dnanexus/in/{0}".format(ref_genome.name) dxpy.download_dxfile(ref_genome.id, ref_name) - docker_call = ['docker', 'run', '-v', '/home/dnanexus/in/:/home/dnanexus/in/', '-v', '/home/dnanexus/out/:/home/dnanexus/out/', 'parliament2', '--bam', bam_name, '-r', ref_name, '--prefix', str(prefix)] + docker_call = ['docker', 'run', '-v', '/home/dnanexus/in/:/home/dnanexus/in/', '-v', '/home/dnanexus/out/:/home/dnanexus/out/', 'dnanexus/parliament2:v0.1.9-13-g37d63065', '--bam', bam_name, '-r', ref_name, '--prefix', str(prefix)] # docker_call = ['dx-docker', 'run', '-v', '/home/dnanexus/in/:/home/dnanexus/in/', '-v', '/home/dnanexus/out/:/home/dnanexus/out/', 'parliament2:0.1.9', '--bam', bam_name, '-r', ref_name, '--prefix', str(prefix)] if 'illumina_bai' in job_inputs: @@ -93,8 +93,6 @@ def main(**job_inputs): 'sv_caller_results' : sv_caller_results_upload } - subprocess.check_call(['ls', '-sh', '/home/dnanexus/out/svtyped_vcfs/']) - # Uploading log files if job_inputs['output_log_files'] and os.listdir('/home/dnanexus/out/log_files/'): log_file_names = glob.glob('/home/dnanexus/out/log_files/*') diff --git a/parliament2.sh b/parliament2.sh index 5084d7f3..9916678e 100644 --- a/parliament2.sh +++ b/parliament2.sh @@ -433,7 +433,6 @@ if [[ "${run_genotype_candidates}" == "True" ]]; then source /miniconda/etc/profile.d/conda.sh conda activate svtyper_env - echo "Running SVTyper" mkdir -p /home/dnanexus/out/svtyped_vcfs/