SVTyper bug fix (#65)

* Bug fixes re: svtyper (would hang forever) * Bug fix
dnanexus-archive · Jun 4, 2019 · 4ea10cd · 4ea10cd
1 parent 37d6306
commit 4ea10cd
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diff --git 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
@@ -271,78 +271,38 @@
       "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"
         }
       }
     },
     "aws:cn-north-1": {
-      "assetDepends": [
-        {
-          "project": "project-F3vk1f02GyKbj2JF0q1kQfV3",
-          "folder": "/parliament2/",
-          "name": "parliament2:0.1.9",
-          "version": "0.0.1"
-        }
-      ],
       "systemRequirements": {
         "*": {
           "instanceType": "mem1_ssd1_x16"
         }
       }
     },
     "aws:ap-southeast-2": {
-      "assetDepends": [
-        {
-          "project": "project-F4gVXbj5qkxXq3v038V7qjxq",
-          "folder": "/parliament2/",
-          "name": "parliament2:0.1.9",
-          "version": "0.0.1"
-        }
-      ],
       "systemRequirements": {
         "*": {
           "instanceType": "mem1_ssd1_x16"
         }
       }
     },
     "aws:eu-central-1": {
-      "assetDepends": [
-        {
-          "project": "project-FPXF2x84qJf3P5Fx8qpBZk1y",
-          "folder": "/",
-          "name": "parliament2:0.1.9",
-          "version": "0.0.1"
-        }
-      ],
       "systemRequirements": {
         "*": {
           "instanceType": "mem1_ssd1_x16"
         }
       }
     },
     "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
@@ -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
@@ -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/