Merge pull request #5 from wtsi-hgi/change_docker_dependency

v1.3 (Change docker dependency)

CHANGELOG

@@ -1,3 +1,6 @@
+v1.3
+- Changed the docker container to be broad institute's official docker container, not wtsi-hgi own container
+
 v1.2.2
 - Resolving secondaryFiles to a relative path, to work with newer cwl-runner versions and the advice in "secondaryFiles" of http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter 
 

README.md

@@ -13,29 +13,13 @@ python setup.py install
 
 You may also want to install [cwltool](https://github.com/common-workflow-language/cwltool) to run the generated CWL files
 
-### Docker Requirements
-
-The generated CWL files have a dependency on a GATK docker container. These can be found at https://github.com/wtsi-hgi/arvados-pipelines/tree/master/docker/
-
-As Oracle have discontinued public downloading of JDK 7, to install the docker image you need to install jdk-7u25-linux-x64.tar.gz from http://www.oracle.com/technetwork/java/javase/downloads/java-archive-downloads-javase7-521261.html and put it in the same directory as the Dockerfile (see https://github.com/wtsi-hgi/arvados-pipelines/blob/master/docker/gatk-3.5/Dockerfile#L44)
-```bash
-git clone https://github.com/wtsi-hgi/arvados-pipelines
-cd arvados-pipelines/docker
-... add jdk-7u25-linux-x64.tar to the directory ...
-docker build gatk-3.5 -t gatk
-```
-
-To enter the container, run:
-```bash
-docker run --name='gatk' -it gatk /bin/bash
-```
-
 ## Usage
 
 ```
 usage: gatkcwlgenerator [-h] [--version GATKVERSION] [--out OUTPUTDIR]
                         [--include INCLUDE_FILE] [--dev]
                         [--docker_container_name DOCKER_CONTAINER_NAME]
+                        [--gatk_location GATK_LOCATION]
 
 Generates CWL files from the GATK documentation
 
@@ -54,14 +38,18 @@ optional arguments:
                         generated files (for development purposes). Requires
                         requests_cache to be installed
   --docker_container_name DOCKER_CONTAINER_NAME, -c DOCKER_CONTAINER_NAME
-                        Enable network caching and overwriting of the
-                        generated files (for development purposes). Default is
-                        'gatk'
+                        Docker container name for generated cwl files. Default
+                        is 'broadinstitute/gatk3:<VERSION>' for version 3.x and
+                        'broadinstitute/gatk:<VERSION>' for 4.x
+  --gatk_location GATK_LOCATION, -l GATK_LOCATION
+                        Location of the gatk jar file. Default is
+                        '/usr/GenomeAnalysisTK.jar' for gatk 3.x and
+                        '/gatk/gatk.jar' for gatk 4.x
 ```
 
 This has been tested on versions 3.5-3.8 and generates files for version 4 (though some parameters are unknown and default to outputting a string).
 
-The input parameters are the same as in the documentation, with the addition of `refIndex` and `refDict` which are required parameters that specify the index and dict file of the reference genome. 
+The input parameters are the same as in the documentation, with the addition of `refIndex` and `refDict` which are required parameters that specify the index and dict file of the reference genome.
 
 To add tags to arguments that have a file type, add to the parameter `<NAME>_tags`. e.g. to output the parameter `--variant:vcf path\to\file`, use the input:
 ```yml

gatkcwlgenerator/json2cwl.py

@@ -57,12 +57,17 @@ def json2cwl(GATK_json, cwl_dir, cmd_line_options):
     skeleton_cwl = {
         'id': GATK_json['name'],
         'cwlVersion': 'v1.0',
-        'baseCommand': ['java', '-jar', '/gatk/GenomeAnalysisTK.jar'],
+        'baseCommand': ['java', '-jar', cmd_line_options.gatk_location],
         'class': 'CommandLineTool',
+        'hints': [{
+            "class": "DockerRequirement",
+            "dockerPull": cmd_line_options.docker_container_name
+        }],
         'requirements': [
             {
                 "class": "ShellCommandRequirement"
-            }, {
+            },
+            {
                 "class": "InlineJavascriptRequirement",
                 "expressionLib": [
                     # Allows you to add annotations
@@ -75,10 +80,6 @@ def json2cwl(GATK_json, cwl_dir, cmd_line_options):
                         }
                     }""".replace("    ", "").replace("\n", "")
                 ]
-            },
-            {
-                "dockerPull": cmd_line_options.docker_container_name + ":latest",
-                "class": "DockerRequirement"
             }
         ]
     }

gatkcwlgenerator/main.py

@@ -186,9 +186,11 @@ def main():
     parser.add_argument("--dev", dest="dev", action="store_true",
         help="Enable network caching and overwriting of the generated files (for development purposes). " + 
         "Requires requests_cache to be installed")
-    parser.add_argument("--docker_container_name", "-c", dest="docker_container_name", default="gatk",
-        help="Enable network caching and overwriting of the generated files (for development purposes). " + 
-        "Default is 'gatk'")
+    parser.add_argument("--docker_container_name", "-c", dest="docker_container_name",
+        help="Docker container name for generated cwl files. Default is 'broadinstitute/gatk3:<VERSION>-0' " + 
+        "for version 3.x and 'broadinstitute/gatk:<VERSION>' for 4.x")
+    parser.add_argument("--gatk_location", "-l", dest="gatk_location",
+        help="Location of the gatk jar file. Default is '/usr/GenomeAnalysisTK.jar' for gatk 3.x and '/gatk/gatk.jar' for gatk 4.x")
     cmd_line_options = parser.parse_args()
 
 
@@ -197,7 +199,19 @@ def main():
         requests_cache.install_cache() # Decreases the time to run dramatically
 
     if not cmd_line_options.outputdir:
-      cmd_line_options.outputdir = os.getcwd() + '/gatk_cmdline_tools/%s' % cmd_line_options.gatkversion
+        cmd_line_options.outputdir = os.getcwd() + '/gatk_cmdline_tools/' + cmd_line_options.gatkversion
+
+    if not cmd_line_options.docker_container_name:
+        if is_version_3(cmd_line_options.gatkversion):
+            cmd_line_options.docker_container_name = "broadinstitute/gatk3:" + cmd_line_options.gatkversion + "-0"
+        else:
+            cmd_line_options.docker_container_name = "broadinstitute/gatk:" + cmd_line_options.gatkversion
+
+    if not cmd_line_options.gatk_location:
+        if is_version_3(cmd_line_options.gatkversion):
+            cmd_line_options.gatk_location = "/usr/GenomeAnalysisTK.jar"
+        else:
+            cmd_line_options.gatk_location = "/gatk/gatk.jar"
 
     print("Your chosen directory is: %s" % cmd_line_options.outputdir)
     grouped_urls = get_json_links(cmd_line_options.gatkversion)

setup.py

@@ -10,7 +10,7 @@ def read_markdown(file):
 
 setup(
     name="gatk_cwl_generator",
-    version="1.2.2",
+    version="1.3.0",
     packages=find_packages(exclude=["tests"]),
     install_requires=open("requirements.txt", "r").readlines(),
     tests_require=open("test_requirements.txt", "r").readlines(),