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Merge pull request #203 from 4dn-dcic/0.8.1
0.8.1
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,52 @@ | ||
| #!/usr/bin/python | ||
| import os | ||
| import subprocess | ||
| import boto3 | ||
|
|
||
|
|
||
| def main(): | ||
| language = os.environ.get('LANGUAGE') | ||
| local_wfdir = os.environ.get('LOCAL_WFDIR') | ||
| subprocess.call(['mkdir', '-p', local_wfdir]) | ||
|
|
||
| if language == 'wdl': | ||
| main_wf = os.environ.get('MAIN_WDL', '') | ||
| wf_files = os.environ.get('WDL_FILES', '') | ||
| wf_url = os.environ.get('WDL_URL') | ||
| else: | ||
| main_wf = os.environ.get('MAIN_CWL', '') | ||
| wf_files = os.environ.get('CWL_FILES', '') | ||
| wf_url = os.environ.get('CWL_URL') | ||
| # turn into a list | ||
| if not wf_files: | ||
| wf_files = [] | ||
| elif ' ' in wf_files: | ||
| wf_files = wf_files.split(' ') | ||
| else: | ||
| wf_files = [wf_files] | ||
| wf_files.append(main_wf) | ||
| wf_url = wf_url.strip('/') | ||
|
|
||
| print("main workflow file: %s" % main_wf) | ||
| print("workflow files: " + str(wf_files)) | ||
|
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| s3 = boto3.client('s3') | ||
| for wf_file in wf_files: | ||
| target = "%s/%s" % (local_wfdir, wf_file) | ||
| source = "%s/%s" % (wf_url, wf_file) | ||
| if wf_url.startswith('http'): | ||
| subprocess.call(["wget", "-O" + target, source]) | ||
| elif wf_url.startswith('s3'): | ||
| wf_loc = wf_url.replace('s3://', '') | ||
| bucket_name = wf_loc.split('/')[0] | ||
| if len(wf_loc.split('/')) > 1: | ||
| subdirectory = wf_loc.replace(bucket_name + '/', '') | ||
| key = subdirectory + '/' + wf_file | ||
| else: | ||
| key = wf_file | ||
| print("downloading key %s from bucket %s to target %s" % (key, bucket_name, target)) | ||
| s3.download_file(Bucket=bucket_name, Key=key, Filename=target) | ||
|
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|
|
||
| if __name__ == '__main__': | ||
| main() |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1 @@ | ||
| python-lambda-4dn==0.12.0 | ||
| dcicutils==0.6.0 | ||
| Benchmark-4dn==0.5.2 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -23,7 +23,7 @@ include = | |
| */tibanna/* | ||
| */tibanna_4dn/* | ||
| [aliases] | ||
| test=pytest | ||
| test=check | ||
|
|
||
| [tool:pytest] | ||
| addopts = | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| { | ||
| "args": { | ||
| "app_name": "bwa-mem", | ||
| "input_parameters": {}, | ||
| "cwl_child_filenames": [], | ||
| "output_target": { | ||
| "out_bam": "lalala/out.bam" | ||
| }, | ||
| "secondary_output_target": {}, | ||
| "cwl_main_filename": "bwa-mem.cwl", | ||
| "secondary_files": {}, | ||
| "output_S3_bucket": "tibanna-output", | ||
| "app_version": "5", | ||
| "cwl_directory_local": "tests/files/cwl_upload/", | ||
| "cwl_version": "v1", | ||
| "input_files": { | ||
| "fastq1": { | ||
| "bucket_name": "4dn-tool-evaluation-files", | ||
| "object_key": "GM12878_SRR1658581_1pc_1_R1.fastq.h10000" | ||
| }, | ||
| "fastq2": { | ||
| "bucket_name": "4dn-tool-evaluation-files", | ||
| "object_key": "GM12878_SRR1658581_1pc_1_R2.fastq.h10000" | ||
| }, | ||
| "bwa_index": { | ||
| "bucket_name": "elasticbeanstalk-fourfront-webdev-files", | ||
| "object_key": "1f53df95-4cf3-41cc-971d-81bb16c486dd/4DNFIZQZ39L9.bwaIndex.tgz" | ||
| } | ||
| }, | ||
| "input_parameters": { | ||
| "nThreads": 2 | ||
| } | ||
| }, | ||
| "config": { | ||
| "ebs_size": 30, | ||
| "ebs_type": "io1", | ||
| "json_bucket": "4dn-aws-pipeline-run-json", | ||
| "EBS_optimized": false, | ||
| "ebs_iops": 500, | ||
| "shutdown_min": 30, | ||
| "instance_type": "t2.large", | ||
| "password": "dragonfly", | ||
| "log_bucket": "tibanna-output", | ||
| "key_name": "4dn-encode", | ||
| "cloudwatch_dashboard": true | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,98 @@ | ||
| { | ||
| "hints": [ | ||
| { | ||
| "dockerPull": "duplexa/4dn-hic:v42.1", | ||
| "class": "DockerRequirement" | ||
| } | ||
| ], | ||
| "arguments": [], | ||
| "class": "CommandLineTool", | ||
| "inputs": [ | ||
| { | ||
| "type": [ | ||
| "File" | ||
| ], | ||
| "id": "#fastq1", | ||
| "inputBinding": { | ||
| "position": 1, | ||
| "separate": true | ||
| } | ||
| }, | ||
| { | ||
| "type": [ | ||
| "File" | ||
| ], | ||
| "id": "#fastq2", | ||
| "inputBinding": { | ||
| "position": 2, | ||
| "separate": true | ||
| } | ||
| }, | ||
| { | ||
| "type": [ | ||
| "File" | ||
| ], | ||
| "id": "#bwa_index", | ||
| "inputBinding": { | ||
| "position": 3, | ||
| "separate": true | ||
| } | ||
| }, | ||
| { | ||
| "type": [ | ||
| "int" | ||
| ], | ||
| "id": "#nThreads", | ||
| "inputBinding": { | ||
| "position": 6, | ||
| "separate": true | ||
| }, | ||
| "default": 4 | ||
| }, | ||
| { | ||
| "type": [ | ||
| "null", | ||
| "string" | ||
| ], | ||
| "id": "#prefix", | ||
| "inputBinding": { | ||
| "position": 5, | ||
| "separate": true | ||
| }, | ||
| "default": "out" | ||
| }, | ||
| { | ||
| "type": [ | ||
| "null", | ||
| "string" | ||
| ], | ||
| "id": "#outdir", | ||
| "inputBinding": { | ||
| "position": 4, | ||
| "separate": true | ||
| }, | ||
| "default": "." | ||
| } | ||
| ], | ||
| "outputs": [ | ||
| { | ||
| "type": [ | ||
| "null", | ||
| "File" | ||
| ], | ||
| "id": "#out_bam", | ||
| "outputBinding": { | ||
| "glob": "*.bam" | ||
| } | ||
| } | ||
| ], | ||
| "baseCommand": [ | ||
| "run-bwa-mem.sh" | ||
| ], | ||
| "requirements": [ | ||
| { | ||
| "class": "InlineJavascriptRequirement" | ||
| } | ||
| ], | ||
| "cwlVersion": "v1.0" | ||
| } |
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37 changes: 37 additions & 0 deletions
37
tests/tibanna/unicorn/run_task_awsem/event_cwl_upload.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,37 @@ | ||
| { | ||
| "args": { | ||
| "app_name": "md5", | ||
| "language": "cwl draft-3", | ||
| "input_parameters": {}, | ||
| "cwl_version": "draft-3", | ||
| "output_target": { | ||
| "report": "ac18f2bb-c256-40bf-9562-cdc6179d6f9a/report" | ||
| }, | ||
| "secondary_output_target": {}, | ||
| "cwl_main_filename": "main.cwl", | ||
| "cwl_child_filenames": ["child1.cwl", "child2.cwl"], | ||
| "secondary_files": {}, | ||
| "output_S3_bucket": "elasticbeanstalk-fourfront-webdev-wfoutput", | ||
| "app_version": "0.0.4", | ||
| "cwl_directory_local": "tests/tibanna/unicorn/run_task_awsem/cwl_upload/", | ||
| "input_files": { | ||
| "input_file": { | ||
| "bucket_name": "elasticbeanstalk-fourfront-webdev-files", | ||
| "object_key": "f4864029-a8ad-4bb8-93e7-5108f462ccaa/4DNFIRSRJH45.fastq.gz" | ||
| } | ||
| }, | ||
| "input_env": {"TESTENV": 1234} | ||
| }, | ||
| "config": { | ||
| "ebs_size": 0, | ||
| "ebs_type": "io1", | ||
| "json_bucket": "4dn-aws-pipeline-run-json", | ||
| "EBS_optimized": "", | ||
| "ebs_iops": 500, | ||
| "shutdown_min": 30, | ||
| "instance_type": "", | ||
| "password": "", | ||
| "log_bucket": "tibanna-output", | ||
| "key_name": "4dn-encode" | ||
| } | ||
| } |
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