Add cmo_list2bed 1.0.1

REVISION

@@ -1 +1 @@
-23
+24

build/containers/list2bed/1.0.1/.dockerignore

@@ -0,0 +1 @@
+*

build/containers/list2bed/1.0.1/Dockerfile

@@ -0,0 +1,25 @@
+FROM python:2.7.13-alpine
+MAINTAINER Jaeyoung Chun ([email protected])
+
+LABEL maintainer="Jaeyoung Chun ([email protected])" \
+      version.container="1.0" \
+      version.list2bed="1.0.1" \
+      version.alpine="3.4.6" \
+      source.gatk="https://github.com/mskcc/list2bed/releases/tag/1.0.1"
+
+ENV LIST2BED_VERSION 1.0.1
+
+# to build pybedtools : build-base musl-dev zlib-dev cython
+RUN apk add --update \
+      && apk add ca-certificates openssl \
+      && apk add build-base musl-dev zlib-dev bzip2-dev xz-dev cython \
+      && pip install pybedtools \
+      && cd /tmp && wget https://github.com/mskcc/list2bed/archive/${LIST2BED_VERSION}.zip \
+      && unzip ${LIST2BED_VERSION}.zip \
+      && mv /tmp/list2bed-${LIST2BED_VERSION}/list2bed.py /usr/bin/ \
+      && rm -rf /var/cache/apk/* /tmp/*
+
+# disable per-user site-packages before run
+ENV PYTHONNOUSERSITE set
+
+ENTRYPOINT ["python", "/usr/bin/list2bed.py"]

build/containers/list2bed/1.0.1/Singularity

@@ -0,0 +1,44 @@
+Bootstrap: docker
+From: /pipeline-list2bed:1.0.1
+Registry: http://localhost:5000
+
+%setup
+
+    # copy settings-container.sh from the host to the container
+    cp /vagrant/build/scripts/settings-container.sh $SINGULARITY_ROOTFS/tmp
+
+%post
+
+    # load the settings-container.sh which was copied in the %setup step
+    source /tmp/settings-container.sh
+
+    # create an empty directory for each bind point defined
+    for dir in $SINGULARITY_BIND_POINTS
+    do
+        mkdir -p $dir
+    done
+
+    # remove settings-container.sh
+    rm -rf /tmp/settings-container.sh
+
+%runscript
+
+    # disable per-user site-packages before run
+    export PYTHONNOUSERSITE="set"
+    python /usr/bin/list2bed.py "$@"
+
+%test
+
+    # get actual output of the tool
+    python /usr/bin/list2bed.py 2>&1 | head -1 > /tmp/actual.diff.txt
+
+# expected output
+cat > /tmp/expected.diff.txt << EOM
+usage: list2bed.py [-h] -i INPUT_FILE -o OUTPUT_FILE [-ns]
+EOM
+
+    # diff
+    diff /tmp/actual.diff.txt /tmp/expected.diff.txt
+
+    # delete tmp
+    rm -rf /tmp/*.diff.txt

build/cwl-wrappers/cmo-list2bed/1.0.1/cmo-list2bed.cwl

@@ -0,0 +1,89 @@
+#!/usr/bin/env cwl-runner
+
+$namespaces:
+  dct: http://purl.org/dc/terms/
+  foaf: http://xmlns.com/foaf/0.1/
+  doap: http://usefulinc.com/ns/doap#
+
+$schemas:
+- http://dublincore.org/2012/06/14/dcterms.rdf
+- http://xmlns.com/foaf/spec/20140114.rdf
+- http://usefulinc.com/ns/doap#
+
+doap:name: cmo-list2bed.cwl
+doap:release:
+- class: doap:Version
+  doap:revision: 1.0.1
+
+dct:creator:
+- class: foaf:Organization
+  foaf:name: Memorial Sloan Kettering Cancer Center
+  foaf:member:
+  - class: foaf:Person
+    foaf:name: Jaeyoung Chun
+    foaf:mbox: mailto:[email protected]
+
+dct:contributor:
+- class: foaf:Organization
+  foaf:name: Memorial Sloan Kettering Cancer Center
+  foaf:member:
+  - class: foaf:Person
+    foaf:name: Jaeyoung Chun
+    foaf:mbox: mailto:[email protected]
+
+# This tool description was generated automatically by argparse2cwl ver. 0.3.1
+# To generate again: $ cmo_list2bed -o FILENAME --generate_cwl_tool
+# Help: $ cmo_list2bed  --help_arg2cwl
+
+cwlVersion: cwl:v1.0
+
+class: CommandLineTool
+baseCommand: [cmo_list2bed]
+
+requirements:
+  InlineJavascriptRequirement: {}
+  ResourceRequirement:
+    ramMin: 2
+    coresMin: 1
+
+
+doc: |
+  rerun a FIZZLED Job
+
+inputs:
+  input_file:
+    type: 
+
+      - string
+      - File
+      - type: array
+        items: string
+    doc: picard interval list
+    inputBinding:
+      prefix: --input_file
+
+  output_file:
+    type: string
+
+    doc: output bed file
+    inputBinding:
+      prefix: --output_file
+
+  no_sort:
+    type: ['null', boolean]
+    default: true
+    doc: sort bed file output
+    inputBinding:
+      prefix: --no_sort
+
+
+outputs:
+  output_file:
+    type: File
+    outputBinding:
+      glob: |
+        ${
+          if (inputs.output_file)
+            return inputs.output_file;
+          return null;
+        }

build/cwl-wrappers/cmo-list2bed/1.0.1/metadata.yaml

@@ -0,0 +1,30 @@
+$namespaces:
+  dct: http://purl.org/dc/terms/
+  foaf: http://xmlns.com/foaf/0.1/
+  doap: http://usefulinc.com/ns/doap#
+
+$schemas:
+  - http://dublincore.org/2012/06/14/dcterms.rdf
+  - http://xmlns.com/foaf/spec/20140114.rdf
+  - http://usefulinc.com/ns/doap#
+
+doap:name: cmo-list2bed.cwl
+doap:release:
+  - class: doap:Version
+    doap:revision: '1.0.1'
+
+dct:creator:
+- class: foaf:Organization
+  foaf:name: Memorial Sloan Kettering Cancer Center
+  foaf:member:
+  - class: foaf:Person
+    foaf:name: Jaeyoung Chun
+    foaf:mbox: mailto:[email protected]
+
+dct:contributor:
+- class: foaf:Organization
+  foaf:name: Memorial Sloan Kettering Cancer Center
+  foaf:member:
+  - class: foaf:Person
+    foaf:name: Jaeyoung Chun
+    foaf:mbox: mailto:[email protected]

build/cwl-wrappers/cmo-list2bed/1.0.1/outputs.yaml

@@ -0,0 +1,10 @@
+outputs:
+  output_file:
+    type: File
+    outputBinding:
+      glob: |
+        ${
+          if (inputs.output_file)
+            return inputs.output_file;
+          return null;
+        }

build/cwl-wrappers/cmo-list2bed/1.0.1/postprocess.py

@@ -0,0 +1,56 @@
+#!/usr/bin/python
+"""postprocess"""
+
+import argparse
+import ruamel.yaml
+
+
+def read(filename):
+    """return file contents"""
+
+    with open(filename, 'r') as file_in:
+        return file_in.read()
+
+
+def write(filename, cwl):
+    """write to file"""
+
+    with open(filename, 'w') as file_out:
+        file_out.write(cwl)
+
+
+def main():
+    """main function"""
+
+    parser = argparse.ArgumentParser(description='postprocess')
+
+    parser.add_argument(
+        '-f',
+        action="store",
+        dest="filename_cwl",
+        help='Name of the cwl file',
+        required=True
+    )
+
+    params = parser.parse_args()
+
+    cwl = ruamel.yaml.load(read(params.filename_cwl),
+                           ruamel.yaml.RoundTripLoader)
+
+# we're doing this way to preserve the order
+# can't figure out other ways.
+    input_file_type = """
+- string
+- File
+- type: array
+  items: string
+"""
+    cwl['inputs']['input_file']['type'] = ruamel.yaml.load(input_file_type, ruamel.yaml.RoundTripLoader)
+
+    write(params.filename_cwl, ruamel.yaml.dump(
+        cwl, Dumper=ruamel.yaml.RoundTripDumper))
+
+
+if __name__ == "__main__":
+
+    main()

build/cwl-wrappers/cmo-list2bed/1.0.1/requirements.yaml

@@ -0,0 +1,5 @@
+requirements:
+  InlineJavascriptRequirement: {}
+  ResourceRequirement:
+    ramMin: 2
+    coresMin: 1

build/cwl-wrappers/cmo_resources.json

@@ -187,7 +187,7 @@
         }, 
         "list2bed": {
             "1.0.0": "sudo docker run -i list2bed:1.0.0", 
-            "default": "sudo docker run -i list2bed:1.0.0"
+            "default": "sudo docker run -i list2bed:1.0.1"
         }, 
         "matlab": {
             "default": "/opt/common/CentOS_6-dev/matlab/R2013a/v81/"

build/cwl-wrappers/prism_resources.json

@@ -222,7 +222,8 @@
         }, 
         "list2bed": {
             "1.0.0": "sing.sh list2bed 1.0.0", 
-            "default": "sing.sh list2bed 1.0.0"
+            "1.0.1": "sing.sh list2bed 1.0.1", 
+            "default": "sing.sh list2bed 1.0.1"
         }, 
         "matlab": {
             "R2014b": "/opt/common/CentOS_6-dev/matlab/R2014b/", 

build/scripts/tools.json

@@ -33,7 +33,7 @@
             "0.2.5a7"
         ],
         "list2bed": [
-            "1.0.0"
+            "1.0.1"
         ]
     },
     "containerDependency": {

docs/workspace/setup.md

@@ -191,7 +191,7 @@ cmo-gatk.BaseRecalibrator/3.3-0/cmo-gatk.BaseRecalibrator.cwl
 cmo-gatk.FindCoveredIntervals/3.3-0/cmo-gatk.FindCoveredIntervals.cwl
 cmo-gatk.PrintReads/3.3-0/cmo-gatk.PrintReads.cwl
 cmo-gatk.SomaticIndelDetector/2.3-9/cmo-gatk.SomaticIndelDetector.cwl
-cmo-list2bed/1.0.0/cmo-list2bed.cwl
+cmo-list2bed/1.0.1/cmo-list2bed.cwl
 cmo-mutect/1.1.4/cmo-mutect.cwl
 cmo-picard.AddOrReplaceReadGroups/1.129/cmo-picard.AddOrReplaceReadGroups.cwl
 cmo-picard.AddOrReplaceReadGroups/1.96/cmo-picard.AddOrReplaceReadGroups.cwl

setup/cwl-wrappers/1.0.0/checksum.dat

@@ -7,6 +7,7 @@ e62ebe8851dd55f1cc85aac984bc2e98  ./cmo-bwa-mem/0.7.12/cmo-bwa-mem.cwl
 c748bb7cec67c5438274166123d3d2fe  ./cmo-gatk.PrintReads/3.3-0/cmo-gatk.PrintReads.cwl
 4585769701d4b50515be35dd49785b2f  ./cmo-gatk.SomaticIndelDetector/2.3-9/cmo-gatk.SomaticIndelDetector.cwl
 e2b0fd33ed04dbe709a6017d6a72c5e7  ./cmo-list2bed/1.0.0/cmo-list2bed.cwl
+9397490df4170fbb1a25ce3c508f9d95  ./cmo-list2bed/1.0.1/cmo-list2bed.cwl
 126949ee37cbf7aefbad9bc19ae9426b  ./cmo-mutect/1.1.4/cmo-mutect.cwl
 86cfca0e3fbcd0cd3ec6cc16293777b2  ./cmo-picard.AddOrReplaceReadGroups/1.129/cmo-picard.AddOrReplaceReadGroups.cwl
 ed873a7dc75dcc9c26788834fa1ab043  ./cmo-picard.AddOrReplaceReadGroups/1.96/cmo-picard.AddOrReplaceReadGroups.cwl