<commit_before>name: diamond
pegasus: "5.0"

hooks:
    shell:
        - _on: error
          cmd: /bin/mailx -s &apos;diamond failed&apos; <EMAIL>

siteCatalog:
    $ref: "https://pegasus.isi.edu/hosted/site/catalog"

replicaCatalog:
    replicas:
        - lfn: f.a
          pfn: file:///lfs/voeckler/src/svn/pegasus/trunk/examples/grid-blackdiamond-perl/f.a
          site: local


transformationCatalog:
    transformations:
        - namespace: example
          name: keg
          version: "1.0"
          profiles:
              env:
                  APP_HOME: /tmp/myscratch
                  JAVA_HOME: /opt/java/1.6

          requires:
              - anotherTr

          sites:
            - name: isi
              type: installed
              pfn: /path/to/keg
              arch: x86_64
              os.type: linux
              os.release: fc
              os.version: "4"
              profiles:
                env:
                    Hello: World
                    JAVA_HOME: /bin/java.1.6
                condor:
                    FOO: bar
              container: centos-pegasus

        - namespace: example
          name: anotherTr
          version: "1.2.3"

          sites:
              - name: isi
                type: installed
                pfn: /path/to/anotherTr

    containers:
        - name: centos-pegasus
          type: docker
          image: docker:///rynge/montage:latest
          mounts:
            - /Volumes/Work/lfs1:/shared-data/:ro
          profiles:
            env:
                JAVA_HOME: /opt/java/1.6

jobs:
    - id: ID000001
      name: preprocess
      namespace: diamond
      version: "2.0"
      arguments: ["-a", "preprocess", "-T60", "-i", lfn: f.a, "-o", "f.b1", "f.b2"]
      uses:
          - file:
              lfn: f.b2
            type: output
            registerReplica: false
            stageOut: true
          - file:
              lfn: f.b1
              metadata:
                size: "2048"
            type: output
            registerReplica: false
            stageOut: true
          - file:
              lfn: f.a
            type: input

    - id: ID000002
      name: findrange
      namespace: diamond
      version: "2.0"
      arguments: ["-a", "findrange", "-T60", "-i", "f.b1", "-o", "f.c1"]
      uses:
          - file:
              lfn: f.b1
            type: input
          - file:
              lfn: f.c1
            type: output
            registerReplica: false
            stageOut: true

    - id: ID000003
      name: findrange
      namespace: diamond
      version: "2.0"
      arguments: ["-a", "findrange", "-T60", "-i", "f.b2", "-o", "f.c2"]
      uses:
          - file:
              lfn: f.b2
            type: input
          - file:
              lfn: f.c2
            type: output
            registerReplica: false
            stageOut: true

    - id: ID000004
      name: analyze
      namespace: diamond
      version: "2.0"
      arguments: ["-a", "analyze", "-T60", "-i", "f.c1", "f.c2", "-o", "f.d"]
      uses:
          - file:
              lfn: f.c2
            type: input
          - file:
              lfn: f.c1
            type: input
          - file:
              lfn: f.d
            type: output
            registerReplica: false
            stageOut: true

jobDependencies:
    - id: ID000001
      children:
        - ID000002
        - ID000003
    - id: ID000002
      children:
        - ID000004
    - id: ID000003
      children:
        - ID000004
<commit_msg>PM-1501 pegasus should be the first key<commit_after>pegasus: "5.0"
name: diamond

hooks:
    shell:
        - _on: error
          cmd: /bin/mailx -s &apos;diamond failed&apos; <EMAIL>

siteCatalog:
    $ref: "https://pegasus.isi.edu/hosted/site/catalog"

replicaCatalog:
    replicas:
        - lfn: f.a
          pfn: file:///lfs/voeckler/src/svn/pegasus/trunk/examples/grid-blackdiamond-perl/f.a
          site: local


transformationCatalog:
    transformations:
        - namespace: example
          name: keg
          version: "1.0"
          profiles:
              env:
                  APP_HOME: /tmp/myscratch
                  JAVA_HOME: /opt/java/1.6

          requires:
              - anotherTr

          sites:
            - name: isi
              type: installed
              pfn: /path/to/keg
              arch: x86_64
              os.type: linux
              os.release: fc
              os.version: "4"
              profiles:
                env:
                    Hello: World
                    JAVA_HOME: /bin/java.1.6
                condor:
                    FOO: bar
              container: centos-pegasus

        - namespace: example
          name: anotherTr
          version: "1.2.3"

          sites:
              - name: isi
                type: installed
                pfn: /path/to/anotherTr

    containers:
        - name: centos-pegasus
          type: docker
          image: docker:///rynge/montage:latest
          mounts:
            - /Volumes/Work/lfs1:/shared-data/:ro
          profiles:
            env:
                JAVA_HOME: /opt/java/1.6

jobs:
    - id: ID000001
      name: preprocess
      namespace: diamond
      version: "2.0"
      arguments: ["-a", "preprocess", "-T60", "-i", lfn: f.a, "-o", "f.b1", "f.b2"]
      uses:
          - file:
              lfn: f.b2
            type: output
            registerReplica: false
            stageOut: true
          - file:
              lfn: f.b1
              metadata:
                size: "2048"
            type: output
            registerReplica: false
            stageOut: true
          - file:
              lfn: f.a
            type: input

    - id: ID000002
      name: findrange
      namespace: diamond
      version: "2.0"
      arguments: ["-a", "findrange", "-T60", "-i", "f.b1", "-o", "f.c1"]
      uses:
          - file:
              lfn: f.b1
            type: input
          - file:
              lfn: f.c1
            type: output
            registerReplica: false
            stageOut: true

    - id: ID000003
      name: findrange
      namespace: diamond
      version: "2.0"
      arguments: ["-a", "findrange", "-T60", "-i", "f.b2", "-o", "f.c2"]
      uses:
          - file:
              lfn: f.b2
            type: input
          - file:
              lfn: f.c2
            type: output
            registerReplica: false
            stageOut: true

    - id: ID000004
      name: analyze
      namespace: diamond
      version: "2.0"
      arguments: ["-a", "analyze", "-T60", "-i", "f.c1", "f.c2", "-o", "f.d"]
      uses:
          - file:
              lfn: f.c2
            type: input
          - file:
              lfn: f.c1
            type: input
          - file:
              lfn: f.d
            type: output
            registerReplica: false
            stageOut: true

jobDependencies:
    - id: ID000001
      children:
        - ID000002
        - ID000003
    - id: ID000002
      children:
        - ID000004
    - id: ID000003
      children:
        - ID000004

{'fraction_non_alphanumeric': 0.11037309214245336, 'fraction_numerical': 0.034765404183154325, 'mean_word_length': 1.0584642233856894, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6623923', 'n_tokens_mistral': 2352, 'n_tokens_neox': 2189, 'n_words': 510}