Arvados

h1. Pipeline template template

h2. Run-Command Template

<pre>

  "NAME":{

   "script_version":"29009a1c1f8a9653042c5853832881aca4141cf2",

   "repository":"arvados",

   "script":"run-command",

   "script_parameters":{

    "input":{

     "output_of":"OUTPUT_OF_PREVIOUS_JOB_NAME"

    },

    "reference":{

     "dataclass":"Collection",

     "default":"3514b8e5da0e8d109946bc809b20a78a+5698",

     "link_name":"human_g1k_v37 reference data",

     "title":"NAME Input Reference genome (FASTA)"

    },

    "command":[

     "java",

     "-Xmx60g",

     "-jar",

     "$(dir $(gatk3))/GenomeAnalysisTK.jar",

     "-T",

     "PrintReads",

     "-R",

     "$(glob $(dir $(reference))/*.fasta)",

     {

      "foreach":"iterator",

      "command":[

       "-I",

       "$(iterator)"

      ]

     },

     "-BQSR",

     "$(bqsr_table)",

     "-nct",

     "16",

     "-o",

     "$(outputname)"

    ],

    "outputname":{

     "value":{

      "list":"iterator",

      "index":"0",

      "command":"$(basename $(iterator)).bqsrCal.bam"

     }

    },

    "bqsr_table":{

     "value":{

      "list":"iterator",

      "index":"0",

      "command":"$(dir $(bqsr))/$(basename $(basename $(iterator))).recal_data.table"

     }

    },

    "input_dir":"$(dir $(input))",

    "task.foreach":[

     "iterator"

    ],

    "iterator":{

     "value":{

      "group":"input_dir",

      "regex":"(.*)\\.realigned.bam"

     }

    },

    "gatk3":{

     "dataclass":"Collection",

     "default":"2e98fdc8e90f4c48a0714b711767c9ce+76",

     "link_name":"Genome Analysis Toolkit 3.2-2",

     "title":"NAME Input Version of GATK3 jar"

    },

    "dbsnp":{

     "dataclass":"Collection",

     "default":"8ac324bfa3dfff1ff81ed34b433869b1+6712",

     "title":"Single Nucleotide Polymorphism database",

     "description":"NAME Input DBsnp"

    }

   },

   "runtime_constraints":{

    "max_tasks_per_node":1,

    "min_nodes":1,

    "docker_image":"bcosc/arv-base-java",

    "arvados_sdk_version":"29009a1c1f8a9653042c5853832881aca4141cf2" 

   },

   "output_name":false

</pre>

h2. Crunch Script Template Template

<pre>

 "NAME":{

   "script_version":"GIT_BRANCH_NAME",

   "repository":"GIT_REPO_NAME",

   "script":"GIT_SCRIPT_NAME",

   "script_parameters":{

    "input":{

     "output_of":"PREVIOUS_JOB_NAME"

    },

    "samtools":{

     "required":true,

     "dataclass":"Collection",

     "default":"0b5dd5ad3fd555dbb9ef81a027b69dec+18147",

     "title":"NAME Input Samtools Collection"

    },

    "bcftools":{

     "required":true,

     "dataclass":"Collection",

     "default":"6a0c51bea360b487aa5c9d130435cd00+14097",

     "title":"NAME Input BCFtools Collection"

    },

    "gatk_jar":{

     "required":true,

     "dataclass":"Collection",

     "default":"2e98fdc8e90f4c48a0714b711767c9ce+76",

     "title":"NAME Input GATK Collection"

    },

    "reference":{

     "required":true,

     "dataclass":"Collection",

     "default":"3514b8e5da0e8d109946bc809b20a78a+5698",

     "title":"NAME Input Reference Collection"

    },

    "picard":{

     "required":true,

     "dataclass":"Collection",

     "default":"0eaa58017c3689414a9e644a2297df5c+165",

     "title":"NAME Input Picard Collection"

    },

    "bedtools_bin":{

     "required":true,

     "dataclass":"Collection",

     "default":"b2f86c26e05e7a0686e7f39a86d406bf+34584",

     "title":"NAME Input Bedtools Collection"

    },

    "bed_path":{

     "required":true,

     "dataclass":"Collection",

     "default":"a0e2c5057d64bfb9ce2cdefd46f71b27+516",

     "title":"NAME Input Bed Collection"

    },

    "bwa_bin": {

     "required": true,

     "dataclass": "Collection",

     "default": "39c6f22d40001074f4200a72559ae7eb+5745",

     "title": "NAME Input BWA Binary"

    },

    "gatk_ref":{

     "required":true,

     "dataclass":"Collection",

     "default":"25b68283b442c1a921ac826296103426+9636",

     "title":"NAME GATK Reference Collection"

    }

   },

   "runtime_constraints":{

    "max_tasks_per_node":1,

    "min_nodes":1,

    "docker_image":"bcosc/arv-base-java",

    "arvados_sdk_version":"749b87143ebb0bdcbe2d49deee9c66f6de9f86dd"

   },

   "output_name":false

  },

</pre>

h2. Crunch Script Template

<pre>

#!/usr/bin/env python

import arvados

import subprocess

import os

import sys

import re

from arvados.collection import Collection as coll

import arvados_tools

import shutil

arvados_tools.spawn_new_task_per_file('input','.*realigned.bqsrCal.bam$',if_sequence=0, and_end_task=True)

this_job = arvados.current_job()

this_task = arvados.current_task()

tmpdir = arvados.current_task().tmpdir

input_1 = this_task['parameters']['input_1']

input_1_path = os.path.join(arvados.get_job_param_mount("input"),input_1)

tmp_input_1_path = os.path.join(tmpdir,input_1) # If we need to copy to tmpdir

shutil.copyfile(input_1_path,tmp_input_1_path) # If we need to copy to tmpdir

</pre> 

<pre>

samtools_path = arvados_tools.get_file_path('samtools','^samtools$')

gatk_path = arvados_tools.get_file_path('gatk_jar','^GenomeAnalysisTK.jar$')

reference_path = arvados_tools.get_file_path('reference','.*f(ast)?a(.gz)?$')

dbsnp_path = arvados_tools.get_file_path('dbsnp','^dbsnp.*vcf$')

bgzip_path = arvados_tools.get_file_path('tabix','^bgzip$')

tabix_path = arvados_tools.get_file_path('tabix','^tabix$')

tmp_picard_path = arvados_tools.get_file_path('picard','^picard.jar$')

# Copy picard over to tmpdir because java cannot hand "+" characters

picard_path = os.path.join(tmpdir,"picard.jar")

shutil.copyfile(tmp_picard_path,picard_path)

others:

bed56Gb37_path = arvados_tools.get_file_path('bed_path','.*bed$')

</pre>

<pre>

gatk_inserttool_args = []

gatk_inserttool_output_name

gatk_inserttool_output_path

gatk_inserttool_pipe = subprocess.check_output()

</pre>

<pre>

samtools_inserttool_args = []

</pre>

h2. Script Parameter Template

h2. Random stuff

h2. Latest arvados_sdk_version: 

https://arvados.org/projects/arvados/repository/revisions/master/show/sdk/python

h2. Random tools I use

os.path.join(arvados.get_job_param_mount("param"),name)

h2. Pipe through tools

bwa_pipe = subprocess.Popen(args,stdout=subprocess.PIPE)

output_file = open(output_bam_path,'w')

samtools_pipe = subprocess.Popen(sam_args, stdin=bwa_pipe.stdout, stdout=output_file)

bwa_pipe.wait()

samtools_pipe.wait()

output_file.close()

h2. Get name of file without n extensions

base_input_split = re.split('(\.)',input_1)

base_input_list = base_input_split[0:len(base_input_split)-n*2]

base_name = ''.join(base_input_list)

print base_name