MatthewRalston

require 'log4r'
require 'log4r/yamlconfigurator'
include Log4r

ycfg = YamlConfigurator
ycfg["LOGFILE"] = "/home/matt/logs/myapp.log"
ycfg.load_yaml_file("/home/matt/.config/ruby/logger.yaml")
root_logger = Logger['root_logger']

MatthewRalston

import logging
import logging.config

def get_root_logger(loglevel, logfile=None, log_config="log.conf"):
    # Requires 'import logging' and 'import logging.config'

    def log_level(loglevel):
        case = {"DEBUG": logging.DEBUG,
                "INFO": logging.INFO,
                "WARNING": logging.WARNING,

MatthewRalston

<tool name="Summarize FastQC" id="summarizeFastQCMetrics" version="0.0.1">
  <description>summarizes data from FastQC</description>
  <command>

    #def pairfunc($theList)
    #set $left = []
    #set $right = []
    #for $file1, $file2 in $theList
        #$left.append(str($file1))
        #$right.append(str($file2))

MatthewRalston

<tool name="Random Subsample" id="subsample_fastq" version="0.0.1">
  <description>Subsamples a fastq file</description>
  <command>

    RandomSubFq -w $readsRequested
    -i $paired_fastq_files.forward
    -i $paired_fastq_files.reverse
    -o $paired_list_output.forward
    -o $paired_list_output.reverse
  </command>