drio

#!/bin/bash
#

#$coverage_bin -in $a_out_bin -ia $hsap_ref -od $plots_dir -cg #-u
mosaik_dir="$HOME/mosaik/bin"
build_bin="$mosaik_dir/MosaikBuild"
align_bin="$mosaik_dir/MosaikAligner"
text_bin="$mosaik_dir/MosaikText"
jump_bin="$mosaik_dir/MosaikJump"
coverage_bin="$mosaik_dir/MosaikCoverage"

drio

deiros@rsync1:/data/bucket2/solid_offline/solid0083_20090429_1_Ovarian_13_0720_Normal_Fragment $ cat /tmp/foo 
cp_file.txt
input.txt
JOB_LIST.txt
PBS_General.input
r.o
run
scripts
solid0083_20090429_1_Ovarian_13_0720_Normal_Fragment_Ovarian_13_0720_Normal_Fragment_F3.csfasta.ma.50.6.gz
solid0083_20090429_1_Ovarian_13_0720_Normal_Fragment_Ovarian_13_0720_Normal_Fragment_F3.csfasta.ma.50.6.idx.gz

drio

require 'dm-core'
require 'dm-validations'
require 'dm-timestamps'

DataMapper.setup(:default, "sqlite3://#{Dir.pwd}/mydb.sqlite3")

class Post
  include DataMapper::Resource

  has n, :comments

drio

require 'sinatra/base'
require 'sequel'
require 'scaffolding_extensions'

DB = Sequel.connect('sqlite://sca.db')

class SeqEvent < Sequel::Model(:seq_events)
end

# Change some basic behaviour in sinatra

drio

$ jrubyc ./file_read_parse.rb
$ java -Djruby.home=/stornext/snfs1/next-gen/software/jruby-1.3.1 \
-cp .:/stornext/snfs1/next-gen/software/jruby-1.3.1/lib/jruby.jar file_read_parse

drio

#!/bin/bash

ec_ref="./E.coli.K12strainMG1655.fa"
dc_plas_ref="ecoli_plasmid.fa"

rm -f *.brg
rm -f *.bif

for space in 0 1
do

drio

#!/bin/bash

bf_bin="/stornext/snfs1/next-gen/drio-scratch/bfast_related/versions/production/bfast/bfast"
fq="/stornext/snfs4/next-gen/solid/analysis/solid0099/0099_20100104_2_SL_AWG_HCC_L09_0150_T_000pA_01003244695_1/reads/0099_20100104_2_SL_AWG_HCC_L09_0150_T_000pA_01003244695_1.21.fastq"


for i in `seq 1 72`
do
  cat <<-EOF
  bsub -q normal \

drio

 def self.dir_exists?(sea)
    found = []
    SNFS.each do |s|
      path = SEA_DIR_TEMPLATE.gsub(/SS/, s).gsub(/II/, sea.instrument)
      log("I can't find #{path}", 1) unless File.exists?(path)
      re = %r{ ^#{path}/\d+/\d+/#{sea}$ }
      puts re
      Find.find(path) do |p|
        puts p
        #sea_dir = a_dir_for(sea)

drio

1

Sun Apr 11 21:41:42 CDT 2010

drio

Copyright (c) 2008 Chris Wanstrath

Permission is hereby granted, free of charge, to any person obtaining a copy of 
this software and associated documentation files (the "Software"), to deal in 
the Software without restriction, including without limitation the rights to 
use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of 
the Software, and to permit persons to whom the Software is furnished to do so, 
subject to the following conditions:

The above copyright notice and this permission notice shall be included in all