gawbul

#  ---------------------------------------------------------------------------
#
#  Description:  This file holds all my BASH configurations and aliases.
#                Much of this was originally copied from:
#                http://natelandau.com/my-mac-osx-bash_profile/
#
#  Sections:
#  1.   Environment Configuration
#  2.   Make Terminal Better (remapping defaults and adding functionality)
#  3.   File and Folder Management

gawbul

cd /tmp/kitchen.
/opt/chef/embedded/bin/gem install chef-zero
/opt/chef/embedded/bin/chef-zero -d
knife cookbook upload -a -c solo.rb
knife environment from file environments/DEV.json -c solo.rb
chef-shell -z -c solo.rb -o '<YOUR RECIPE>'

gawbul

Unfortunately, the Cisco AnyConnect client for Mac conflicts with Pow. And by "conflicts", I mean it causes a grey-screen-of-death kernel panic anytime you connect to the VPN and Pow is installed.

As an alternative, there is OpenConnect, a command-line client for Cisco's AnyConnect SSL VPN.

Here's how to get it set up on Mac OS X:

1. OpenConnect can be installed via homebrew:

    brew update
   

brew install openconnect

gawbul

[smoss@bioservd ~]$ poretools
Warning! ***HDF5 library version mismatched error***
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment

gawbul

class Poretools < Formula
  desc "Tools for working with nanopore sequencing data"
  homepage "http://poretools.readthedocs.org/"
  url "https://github.com/arq5x/poretools/archive/v0.5.1.tar.gz"
  sha256 "7cd55a8f30290992dcf8d7792401e7f21efadfde02b3f4604d6680d2f8300479"
  head "https://github.com/arq5x/poretools.git"

  depends_on "hdf5"
  depends_on "r"
  depends_on :python if MacOS.version <= :snow_leopard

gawbul

#!/usr/bin/env python
# import modules
import mmap, os, random, re, sys

# parse arguments
if len(sys.argv) != 3:
  print "Requires an input filename and integer as arguments."
  sys.exit()
filename = sys.argv[1]
try:

gawbul

#!/usr/bin/env python
# import modules
import mmap, os, random, sys
from Bio import SeqIO
from StringIO import StringIO

# parse arguments
if len(sys.argv) != 3:
  print "Requires an input filename and integer as arguments."
  sys.exit()

gawbul

#!/usr/bin/env python
# import modules
import os, random, sys

# parse arguments
if len(sys.argv) != 2:
  print "Requires one input filename as an argument."
  sys.exit()
filename = sys.argv[1]

gawbul

==> Installing mira from homebrew/homebrew-science
couldn't understand kern.osversion `14.3.0'
==> Downloading https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira-4.0.2.tar.bz2
Already downloaded: /Library/Caches/Homebrew/mira-4.0.2.tar.bz2
==> Verifying mira-4.0.2.tar.bz2 checksum
tar xf /Library/Caches/Homebrew/mira-4.0.2.tar.bz2
==> ./configure --disable-debug --disable-dependency-tracking --prefix=/usr/local/Cellar/mira/4.0.2 --with-expat=/usr/local/opt/expat --with-expat-lib=-L/usr/local/opt/expat/lib --with-boost=/usr/local/opt/boost --with-boost-libdir=/usr/local/opt/boost/lib --with-boost-regex=boost_regex-mt --with-boost-system=boost_system-mt --with-boost-filesystem=boost_filesystem-mt --with-boost-iostreams=boost_iostreams-mt --with-tcmalloc --with-tcmalloc-dir=/usr/local/opt/google-perftools/lib
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d

gawbul

==> Installing maker from homebrew/homebrew-science
/usr/bin/env perl -e use Bio::Perl
/usr/bin/env perl -e use Bit::Vector
/usr/bin/env perl -e use DBD::SQLite
/usr/bin/env perl -e use DBI
/usr/bin/env perl -e use File::Which
/usr/bin/env perl -e use IO::All
/usr/bin/env perl -e use IO::Prompt
/usr/bin/env perl -e use Inline
/usr/bin/env perl -e use Perl::Unsafe::Signals