gawbul

GNU GENERAL PUBLIC LICENSE

Version 3, 29 June 2007

Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/>

Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.

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

#!/usr/bin/python
'''
Launch codeml on all the alignments

Marco Galardini 2012
University of Florence
GPL v3.0
'''
from optparse import OptionParser, OptionGroup
from time import strftime

gawbul

#!/usr/bin/ruby
require 'sqlite3'

cite_part = ARGV[0]
db_name = "/Users/nernst/Library/Application\ Support/Mendeley\ Desktop/neil\@neilernst.net\@www.mendeley.com.sqlite"
db = SQLite3::Database.new( db_name )
db.results_as_hash = true
query = "select citationkey, title, year from Documents where citationkey like '%#{cite_part}%'"#MATCH '#{cite_part}'"#{}like '%#{cite_part}%'"
db.execute( query ) do |row|
  print row['citationKey'] + '|'

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