mscook

192.168.1.71	mini
192.168.1.1	erx

mscook

Keybase proof

I hereby claim:

• I am mscook on github.
• I am mscook (https://keybase.io/mscook) on keybase.
• I have a public key whose fingerprint is 753D EE5F F52A 8D99 D5CE 6F9E 3250 99BF BFC2 08D4

To claim this, I am signing this object:

mscook

015-06-18T04:20:30.719185558 0.017922s error: Error in src/arch/io/timer/timerfd_provider.cc at line 18:
2015-06-18T04:20:30.719599764 0.018326s error: Guarantee failed: [fd != -1]  (errno 1 - Operation not permitted) Could not create timer
2015-06-18T04:20:30.719676100 0.018402s error: Backtrace:
2015-06-18T04:20:30.720274794 0.019002s error: Error in src/arch/io/timer/timerfd_provider.cc at line 18:
2015-06-18T04:20:30.720465822 0.019192s error: Guarantee failed: [fd != -1]  (errno 1 - Operation not permitted) Could not create timer
2015-06-18T04:20:30.720554637 0.019281s error: Backtrace:
2015-06-18T04:20:30.737817554 0.036561s error: Error in src/arch/io/timer/timerfd_provider.cc at line 18:
2015-06-18T04:20:30.738007288 0.036733s error: Guarantee failed: [fd != -1]  (errno 1 - Operation not permitted) Could not create timer
2015-06-18T04:20:30.738081646 0.036807s error: Backtrace:
2015-06-18T04:20:30.777285267 0.076028s error: Error in src/arch/io/timer/timerfd_provider.cc at line 18:

mscook

print 80*"="+"\nThe 'counter' decorator\n"+80*"="

def scount(wrapped):
    def inner(*args, **kwargs):
        inner.counter +=1
        return wrapped(*args, **kwargs)
    inner.counter = 0
    return inner

@scount

mscook

##############################################################################
#
# Handling arguments
#
# This is a wrapt decorator equivalent to Colton Meyers' skipIf presented
# from about the 15 minute mark in his PyCon 2014 talk
#
##############################################################################

import wrapt

mscook

| => brew list
ansible			blast			cd-hit			freetype		glibmm			harfbuzz		intltool		libpng			open-mpi		pkg-config		ray			tmux
aspell			boost			cloog			gcc			gmp			hicolor-icon-theme	isl			libsigc++		openssl			popt			readline		vcftools
atk			boost-build		cmake			gdbm			gobject-introspection	icu4c			jpeg			libtiff			pango			python			samtools		velvet
atkmm			bwa			coreutils		gdk-pixbuf		gsl			igv			libevent		libyaml			pangomm			python3			spades			vim
autoenv			cairo			ctags			gettext			gtk+			igvtools		libffi			little-cms		pcre			qualimap		sqlite			wget
bdw-gc			cairomm			fontconfig		glib			gtkmm			inkscape		libmpc			mpfr			pixman			quast			sratoolkit		xz

mscook

diff --git a/SeqFindR/blast.py b/SeqFindR/blast.py
index 62fb750..cfee667 100644
--- a/SeqFindR/blast.py
+++ b/SeqFindR/blast.py
@@ -77,6 +77,7 @@ def run_BLAST(query, database, args):

     :returns: the path of the blast.xml file
     """
+    out_xml = database.split('/')[-1]+"_blast.xml"
     protein = False

mscook

(function(){if (!Date.now) Date.now = function() {
  return +new Date;
};
try {
  document.createElement("div").style.setProperty("opacity", 0, "");
} catch (error) {
  var d3_style_prototype = CSSStyleDeclaration.prototype,
      d3_style_setProperty = d3_style_prototype.setProperty;
  d3_style_prototype.setProperty = function(name, value, priority) {
    d3_style_setProperty.call(this, name, value + "", priority);

mscook

#!/usr/bin/env python

# Copyright 2014 Beatson Laboratory Licensed under the
# Educational Community License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may
# obtain a copy of the License at
#
# http://www.osedu.org/licenses/ECL-2.0
#
# Unless required by applicable law or agreed to in writing,

mscook

import glob
import os

inf = glob.glob("*.gz")

for f in inf:
    tmp = f.split(".gz")[0]
    os.system("cp "+f+" .original/")
    os.system("gunzip "+f)
    os.system("seqret fastq-illumina::"+tmp+" fastq::"+tmp+".33")