arraytools’s gists

arraytools / BR5250_2.ppd

Created December 30, 2015 15:51

Brother-HL-5250DN-Postscript-Brother.ppd

	*PPD-Adobe: "4.3"
	*% This program is free software; you can redistribute it and/or modify it
	*% under the terms of the GNU General Public License as published by the Free
	*% Software Foundation; either version 2 of the License, or (at your option)
	*% any later version.
	*%
	*% This program is distributed in the hope that it will be useful, but WITHOUT
	*% ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
	*% FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
	*% more details.

arraytools / r.nanorc

Created December 23, 2015 15:13

	################################################################################
	#
	# R.nanorc -- nano syntax-highlighting file for R
	#
	# Origin: This file is part of the pkgutils package for R.
	#
	# Usage: This file should be placed in a directory such as /usr/share/nano/ (on
	# Ubuntu 12.04). That nano uses syntax highlighting at all might need to be
	# enabled separately.
	#

arraytools / qt5.5_configure_output_on_Windows 10

Last active November 4, 2015 15:35

qt5.5 configure output on Windows 10

	c:\qt\qt-everywhere-5.5.1>configure -release -static -confirm-license -nomake examples -opensource
	+ cd qtbase
	+ c:\Qt\qt-everywhere-5.5.1\qtbase\configure.bat -top-level -release -static -confirm-license -nomake examples -opensource
	Please wait while bootstrapping configure ...
	<srcbase> = c:/Qt/qt-everywhere-5.5.1/qtbase
	<outbase> = c:/Qt/qt-everywhere-5.5.1/qtbase

	jom 1.1.0 - empower your cores

	cl -c -Yc -nologo -Zc:wchar_t -W3 -GR -EHsc -w34100 -w34189 -DUNICODE -DQT_NO_CODECS -DQT_NO_TEXTCODEC -DQT_NO_UNICODETABLES -DQT_LITE_COMPONENT -DQT_NO_COMPRESS -DQT_NO_THREAD -DQT_NO_QOBJECT -DQT_NO_GEOM_VARIANT -D_CRT_SECURE_NO_DEPRECATE -DQT_BOOTSTRAPPED -DQT_BUILD_CONFIGURE -I"..\..\include" -I"..\..\include\QtCore" -I"..\..\include\QtCore\5.5.1" -I"..\..\include\QtCore\5.5.1\QtCore" -I"c:\Qt\qt-everywhere-5.5.1\qtbase\tools\shared" -I"c:\Qt\qt-everywhere-5.5.1\qtbase\mkspecs\win32-msvc2008" -Fpconfigure_pch.pch -Foconfigure_pch.obj -TP c:\Qt\qt-everywhere-5.5.1\qtbase\tools\configure\configure_pch.

arraytools / Experiment descriptors

Last active September 8, 2015 17:39

GSE22631 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse22631). Only partial data is put here.

	ExpId title reference_ch1 time point_ch2 replicate_ch2 agent_ch2 description
	GSM561077 F11_FSK2h_rep1 F11 cells, no forskolin 2hrs 1 10ÂµM forskolin gene expression data of regenerating dorsal root ganglion neurons
	GSM561078 F11_FSK2h_rep2 F11 cells, no forskolin 2hrs 2 10ÂµM forskolin gene expression data of regenerating dorsal root ganglion neurons
	GSM561079 F11_FSK2h_rep3 F11 cells, no forskolin 2hrs 3 10ÂµM forskolin gene expression data of regenerating dorsal root ganglion neurons
	GSM561080 F11_FSK4h_rep1 F11 cells, no forskolin 4hrs 1 10ÂµM forskolin gene expression data of regenerating dorsal root ganglion neurons
	GSM561081 F11_FSK4h_rep2 F11 cells, no forskolin 4hrs 2 10ÂµM forskolin gene expression data of regenerating dorsal root ganglion neurons
	GSM561082 F11_FSK4h_rep3 F11 cells, no forskolin 4hrs 3 10ÂµM forskolin gene expression data of regenerating dorsal root ganglion neurons
	GSM561083 F11_FSK24h_rep1 F11 cells, no forskolin 24hrs 1 10ÂµM forskolin gene expression data of regenerating dorsal r

arraytools / qt5.5_configure

Created July 15, 2015 16:51

qt 5.5 configure options

	brb@brb-VirtualBox:~/qt-everywhere-opensource-src-5.5.0$ ./configure -h
	+ cd qtbase
	+ /home/brb/qt-everywhere-opensource-src-5.5.0/qtbase/configure -top-level -h
	Usage: configure [options]

	Installation options:

	These are optional, but you may specify install directories.

	-prefix <dir> ...... The deployment directory, as seen on the target device.

arraytools / tophat2_Lesson

Last active August 29, 2015 14:22

tophat2 with -G and --transcriptome-index options

	If no fasta file is found alongside the other index files, tophat will use the bowtie index you give
	to build this file and save it to the output directory. This step can take up to an hour for a
	human-sized genome.

	############################################################################################################
	#!/bin/bash
	export PATH=$PATH:/opt/RNA-Seq/bin/bowtie2-2.2.1:/opt/RNA-Seq/bin/tophat-2.0.11.Linux_x86_64
	export PATH=$PATH:/opt/RNA-Seq/bin/tophat-2.0.11.Linux_x86_64
	export PATH=$PATH:/opt/RNA-Seq/bin/samtools-0.1.19/:/opt/RNA-Seq/bin/samtools-0.1.19/bcftools:/opt/RNA-Seq/bin/samtools-0.1.19/misc
	cd /home/brb/Anders2013

arraytools / Home_sapiens_UCSC_hg19

Created May 21, 2015 20:37

Content obtained from the command "tar -tzvf Homo_sapiens_UCSC_hg19.tar.gz"

	10228584083 Homo_sapiens/UCSC/hg19/Annotation/Archives/archive-2014-06-02-13-47-56/Variation/snp137.txt
	12318134451 Homo_sapiens/UCSC/hg19/Annotation/Archives/archive-2014-06-02-13-47-56/Variation/snp138.txt
	0 Homo_sapiens/UCSC/hg19/
	0 Homo_sapiens/UCSC/hg19/Annotation/
	0 Homo_sapiens/UCSC/hg19/Annotation/Genes -> Archives/archive-current/Genes
	0 Homo_sapiens/UCSC/hg19/Annotation/README.txt -> Archives/archive-current/README.txt
	0 Homo_sapiens/UCSC/hg19/Annotation/SmallRNA -> Archives/archive-current/SmallRNA
	0 Homo_sapiens/UCSC/hg19/Annotation/Variation -> Archives/archive-current/Variation
	0 Homo_sapiens/UCSC/hg19/Annotation/Archives/
	0 Homo_sapiens/UCSC/hg19/Annotation/Archives/archive-2011-08-30-21-45-18/

arraytools / build-R-based-on-git

Last active August 29, 2015 14:20

build-R-base-on-git

	# sudo apt-get update
	# sudo apt-get install git
	# sudo apt-get build-dep r-base

	# about 350MB as of R 3.2.0
	git clone https://github.com/wch/r-source.git
	cd r-source

	R_PAPERSIZE=letter \
	R_BATCHSAVE="--no-save --no-restore" \

arraytools / ip.txt

Created September 28, 2013 16:34

Given a list of ip, we want to plot the locations on google map

arraytools / memoryTest.cpp

Last active December 23, 2015 20:29

memory leak test

	#include <iostream>

	using namespace std;

	void foo(unsigned long long n)
	{
	double *ptr = new (std::nothrow) double[n];
	if (!ptr) {
	cout << "Failed to allocate double[n]" << endl;
	} else {