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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
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
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 10µM forskolin gene expression data of regenerating dorsal root ganglion neurons
GSM561078 F11_FSK2h_rep2 F11 cells, no forskolin 2hrs 2 10µM forskolin gene expression data of regenerating dorsal root ganglion neurons
GSM561079 F11_FSK2h_rep3 F11 cells, no forskolin 2hrs 3 10µM forskolin gene expression data of regenerating dorsal root ganglion neurons
GSM561080 F11_FSK4h_rep1 F11 cells, no forskolin 4hrs 1 10µM forskolin gene expression data of regenerating dorsal root ganglion neurons
GSM561081 F11_FSK4h_rep2 F11 cells, no forskolin 4hrs 2 10µM forskolin gene expression data of regenerating dorsal root ganglion neurons
GSM561082 F11_FSK4h_rep3 F11 cells, no forskolin 4hrs 3 10µM forskolin gene expression data of regenerating dorsal root ganglion neurons
GSM561083 F11_FSK24h_rep1 F11 cells, no forskolin 24hrs 1 10µM forskolin gene expression data of regenerating dorsal r
@arraytools
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
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
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
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
arraytools / ip.txt
Created September 28, 2013 16:34
Given a list of ip, we want to plot the locations on google map
66.249.75.44
79.133.216.100
79.133.216.107
46.105.54.115
180.76.5.156
199.30.20.52
199.30.20.105
27.153.249.94
199.30.28.131
199.30.20.130
@arraytools
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 {
@arraytools
arraytools / GeneIDs.txt
Created September 23, 2013 14:19
Simple text file used for testing reading by C++
ProbeSet Symbol
1552266_at ADAM32
1007_s_at DDR1
1487_at ESRRA
1294_at UBA7
1552257_a_at TTLL12
1405_i_at CCL5
1053_at RFC2
1320_at PTPN21
1316_at THRA