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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 / 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=$PATH:/opt/RNA-Seq/bin/samtools-0.1.19/:/opt/RNA-Seq/bin/samtools-0.1.19/bcftools:/opt/RNA-Seq/bin/samtools-0.1.19/misc
cd /home/brb/Anders2013
@arraytools
arraytools / qt5.5_configure
Created July 15, 2015 16:51
qt 5.5 configure options
brb@brb-VirtualBox:~/qt-everywhere-opensource-src-5.5.0$ ./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 / 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_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 / 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 / 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
arraytools / vagrant.nginx.output
Created January 1, 2016 19:26
Running nginx using vagrant
brb@brb-P45T-A:/mnt/bigdisk/mytestbox$ cat > Vagrantfile
VAGRANTFILE_API_VERSION = "2"
Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
config.vm.define "web", primary: true do |web|
web.vm.box = "ubuntu/trusty64"
web.vm.network "forwarded_port", guest:80, host:8888
web.vm.provision "shell", inline: "apt-get install -y nginx"
end
end
brb@brb-P45T-A:/mnt/bigdisk/mytestbox$ vagrant up
@arraytools
arraytools / corebird
Created February 12, 2016 18:38
corebird installation
vagrant@vagrant:~$ sudo apt-get install corebird
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
@arraytools
arraytools / qt4.8_configure
Created September 29, 2016 00:49
Usage: configure [-h] [-prefix <dir>] [-prefix-install] [-bindir <dir>] [-libdir <dir>]
[-docdir <dir>] [-headerdir <dir>] [-plugindir <dir> ] [-importdir <dir>] [-datadir <dir>]
[-translationdir <dir>] [-sysconfdir <dir>] [-examplesdir <dir>]
[-demosdir <dir>] [-buildkey <key>] [-release] [-debug]
[-debug-and-release] [-developer-build] [-shared] [-static] [-no-fast] [-fast] [-no-largefile]
[-largefile] [-no-exceptions] [-exceptions] [-no-accessibility]
[-accessibility] [-no-stl] [-stl] [-no-sql-<driver>] [-sql-<driver>]
[-plugin-sql-<driver>] [-system-sqlite] [-no-qt3support] [-qt3support]
[-platform] [-D <string>] [-I <string>] [-L <string>] [-help]
[-qt-zlib] [-system-zlib] [-no-gif] [-no-libtiff] [-qt-libtiff] [-system-libtiff]