haotu : an open lab notebook


Install Bioconductor R XML

Filed under: Bioconductor, Lynux, R, Ubuntu — S @ 06:08

First install

sudo apt-get install libxml2-dev

then install XML,

The reason I want to install the R XML package is because I wanted to install rtracklayer



Install Bioconductor RCurl Ubuntu

Filed under: Bioconductor, Genomics, Lynux, R, Ubuntu — S @ 06:03
First install libcurl4-gnutls-dev (Ubuntu) package.

Then install RCurl from CRAN


Install Trinity RNA-Seq on Ubuntu

Filed under: De Novo assembly, Genomics, RNAseq — S @ 04:36

I am going to try to install the Trinity RNA-Seq de novo assembler to create contigs of some tadpole RNA-seq data.

1. Download tar ball at sourceforgehttp://sourceforge.net/projects/trinityrnaseq/
2. Then I extracted it to a folder and typed


3. then you can go to the sample data folder and run the example script

sudo ./runMe.sh

This all seemed to work fine on my laptop…

On the Trinity website they refer to left and right reads for paired end files, this corresponded to files 1 and 2, respectively, that I received from BGI.


Install BioPython on Ubuntu

Filed under: BioPython, Lynux, Python, Ubuntu — S @ 05:15

I am following the Byopython instructions on http://biopython.org/DIST/docs/install/Installation.html

1. First first I needed to instal Numpy

I found the tar ball here:  http://sourceforge.net/projects/numpy/files/NumPy/

but could not get that to install following the instructions on the biopython website: http://biopython.org/DIST/docs/install/Installation.html#htoc2
so instead I just typed

sudo apt-get install python-numpy

and this seemed to work… since I was able to type

import numpy

into a python terminal window and get no errors. Some discussion can be found here: http://ubuntuforums.org/showthread.php?t=566456

2. I also installed ReportLab in order to generate pdf graphics again I just typed

sudo apt-get install python-reportlab

3. Then instead of following the more complicated instructions on the website I just typed

sudo apt-get install python-biopython

and this seemed to install it properly.

4. I Checked the instalation following the code written in point 5 on the instructions.

Use Lynux File Mannager to Graphically Create a Link to Run a Program from any Location

Filed under: Lynux, Ubuntu — S @ 05:15

Open the file manager using sudo

right click on the application that you want to use from any location and make a link

cut that link and then in the file manager got to your HD and then the folder bin in your HD and paste the link.

Rename the link the name of the program (or some other command that you want to type to get it to run)


R gedit for Ubuntu

Filed under: Lynux, R, Ubuntu — S @ 12:55

I started using gedit to interact with R and so far it is fine. The instructions can be found here:



Administrator access in Ubuntu GUI File Manager

Filed under: Lynux, Ubuntu — S @ 06:57

in command line type this:

gksu nautilus

Vim Text Editor Instalation for Ubuntu

Filed under: Uncategorized — S @ 06:56


To set up the GUI

sudo apt-get install vim-gnome

Also install the full version

sudo apt-get install vim

Then I just added a shortcut by right clicking on the desktop and creating a launcher. Then you can select “Application in terminal” and then type gvim into the command line.


Working directory in Python

Filed under: Python — S @ 08:13
The os module has lots of input output functions to get the working directory and a list of the files in the wd use the below

import os
wd = os.getcwd()
dirList = os.listdir(wd)
for fname in dirList:
    print fname

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