haotu : an open lab notebook

2013/01/09

Update R for Ubuntu

Filed under: Lynux, R, Ubuntu — S @ 07:14

The directions are here:
http://stackoverflow.com/questions/10476713/how-to-upgrade-r-in-ubuntu

1.
sudo gedit /etc/apt/sources.list

This will open up your sources.list file in gedit, where you can add the following line.

2.
deb http://cran.cnr.berkeley.edu/bin/linux/ubuntu/ version/

Replace version/ with whatever version of Ubuntu you are using (eg, precise/, oneric/, and so on). If you’re getting a “Malformed line error”, check to see if you have a space between /ubuntu/ and version/.
Note that you dont have to necesasrily use the berkley mirror. You may get a list of all mirrors here : http://cran.r-project.org/mirrors.html

3.
Fetch the secure APT key with gpg –keyserver keyserver.ubuntu.com –recv-key E084DAB9.

4.
Feed it to apt-key with gpg -a –export E084DAB9 | sudo apt-key add –

5.
sudo apt-get update

This may take awhile

6.
sudo apt-get install r-base

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2013/01/08

Make Icons for Ubuntu Commands:Make Desktop Icon for Galaxy Local Install

Filed under: Galaxy, Lynux, Ubuntu — S @ 05:13

I suppose it matters what version you have….

http://www.liberiangeek.net/2011/11/create-desktop-shortcuts-icons-in-ubuntu-11-10-oneiric-ocelot/

Here is for the version I am running….

http://www.geekyboy.com/archives/384

Then use this as the command line

sh galaxy-dist/run.sh

2012/06/29

How to install ABySS on Ubuntu

Filed under: De Novo assembly, Genomics, Lynux, Ubuntu — S @ 05:18

sudo apt-get install abyss

2012/03/09

Search text file Ubuntu, split text file based on marker in text file

Filed under: Lynux, Ubuntu — S @ 05:06

http://allgeeks.info/77/how-to-search-inside-text-files-in-ubuntu/

grep -Rs some-title-or-text /some/directory/*

http://stackoverflow.com/questions/3644238/split-text-file-in-two-using-bash-script

awk -vRS=”MARKER” ‘{print $0>NR”.txt”}’ file

2012/03/08

Set up BLAST Ubuntu

Filed under: BLAST, Genomics, Lynux — S @ 04:45

It is unclear to me how I got blast to work, but it may have just been through synaptic. Install it through there and see if it works.

http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ#expect

http://biodoc.ist.unomaha.edu/wiki/Tutorials/blast

http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html

http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/blastall_node3.html

http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/blastall_node24.html

 

 

2011/05/26

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

source(“http://bioconductor.org/biocLite.R”)
biocLite(“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

2011/05/13

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)

2011/05/12

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:

http://www.stattler.com/article/using-gedit-or-rgedit-r

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