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iAmphioxus

~ It's a long way from Amphioxus

iAmphioxus

Category Archives: Bioinformatics

Installing Git via Macports on Mac OSX

20 Saturday Apr 2013

Posted by iAmphioxus in Bioinformatics, Blogs

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Git, GitHub, Macports

As I wrote more and more scripts for my work, it become difficult to keep tracking different version of my scripts for different specific tasks. Adopting a source control management (SCM) tool has been put on my agenda. An SCM tool will be even more useful if one is participating a collaborative code development project. There are many such tools available today: Subversions, Mercurial, Git, CVS, etc. I choose Git not only because it is a neat solution in terms of version control but also due to the popularity of Git-based online code development platform, GitHub. Continue reading →

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Building UCSC Kent Source Utilities on Rice SUG@R Cluster

17 Thursday May 2012

Posted by iAmphioxus in Bioinformatics, Blogs

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CMake, Ensembl, Kent Utilities, MySQL, UCSC Genome Browser

UCSC Genome Browser website surely is one of the must-know sites for both experimental and computational biologists. As their name suggested, it is pretty nice for visualizing and analyzing genomics data without getting bogged down in bioinformatics details. You can even do quite powerful data-mining on your favorite organisms or genes by just a few clicks. A good tutorial for UCSC Genome Browser and also another powerful genome browser called Ensembl can be found here. With the nice, intuitively designed web interface in the front, what happens behind scenes is many programs or utilities being organized together and doing their jobs as integrated pipelines. These utilities (called Kent Source Utilities since they were originally written by Dr. Jim Kent) can be of great help to our own data analysis if we can have a copy of them installed on our local machine. On the UCSC Genome Browser website, they provided access to some of those most commonly used tools for stand alone use. However, this is only a subset of all their tools. If we need to use other tools, we have no choice but to build a copy of our own from their source code. This is what we gonna do in this blog. Continue reading →

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Installing BioPerl-1.6.901 on the SUG@R cluster of Rice University

21 Saturday Apr 2012

Posted by iAmphioxus in Bioinformatics

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BioPerl, CPAN, Perl

BioPerl is a nice collection of Perl modules designed for bioinformatics analysis. Making a good use of BioPerl can greatly facilitate our research. The current version of BioPerl is 1.6.901. The steps are as follows>> Continue reading →

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Installing Python 2.7 on the SUG@R cluster of Rice University

27 Monday Feb 2012

Posted by iAmphioxus in Bioinformatics, Blogs

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Python, Stampy

I am using a software package called Stampy to map illumina sequencing reads against the reference genome for my project. In order to install Stampy, a Python of version 2.6 or 2.7 is prerequisite. The default version of Python on our computing cluster, SUG@R, is 2.4.3 and the optional version is 3.2.1, so neither of them can work with Stampy. So I need to install Python 2.7 on SUG@R by myself. The step is as follows>> Continue reading →

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