https://info.gersteinlab.org/index.php?action=history&feed=atom&title=Software_Requirements 2026-06-19T04:49:46Z Revision history for this page on the wiki MediaWiki 1.42.6 https://info.gersteinlab.org/index.php?title=Software_Requirements&diff=296&oldid=prev 2010-08-19T13:03:15Z

<p>Created page with &#039;{{FusionSeqHeader}} FusionSeq requires several additional packages to be installed in order to carry out the analysis and visualize the results. Moreover, since its modularity, d…&#039;</p> <p><b>New page</b></p><div>{{FusionSeqHeader}}<br /> FusionSeq requires several additional packages to be installed in order to carry out the analysis and visualize the results. Moreover, since its modularity, different programs would need specific libraries. Moreover, some data set are also required for the analysis (see [[#Data Requirements|Data Requirements]]). Here we describe the complete set of tools that one would need to run the analysis as we do in our lab. The modules should be installed in the listed order.<br /> <br /> ===Alignment tools===<br /> * [http://bowtie-bio.sourceforge.net/index.shtml bowtie] (64bit)<br /> * [http://users.soe.ucsc.edu/~kent/src/ Blat (source)] [http://genome-test.cse.ucsc.edu/~kent/exe/ (binaries)]<br /> Please make sure that blat and bowtie executables are part of the PATH, i.e. they can be accessed and executed from any location on your file system. Moreover, make sure that twoBit2fa is also downloaded from the blat package and part of the PATH.<br /> <br /> ===Scientific and bioinformatics libraries===<br /> * [http://www.gnu.org/software/gsl/ GNU Scientific Library]<br /> * [http://rnaseq.gersteinlab.org/doc/bios/ BIOS]<br /> <br /> ===Drawing tools===<br /> * [http://www.libgd.org/Main_Page GD library]<br /> <br /> ===Data analysis===<br /> * [http://root.cern.ch/drupal/ ROOT]</div>

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