https://sourceforge.net/p/tuque/wiki/Install/Recent changes to InstallenFri, 17 May 2013 17:48:53 -0000https://sourceforge.net/p/tuque/wiki/Install/<div class="markdown_content"><pre>--- v2 +++ v3 @@ -21,4 +21,4 @@ PATH. e.g. ln -s $(pwd)/tuque/tuqueSplice ~/bin Edit the file tuque.cfg in the tuque folder so that the program paths correspond to the locations on your -system. Customized copies of tuque.cfg can be saved elsewhere, and invoked with the -c option to the tuque programs +system. Customized copies of tuque.cfg can be saved under another name and invoked with the -c option to the tuque programs </pre> </div>Ian ReidFri, 17 May 2013 17:48:53 -0000https://sourceforge.net54ea414fb42c5618961001722fd415f783fb40behttps://sourceforge.net/p/tuque/wiki/Install/<div class="markdown_content"><pre></pre> </div>Ian ReidWed, 10 Apr 2013 17:33:29 -0000https://sourceforge.net99c3a813f872cee8fe22766bb46ea91bb9047d79https://sourceforge.net/p/tuque/wiki/Install/<div class="markdown_content"><h1 id="installation">Installation</h1> <p>Tuque depends on other open-source software. Before using any of the Tuque programs,<br /> ensure that these programs are available on your system:</p> <ul> <li>A <strong>Unix</strong> operating system, with bash, sort, awk, and grep</li> <li><strong>Python</strong> 2.7 or newer - Available from <a href="http://www.python.org/">http://www.python.org/</a> <em>Don't use Python 3</em></li> <li><strong>Biopython</strong> - Available from <a href="http://biopython.org/wiki/Download">http://biopython.org/wiki/Download</a></li> <li><strong>bowtie</strong> and <strong>bowtie-build</strong> - Available from <a href="http://bowtie-bio.sourceforge.net/index.shtml">http://bowtie-bio.sourceforge.net/index.shtml</a> <em>Don't use Bowtie 2</em></li> <li><strong>blat</strong> and <strong>pslCDnaFilter</strong> - Available from <a href="http://hgdownload.cse.ucsc.edu/admin/exe/">http://hgdownload.cse.ucsc.edu/admin/exe/</a></li> <li><strong>samtools</strong> and <strong>tabix</strong> - Available from <a href="http://sourceforge.net/projects/samtools/files/">http://sourceforge.net/projects/samtools/files/</a></li> <li><strong>genomeCoverageBed</strong> - Available from <a href="http://code.google.com/p/bedtools/">http://code.google.com/p/bedtools/</a></li> </ul> <p>The programs can be installed anywhere; they do not need to be in a system directory or on the PATH.</p> <p>To install Tuque, download and decompress <a href="http://sourceforge.net/projects/tuque/files/tuque.tar.gz">http://sourceforge.net/projects/tuque/files/tuque.tar.gz</a> in a convenient<br /> location.<br /> Leave the tuque scripts in their installation directory so that they can find their library files. For convenience you<br /> can place symbolic links to tuqueSplice, tuqueSplice_ps, tuqueMap, tuqueIndex, and tuqueCount in a directory on your<br /> PATH. e.g. ln -s $(pwd)/tuque/tuqueSplice ~/bin</p> <p>Edit the file tuque.cfg in the tuque folder so that the program paths correspond to the locations on your<br /> system. Customized copies of tuque.cfg can be saved elsewhere, and invoked with the -c option to the tuque programs</p></div>Ian ReidWed, 10 Apr 2013 16:31:22 -0000https://sourceforge.netcc39edc408338e5262801fd4b99ab7d9e019d3df