https://sourceforge.net/p/dspchip/wiki/Installation/Recent changes to InstallationenThu, 19 Dec 2013 10:10:34 -0000https://sourceforge.net/p/dspchip/wiki/Installation/<div class="markdown_content"><p>Requirements for installation of <code>dspchip</code></p> <h1 id="requirements">Requirements</h1> <p><code>dspchip</code> has been implemented in <a class="" href="http://www.python.org" rel="nofollow">Python</a>, hence you will need this :-) </p> <p>There is a number of libraries you should install as dependencies: </p> <ul> <li><a class="" href="http://numpy.scipy.org/" rel="nofollow">numpy</a></li> <li><a class="" href="http://www.scipy.org/" rel="nofollow">scipy</a>, backbode for most of the processing </li> <li><a class="" href="http://www.pybytes.com/pywavelets/" rel="nofollow">pywt</a>, for wavelet denoising </li> <li><a class="" href="http://code.google.com/p/pysam/" rel="nofollow">pysam</a>, for reading BAM files </li> <li><a class="" href="http://matplotlib.sourceforge.net/">matplotlib</a>, for plotting issues </li> <li><a class="" href="http://bytebucket.org/james_taylor/bx-python/wiki/Home" rel="nofollow">bx-python</a>, for handy readers of wig and interval files </li> </ul> <p>Also, you will beed <code>bigWigInfo</code>, <code>bigWigToBedGraph</code> and <code>wigToBigWig</code> executables to support bigWig file format (until I have native python support). If you can't build from source, there are precompiled versions <a class="" href="http://hgdownload.cse.ucsc.edu/admin/exe/" rel="nofollow">here</a></p> <h1 id="installation">Installation</h1> <p>Install the dependencies above, then get the source (either the tarball or the svn source). Unpack the archive and issue: </p> <div class="codehilite"><pre><span class="err">$</span> <span class="n">python</span> <span class="n">setup</span><span class="p">.</span><span class="n">py</span> <span class="n">build</span> <span class="err">$</span> <span class="n">sudo</span> <span class="n">python</span> <span class="n">setup</span><span class="p">.</span><span class="n">py</span> <span class="n">install</span> </pre></div> <p>within the archive directory. Follow python distutils instruction for additional options, i.e. </p> <div class="codehilite"><pre><span class="err">$</span> <span class="n">python</span> <span class="n">setup</span><span class="p">.</span><span class="n">py</span> <span class="o">--</span><span class="n">help</span><span class="o">-</span><span class="n">commands</span> </pre></div> <p>or </p> <div class="codehilite"><pre><span class="err">$</span> <span class="n">python</span> <span class="n">setup</span><span class="p">.</span><span class="n">py</span> <span class="n">install</span> <span class="o">--</span><span class="n">help</span> </pre></div> </div>AnonymousThu, 19 Dec 2013 10:10:34 -0000https://sourceforge.net62624af48f54778cc0ceccdab089d86deca6f39b