From noreply at r-forge.r-project.org  Thu Aug 22 17:00:49 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 22 Aug 2013 17:00:49 +0200 (CEST)
Subject: [Patchwork-commits] r186 - in www: . css/img
Message-ID: <20130822150049.6CEDF1808E1@r-forge.r-project.org>

Author: sebastian_d
Date: 2013-08-22 17:00:48 +0200 (Thu, 22 Aug 2013)
New Revision: 186

Removed:
   www/css/img/file_struc1.png
   www/css/img/file_struct1.png
   www/css/img/flowPWreq.png
Modified:
   www/changelog.php
   www/pw_requ.php
Log:
updates to homepage

Modified: www/changelog.php
===================================================================
--- www/changelog.php	2013-06-28 13:55:12 UTC (rev 185)
+++ www/changelog.php	2013-08-22 15:00:48 UTC (rev 186)
@@ -7,17 +7,27 @@
 
 <!-- <hr class="alt1" />
 
-<h5 style="display:inline-block;">patchwork v2.3 - </h5><div style="display:inline-block; width:1px;"></div>
+<h5 style="display:inline-block;">patchwork v2.4 - </h5><div style="display:inline-block; width:1px;"></div>
 <h6 style="display:inline-block;">2013</h6>
 <ul>
 	<li>Moved Pysam out of package due to auto-install issues. Now you will have to manually install it.
 	See Patchwork -> Installation </li>
 </ul> -->
 
+<!-- <hr class="alt1" />
+
+<h5 style="display:inline-block;">patchwork v2.4 - </h5><div style="display:inline-block; width:1px;"></div>
+<h6 style="display:inline-block;">20/08/2013</h6>
+<ul>
+	<li>Complete makeover of patchwork plots visualization. Now includes cytoband information. </li>
+	<li>New function: patchwork.region(). Shows a region you specify of a chromosome. Contains Known Gene information </li>
+</ul> -->
+
+
  <hr class="alt1" />
 
 <h5 style="display:inline-block;">patchwork v2.3 - </h5><div style="display:inline-block; width:1px;"></div>
-<h6 style="display:inline-block;">2013</h6>
+<h6 style="display:inline-block;">16/08/2013</h6>
 <ul>
 	<li>Moved Pysam out of package due to auto-install issues. Now you will have to manually install it.
 	See Patchwork -> Installation </li>

Deleted: www/css/img/file_struc1.png
===================================================================
(Binary files differ)

Deleted: www/css/img/file_struct1.png
===================================================================
(Binary files differ)

Deleted: www/css/img/flowPWreq.png
===================================================================
(Binary files differ)

Modified: www/pw_requ.php
===================================================================
--- www/pw_requ.php	2013-06-28 13:55:12 UTC (rev 185)
+++ www/pw_requ.php	2013-08-22 15:00:48 UTC (rev 186)
@@ -9,15 +9,15 @@
 
 <ul class="checks">
 	<!-- <li>A Human Genome fasta file</li> -->
-	<li>An aligned and sorted BAM file of tumor content</li>
-	<li>A BAI index of your BAM file</li>
-	<li>A pileup of your BAM file</li>
-	<li>(optional) A VCF file of your tumor pileup</li>
-	<li>(optional) A matched normal sample to your tumor in BAM format</li>
-	<li>(optional) A pileup of your normal sample BAM</li>
+	<!-- <li>An aligned and sorted BAM file of tumor content</li>
+	<li>A BAI index of your BAM file</li> -->
+	<li><b>An aligned and sorted BAM file of tumor content.</b> <br />A BAI index of your BAM file. <br />A pileup of your BAM file. <br />A VCF file of your tumor pileup (if applicable).</li>
+	<!-- <li>(optional) A VCF file of your tumor pileup</li> -->
+	<li><b>(optional) A matched normal sample to your tumor in BAM format.</b><br /> A BAI index of your normal sample BAM.<br /> A pileup of your normal sample BAM. <br />A VCF file of your normal pileup (if applicable). </li>
+	<!-- <li>(optional) A pileup of your normal sample BAM</li>
 	<li>(optional) A VCF file of your normal pileup</li>
-	<li>(optional) A BAI index of your normal sample BAM</li>
-	<li>(optional) A standard Reference file. (Illumina/Solexa, SOLiD or your own)</li>
+	<li>(optional) A BAI index of your normal sample BAM</li> -->
+	<li><b>(optional) A standard Reference file. (Illumina/Solexa, SOLiD or your own)</b></li>
 </ul>
 
 <!--
@@ -26,15 +26,11 @@
   target="_blank" style="text-decoration:none;">(human_g1k_v37)</a>. <br />
 You probably also used such a file when aligning your tumor sequence.<br /><br /> -->
 
-There are several (optional) files in the list, what we mean by this is that you do not need to have all these
-files. There is really no point in using all of them.
+The (optional) files are interchangeable. If you have a normal sample you do not need to supply a reference file.
 <br /><br />
-If you have a matched normal sample you should make a pileup of this and use those two arguments.
-You should also create a BAI file of it, it will not be a parameter but is
-required for the file to be read by patchwork.
+If you have a matched normal sample you should create a pileup and BAI file and use for execution.
+The BAI file is required for the file to be read by patchwork.
 <br />
-In some cases it may be better to use the reference file and a pileup.
-<br />
 You can also run patchwork.plot() with only a reference file.<br />
 <br />
 


From noreply at r-forge.r-project.org  Thu Aug 22 17:01:48 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 22 Aug 2013 17:01:48 +0200 (CEST)
Subject: [Patchwork-commits] r187 - www/css/img
Message-ID: <20130822150148.E1C5D1808E1@r-forge.r-project.org>

Author: sebastian_d
Date: 2013-08-22 17:01:46 +0200 (Thu, 22 Aug 2013)
New Revision: 187

Added:
   www/css/img/file_struct1.png
Log:
add file_struct1.png

Added: www/css/img/file_struct1.png
===================================================================
(Binary files differ)


Property changes on: www/css/img/file_struct1.png
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream