[Patchwork-commits] r139 - / www

Tue Jun 26 14:26:45 CEST 2012

Author: sebastian_d
Date: 2012-06-26 14:26:45 +0200 (Tue, 26 Jun 2012)
New Revision: 139

Added:
   .gitignore
Modified:
   README
   www/changelog.php
   www/index.php
Log:
post adding to git commit 

Added: .gitignore
===================================================================

--- .gitignore	                        (rev 0)
+++ .gitignore	2012-06-26 12:26:45 UTC (rev 139)
@@ -0,0 +1,2 @@
+.DS_Store
+

Modified: README
===================================================================
--- README	2012-06-25 14:01:50 UTC (rev 138)
+++ README	2012-06-26 12:26:45 UTC (rev 139)
@@ -1,76 +1,10 @@
-			R-Forge SVN README
+Patchwork is a bioinformatic tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes.
+High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid. 
 
-This file explains the repository structure of your project. A more
-detailed guide to R-Forge is available by 
-Theußl and Zeileis (2010) [1] and the R-Forge Administration and 
-Development Team (2009) [2].
+Patchwork is available in two formats. The first, named simply patchwork, takes BAM files as input whereas patchworkCG takes input from CompleteGenomics files. Detailed guides and information regarding these can be found in their respective tabs. 
 
-1. Introduction
------------------------------------------------------------------------
-R is free software distributed under a GNU-style copyleft. R-Forge is
-a central platform for the development of R packages, R-related 
-software and further projects. Among many other web-based features it 
-provides facilities for collaborative source code management via 
-Subversion (SVN) [3].
+If you have any feedback or questions please do not hesitate to contact us! 
 
-2. The directory you're in
------------------------------------------------------------------------
-This is the repository of your project. It contains two important
-pre-defined directories namely 'pkg' and 'www'. These directories must 
-not be deleted otherwise R-Forge's core functionality will not be 
-available (i.e., daily checking and building of your package or the 
-project websites).
-'pkg' and 'www' are standardized and therefore are going to be
-described in this README. The rest of your repository can be used as
-you like.
-
-3. 'pkg' directory
------------------------------------------------------------------------
-To make use of the package building and checking feature the package 
-source code has to be put into the 'pkg' directory of your repository 
-(i.e., 'pkg/DESCRIPTION', 'pkg/R', 'pkg/man', etc.) or, alternatively,
-a subdirectory of 'pkg'. The latter structure allows for having more 
-than one package in a single project, e.g., if a project consists of 
-the packages foo and bar then the source code will be located in 
-'pkg/foo' and 'pkg/bar', respectively.
-
-R-Forge automatically examines the 'pkg' directory of every repository 
-and builds the package sources as well as the package binaries on a
-daily basis for Mac OS X and Windows (if applicable). The package builds
-are provided in the 'R Packages' tab for download or can be installed
-directly in R from a CRAN-style repository using 
-'install.packages("foo", repos="http://R-Forge.R-project.org")'. 
-Furthermore, in the 'R Packages' tab developers can examine logs 
-generated on different platforms by the build and check process.
-
-4. 'www' directory
------------------------------------------------------------------------
-Developers may present their project on a subdomain of R-Forge, e.g.,
-'http://foo.R-Forge.R-project.org', or via a link to an external
-website.
-
-This directory contains the project homepage which gets updated hourly
-on R-Forge, so please take into consideration that it will not be 
-available right after you commit your changes or additions. 
-
-5. Help
------------------------------------------------------------------------
-If you need help don't hesitate to submit a support request at 
-https://r-forge.r-project.org/tracker/?func=add&group_id=34&atid=194, 
-search the forum 
-https://r-forge.r-project.org/forum/forum.php?forum_id=78&group_id=34,
-or contact us at R-Forge at R-project.org.
-
-6. References
------------------------------------------------------------------------
-
-[1] Stefan Theußl and Achim Zeileis. Collaborative software development 
-using R-Forge. The R Journal, 1(1):9-14, May 2009. URL 
-http://journal.r-project.org/2009-1/RJournal_2009-1_Theussl+Zeileis.pdf  
-
-[2] R-Forge Administration and Development Team. RForge User’s Manual, 
-2008. URL http://download.R-Forge.R-project.org/R-Forge.pdf
-
-[3] C. M. Pilato, B. Collins-Sussman, and B. W. Fitzpatrick. Version 
-Control with Subversion. O’Reilly, 2004. Full book available online at 
-http://svnbook.red-bean.com/
+Sebastian.Dilorenzo at medsci.uu.se
+Markus.Mayrhofer at medsci.uu.se
+Anders.Isaksson at medsci.uu.se

Modified: www/changelog.php
===================================================================
--- www/changelog.php	2012-06-25 14:01:50 UTC (rev 138)
+++ www/changelog.php	2012-06-26 12:26:45 UTC (rev 139)
@@ -5,13 +5,25 @@
 Here you can find the recent changes made to the patchwork and patchworkCG packages.
 <br />
 
+<!--
 <hr class="alt1" />
 
+<h5 style="display:inline-block;">patchworkCG v2.1 - </h5><div style="display:inline-block; width:1px;"></div>
+<h6 style="display:inline-block;">25/06/2012</h6>
+<ul>
+	<li>Improved sex-chromosome handling</li>
+	<li>Added support and documentation for HG18</li>
+	<li>Updated naming of files created from running patchwork</li>
+</ul>
+-->
+
+<hr class="alt1" />
+
 <h5 style="display:inline-block;">patchworkCG v2.0 - </h5><div style="display:inline-block; width:1px;"></div>
 <h6 style="display:inline-block;">17/04/2012</h6>
 <ul>
 	<li>Improved segmentation for Allelic Imbalance</li>
-	<li>Changes to onLoad message handling.</li>
+	<li>Changes to onLoad message handling</li>
 </ul>
 
 <hr class="alt1" />

Modified: www/index.php
===================================================================
--- www/index.php	2012-06-25 14:01:50 UTC (rev 138)
+++ www/index.php	2012-06-26 12:26:45 UTC (rev 139)
@@ -95,7 +95,7 @@
 
 <!-- <div id="container"> -->
 	<div id="left">
- 		<h1 style="padding-left:20px; color:#C7C7C7;">Patchwork</h1>
+ 		<h1 style="padding-left:20px; color:#C7C7C7;"><a href="http://patchwork.r-forge.r-project.org/">Patchwork</a></h1>
  	</div>
 
 <!-- 	<div id="right"> -->

