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 @@
+
+
+
patchwork v2.3 -
-2013
+16/08/2013
- Moved Pysam out of package due to auto-install issues. Now you will have to manually install it.
See Patchwork -> Installation
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 @@
- - An aligned and sorted BAM file of tumor content
- - A BAI index of your BAM file
- - A pileup of your BAM file
- - (optional) A VCF file of your tumor pileup
- - (optional) A matched normal sample to your tumor in BAM format
- - (optional) A pileup of your normal sample BAM
+
+ - An aligned and sorted BAM file of tumor content.
A BAI index of your BAM file.
A pileup of your BAM file.
A VCF file of your tumor pileup (if applicable).
+
+ - (optional) A matched normal sample to your tumor in BAM format.
A BAI index of your normal sample BAM.
A pileup of your normal sample BAM.
A VCF file of your normal pileup (if applicable).
+
+ - (optional) A standard Reference file. (Illumina/Solexa, SOLiD or your own)
-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.
-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.
-In some cases it may be better to use the reference file and a pileup.
-
You can also run patchwork.plot() with only a reference file.
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