[hg] galaxy 3203: Smart converter for SOLiD, which takes care of...

5 Jan 2010

details:   http://www.bx.psu.edu/hg/galaxy/rev/b142b116024c
changeset: 3203:b142b116024c
user:      Anton Nekrutenko <anton@bx.psu.edu>
date:      Tue Jan 05 14:33:39 2010 -0500
description:
Smart converter for SOLiD, which takes care of F3-R3 pairing problem. Requires python2.5

diffstat:

 static/welcome.html                       |    95 +-
 test-data/f.fastq                         |  1996 +++++++++++++++++++++++++++++
 test-data/fr.csf                          |  1001 ++++++++++++++
 test-data/fr.qual                         |  1001 ++++++++++++++
 test-data/fr_file1.fastq                  |  1988 ++++++++++++++++++++++++++++
 test-data/fr_file2.fastq                  |  1988 ++++++++++++++++++++++++++++
 test-data/rr.csf                          |  1001 ++++++++++++++
 test-data/rr.qual                         |  1001 ++++++++++++++
 tool_conf.xml.sample                      |     2 +-
 tools/fastx_toolkit/fastq_to_fasta.xml    |     2 +-
 tools/fastx_toolkit/fastx_collapser.xml   |     2 +-
 tools/next_gen_conversion/solid2fastq.py  |   210 +++
 tools/next_gen_conversion/solid2fastq.xml |   159 ++
 13 files changed, 10408 insertions(+), 38 deletions(-)

diffs (truncated from 10545 to 3000 lines):

diff -r 71928a8f9bf9 -r b142b116024c static/welcome.html

--- a/static/welcome.html	Tue Jan 05 10:31:32 2010 -0500
+++ b/static/welcome.html	Tue Jan 05 14:33:39 2010 -0500
@@ -6,15 +6,26 @@
 <meta name="generator" content="Docutils 0.3.9: http://docutils.sourceforge.net/" />
 <link rel="stylesheet" href="style/base.css" type="text/css" />
 <style type="text/css">
+
       .quickie {
 	    text-align: center;
 	    background: black;
 	    margin: 10px;
       }
+
       .current-quickie {
-	    width: 100%;
-	    background: black;
+	    width: 300px;
+	    background: white;
+	    margin: auto;
       }
+
+      .current-quickie img { 
+        padding: 15px; 
+        border: 1px solid #ccc; 
+        margin: auto; 
+        background-color: white; 
+       }
+      
       .previous {
 	    width: 100%;
 	    overflow: auto;
@@ -30,42 +41,35 @@
 	    margin-left: auto;
 	    margin-right: auto;
       }
+
 </style>
+<script type="text/javascript" src="http://galaxy.psu.edu/welcome_img/jquery.min.js"></script>
+<script type="text/javascript" src="http://galaxy.psu.edu/welcome_img/jquery.cycle.all.2.72.js"></script>
+<script type="text/javascript">
+
+$(document).ready(function() {
+    $('.current-quickie').cycle({
+		fx: 'fade', 
+		pause: 1,
+		speed: 100
+	});
+});
+</script>
 </head>
+<body>
+<div class="document">
+<h3 align="center">Galaxy in 2010...</h3>
+<div align="center" class="current-quickie">
+		<img src="http://galaxy.psu.edu/welcome_img/welcome_images.001.png" width="300" height="200" />
+		<img src="http://galaxy.psu.edu/welcome_img/welcome_images.002.png" width="300" height="200" />
+		<img src="http://galaxy.psu.edu/welcome_img/welcome_images.003.png" width="300" height="200" />
+		<img src="http://galaxy.psu.edu/welcome_img/welcome_images.004.png" width="300" height="200" />
+		<img src="http://galaxy.psu.edu/welcome_img/welcome_images.005.png" width="300" height="200" />
+</div>
+<br>
+<hr>
 
-
-<body>
-
-<div class="document">  
-<div class="infomessagelarge">
-      <strong>We are hiring!</strong>
-     <hr>
-    Thanks to your support and an unprecedented level of usage, we are looking for an experienced software developer to join our team. For more information about this position, please, click <a target="_blank" href="https://www.bx.psu.edu/cgi-bin/trac.cgi/galaxy/wiki/PythonDeveloper">here</a>.
-</div>
-<br/>
-
-<div id="screencasts">
-
-<h2>Introducing Galactic Quickies</h2>
-<p>
-    Galactic quickies are <i>super-short</i> screencasts that are <i>always</i> under 5 minutes. We thought it may be a good way to spread the word about Galaxy's functionality while keeping the "annoyance factor" to the minimum. The quickies will be updated weekly.
-</p>
-
-<div class="current-quickie">
-      <table border="0" cellpadding="0" cellspacing="0" width="100%">
-        <tr>
-            <td align="center">
-                <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie5_join/flow.html',width:640,height:500,scroll:'no'})"> 
-                    <img src="images/qk/quickie5_lrg.png" border="0">
-                    <br>
-                </a>
-
-            </td>
-        </tr>
-      </table>
-</div>
-
-<h3>Previous Quickies</h3>
+<h3 align="center">Galaxy Quickies</h3>
 
 <div class="previous" id="previous">
         <table border="0" cellpadding="0" cellspacing="0" width="100%">
@@ -98,6 +102,27 @@
 	                   </div>
                     </a>
                 </td>
+                <td>
+                    <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie5_join/flow.html',width:640,height:500,scroll:'no'})">
+	                   <div class="quickie">
+                        <img src="images/qk/quickie5_small.png" border="0">
+	                   </div>
+                    </a>
+                </td>
+                <td>
+                    <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie6_share/flow.html',width:640,height:500,scroll:'no'})">
+	                   <div class="quickie">
+                        <img src="images/qk/quickie6_small.png" border="0">
+	                   </div>
+                    </a>
+                </td>
+                <td>
+                    <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie7_sr_beta/flow.html',width:640,height:500,scroll:'no'})">
+	                   <div class="quickie">
+                        <img src="images/qk/quickie7_small.png" border="0">
+	                   </div>
+                    </a>
+                </td>
             </tr>
       </table>
 </div>
diff -r 71928a8f9bf9 -r b142b116024c test-data/f.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/f.fastq	Tue Jan 05 14:33:39 2010 -0500
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diff -r 71928a8f9bf9 -r b142b116024c test-data/fr.csf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fr.csf	Tue Jan 05 14:33:39 2010 -0500
@@ -0,0 +1,1001 @@
+# Sun Oct  4 18:40:32 2009 /share/apps/corona/bin/filter_fasta.pl --output=/data/results/solid176/solid176_20090923/Somali_Wild_Ass_a/results.01/primary.20091004212559515 --name=solid176_20090923_Somali_Wild_Ass_a --tag=F3 --minlength=50 --mincalls=25 --prefix=T /data/results/solid176/solid176_20090923/Somali_Wild_Ass_a/jobs/postPrimerSetPrimary.1062/rawseq 
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Greg Von Kuster

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