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From machris...@apache.org
Subject [3/3] airavata-php-gateway git commit: updating for new peak calling
Date Tue, 12 Sep 2017 15:35:33 GMT
updating for new peak calling


Project: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/commit/b38e1fc1
Tree: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/tree/b38e1fc1
Diff: http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/diff/b38e1fc1

Branch: refs/heads/dreg-gateway
Commit: b38e1fc1323b2d7dcbd6fecedde6016abf003b44
Parents: e86a71d
Author: root <root@osboxes>
Authored: Fri Sep 8 20:34:16 2017 +0100
Committer: root <root@osboxes>
Committed: Fri Sep 8 20:34:16 2017 +0100

----------------------------------------------------------------------
 app/libraries/ExperimentUtilities.php          |   4 +-
 app/libraries/FileTransfer.php                 |  83 ++++++++++----------
 app/views/partials/experiment-info.blade.php   |   8 +-
 public/themes/dreg/assets/img/dreg.gbview.png  | Bin 110820 -> 44054 bytes
 public/themes/dreg/partials/doc.blade.php      |  20 ++---
 public/themes/dreg/partials/faq.blade.php      |   2 +
 public/themes/dreg/partials/template.blade.php |   3 +
 7 files changed, 58 insertions(+), 62 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/b38e1fc1/app/libraries/ExperimentUtilities.php
----------------------------------------------------------------------
diff --git a/app/libraries/ExperimentUtilities.php b/app/libraries/ExperimentUtilities.php
index 4d46932..ade7873 100755
--- a/app/libraries/ExperimentUtilities.php
+++ b/app/libraries/ExperimentUtilities.php
@@ -897,7 +897,7 @@ class ExperimentUtilities
                              <div class="file-upload-container">
                                 <input class="file-input" type="file" name="file-' . $input->sanitizedFormName
.'" id="file-' . $input->sanitizedFormName . '" ' . $required . '>
                                 <input type="hidden" class="urlpath" id="' . $input->sanitizedFormName
. '" name="' . $input->sanitizedFormName . '" "'. $required .'" value="">
-                                <div class="file-upload-max-size">Max Upload Size:
' . $allowedFileSize .'M</div>
+                                <!--<div class="file-upload-max-size">Max Upload
Size: ' . $allowedFileSize .'M</div>-->
                              </div>
                             <p class="help-block">' . $input->userFriendlyDescription
. '</p>
                             <div class="progress fadeIn animated" style="display:none">
@@ -921,7 +921,7 @@ class ExperimentUtilities
                 <label>Optional Input Files</label>
                 <div class="file-upload-container">
                     <input type="file" class="file-input" id="optInputFiles" name="optInputFiles[]"
multiple onchange="javascript:updateList()" >
-                    <div class="file-upload-max-size">Max Upload Size: ' . $allowedFileSize
.'M</div>
+                    <!--<div class="file-upload-max-size">Max Upload Size: ' . $allowedFileSize
.'M</div>-->
                 </div>
                 <div id="optFileList"></div>
             </div>';

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/b38e1fc1/app/libraries/FileTransfer.php
----------------------------------------------------------------------
diff --git a/app/libraries/FileTransfer.php b/app/libraries/FileTransfer.php
index b439b67..c59b280 100644
--- a/app/libraries/FileTransfer.php
+++ b/app/libraries/FileTransfer.php
@@ -50,64 +50,65 @@ class FileTransfer {
             mode: "show",
             },'. "\n" ;
 
-        #$content = $content . '{
-        #    type:"bedgraph",
-        #    url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode($folder_path
. '/out.dREG.pred.gz').'",
-        #    name: "dREG informative pos.:",
-        #    mode: "show",
-        #    colorpositive:"#B30086",
-        #    colornegative:"#0000e5",
-        #    backgroundcolor:"#ffffe5",
-        #    height:40,
-        #    #fixedscale:{min:0, max:1},
-        #},'. "\n";
-
         $content = $content . '{
             type:"bedgraph",
-            url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path
. '/out.dREG.peak.gz').'",
-            name: "dREG Peak Calling:",
+            url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path
. '/out.dREG.infp.bed.gz').'",
+            name: "dREG Info. Sites:",
             mode: "show",
             colorpositive:"#B30086",
             colornegative:"#0000e5",
             backgroundcolor:"#ffffe5",
             height:40,
-            fixedscale:{min:0, max:0.6},
-        },'. "\n";
-
-        $content = $content . '{
-            type:"bigwig",
-            url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path
. '/out.dREG.HD.imputedDnase.bw').'",
-            name: "imputed DNase-I signal:",
-            #fixedscale:{min:0,max:20},
-            summarymethod:"max",
-            colorpositive:"#00B306",
-            backgroundcolor:"#ffffe5",
-            height:100,
-            mode: "show",
-        },'. "\n";
-
-        $content = $content . '{
-            type:"bedgraph",
-            url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path
. '/out.dREG.HD.relaxed.bed.gz').'",
-            name: "dREG.HD relaxed peaks:",
-            mode: "show",
-            colorpositive:"#0000e5/#B30086",
-            backgroundcolor:"#ffffe5",
-            height:40,
             fixedscale:{min:0, max:1},
         },'. "\n";
 
         $content = $content . '{
             type:"bedgraph",
-            url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path
. '/out.dREG.HD.stringent.bed.gz').'",
-            name: "dREG.HD stringent peaks:",
+            url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path
. '/out.dREG.peak.score.bed.gz').'",
+            name: "dREG Peak Calling:",
             mode: "show",
-            colorpositive:"#0000e5/#B30086",
+            colorpositive:"#B30086",
+            colornegative:"#0000e5",
             backgroundcolor:"#ffffe5",
             height:40,
-            fixedscale:{min:0, max:1},
+            fixedscale:{min:0.2, max:1.0},
         },'. "\n";
 
+
+        #$content = $content . '{
+        #    type:"bigwig",
+        #    url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path
. '/out.dREG.HD.imputedDnase.bw').'",
+        #    name: "imputed DNase-I signal:",
+        #    #fixedscale:{min:0,max:20},
+        #    summarymethod:"max",
+        #    colorpositive:"#00B306",
+        #    backgroundcolor:"#ffffe5",
+        #    height:100,
+        #    mode: "show",
+        #},'. "\n";
+
+        #$content = $content . '{
+        #    type:"bedgraph",
+        #    url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path
. '/out.dREG.HD.relaxed.bed.gz').'",
+        #    name: "dREG.HD relaxed peaks:",
+        #    mode: "show",
+        #    colorpositive:"#0000e5/#B30086",
+        #    backgroundcolor:"#ffffe5",
+        #    height:40,
+        #    fixedscale:{min:0, max:1},
+        #},'. "\n";
+
+        #$content = $content . '{
+        #    type:"bedgraph",
+        #    url:"'.$protocol.'://'. $_SERVER['HTTP_HOST'] .'/gbfile/'.RBase64::encode( $folder_path
. '/out.dREG.HD.stringent.bed.gz').'",
+        #    name: "dREG.HD stringent peaks:",
+        #    mode: "show",
+        #    colorpositive:"#0000e5/#B30086",
+        #    backgroundcolor:"#ffffe5",
+        #    height:40,
+        #    fixedscale:{min:0, max:1},
+        #},'. "\n";
+
         $content = $content . ']';
         return Response::make($content, 200)
                   ->header('Content-Type', 'text/plain');

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/b38e1fc1/app/views/partials/experiment-info.blade.php
----------------------------------------------------------------------
diff --git a/app/views/partials/experiment-info.blade.php b/app/views/partials/experiment-info.blade.php
index fdf6e55..4f43aee 100755
--- a/app/views/partials/experiment-info.blade.php
+++ b/app/views/partials/experiment-info.blade.php
@@ -207,11 +207,9 @@
 @if(file_exists($dataRoot . '/' . $expDataDir. '/ARCHIVE/out.dREG.tar.gz') )
                     <option value="out.dREG.tar.gz">Full results</option>  
 @endif
-                    <option value="out.dREG.HD.stringent.bed.gz">Stringent Bed regions</option>
-                    <option value="out.dREG.HD.relaxed.bed.gz">Relaxed Bed regions</option>

-                    <option value="out.dREG.HD.imputedDnase.bw">Imputed DNase-I</option>
-                    <option value="out.dREG.peak.gz">dREG regions</option>  
      
-                    <option value="out.dREG.pred.gz">dREG scores</option>  
+                    <option value="out.dREG.infp.bed.gz">dREG informative sites</option>
+                    <option value="out.dREG.peak.full.bed.gz">dREG peaks </option>

+                    <option value="out.dREG.peak.score.bed.gz">dREG peak(only with
scores)</option>
                 </select> &nbsp;&nbsp;&nbsp;&nbsp;
 
    	       <a href="" target="_blank" id="retLinks">Download&nbsp;<span class="glyphicon
glyphicon-save"  style="width:20px"></span></a>

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/b38e1fc1/public/themes/dreg/assets/img/dreg.gbview.png
----------------------------------------------------------------------
diff --git a/public/themes/dreg/assets/img/dreg.gbview.png b/public/themes/dreg/assets/img/dreg.gbview.png
index 136c5ae..2a8e711 100644
Binary files a/public/themes/dreg/assets/img/dreg.gbview.png and b/public/themes/dreg/assets/img/dreg.gbview.png
differ

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/b38e1fc1/public/themes/dreg/partials/doc.blade.php
----------------------------------------------------------------------
diff --git a/public/themes/dreg/partials/doc.blade.php b/public/themes/dreg/partials/doc.blade.php
index 5b5fb36..ae77e01 100755
--- a/public/themes/dreg/partials/doc.blade.php
+++ b/public/themes/dreg/partials/doc.blade.php
@@ -115,26 +115,18 @@ dREG run generates a compressed file including the dREG and dREG.HD
results as f
                     <th>Description</th>
               </tr>
               <tr>
-                    <td>out.dREG.pred.gz</td>
+                    <td>out.dREG.infp.bed.gz</td>
                     <td>Informative positions with the scores predicted by the dREG
model</td>
               </tr>
               <tr>
-                    <td>out.dREG.peak.gz</td>
-                    <td>dREG peaks called using the threshold 0.8 </td>
+                    <td>out.dREG.peak.full.bed.gz</td>
+                    <td>dREG peaks calling results with score, probability and center
position information. </td>
               </tr>
               <tr>
-                    <td>out.dREG.HD.imputedDnase.bw</td>
-                    <td>The imputed DNase-I signal called by dREG.HD.</td>
+                    <td>out.dREG.peak.score.bed.gz</td>
+                    <td>dREG peaks calling results only with score.</td>
               </tr>
-              <tr>
-                    <td>out.dREG.HD.relaxed.bed</td>
-                    <td>dREG.HD peaks called under relaxed condition (FDR=16%)</td>
-              </tr>
-              <tr>
-                    <td>out.dREG.HD.stringent.bed</td>
-                    <td>dREG.HD peaks called under stringent condition (FDR=10%)</td>
-              </tr>
-        </table>
+            </table>
 
         </div>
       </div>

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/b38e1fc1/public/themes/dreg/partials/faq.blade.php
----------------------------------------------------------------------
diff --git a/public/themes/dreg/partials/faq.blade.php b/public/themes/dreg/partials/faq.blade.php
index 09e508a..e92be49 100755
--- a/public/themes/dreg/partials/faq.blade.php
+++ b/public/themes/dreg/partials/faq.blade.php
@@ -22,6 +22,8 @@
 Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., ...
& Siepel, A. (2015). Identification of active transcriptional regulatory elements from
GRO-seq data. Nature methods, 12(5), 433-438. </A></p> 
 <p><b>Q: Do I have to create account before using this service?</b></p>
 <p>A: Yes, this system is supported by an NSF funded supercomputing resource known
as <A title="XSEDE" href="http://www.xsede.org">XSEDE</A>, who regularly needs
to report bulk usage statistics to NSF.  Nevertheless, data that you provide are completely
safe.</p>
+<p><b>Q: How do I know the status of the computational nodes? </b></p>
+<p>A: Since we can't update this web site very often, the gateway status is updated
<A target=_blank href="https://github.com/Danko-Lab/dREG/blob/master/gateway-update.md">here</A>
on the dREG page based on the notifications of the XSEDE community. </p>
 <p><b>Q: Who do I thank for the computing power? </b></p>
 <p>A: This web-based tool is powered by <A title="SciGaP" href="http://www.scigap.org">SciGaP</A>
and <A title="Apache Airavata"  href="http://airavata.apache.org/">Apache Airavata</A>
and the GPU servers are supported by the <A title="XSEDE" href="http://www.xsede.org">XSEDE</A>.</p>
 <p><b>Q: I have another question that is not on this FAQ.  How can I contact
you?</b></p>

http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/b38e1fc1/public/themes/dreg/partials/template.blade.php
----------------------------------------------------------------------
diff --git a/public/themes/dreg/partials/template.blade.php b/public/themes/dreg/partials/template.blade.php
index d1c5099..643ed78 100755
--- a/public/themes/dreg/partials/template.blade.php
+++ b/public/themes/dreg/partials/template.blade.php
@@ -5,6 +5,9 @@
 	<p class="text-center" style="color:#cccccc;">
 	Find the location of enhancers and promoters using PRO-seq, GRO-seq, and ChRO-seq data.<br/>
 	</p>
+	<p class="text-center" style="color:#444444;">
+The gateway status and updates are <A target=_blank href="https://github.com/Danko-Lab/dREG/blob/master/gateway-update.md"><B>here!</b></A>
+</p>
 	<hr/>
 
 	<div class="col-md-5"  style="margin-left: 5%">


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