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Posted to commits@airavata.apache.org by ma...@apache.org on 2017/09/12 15:35:33 UTC
[3/3] airavata-php-gateway git commit: updating for new peak calling
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 <ro...@osboxes>
Authored: Fri Sep 8 20:34:16 2017 +0100
Committer: root <ro...@osboxes>
Committed: Fri Sep 8 20:34:16 2017 +0100
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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
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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>
<a href="" target="_blank" id="retLinks">Download <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
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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
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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
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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
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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%">