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> <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 ---------------------------------------------------------------------- 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%">
