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Posted to commits@airavata.apache.org by ma...@apache.org on 2019/06/02 17:22:52 UTC
[airavata-php-gateway] 05/14: changing document
This is an automated email from the ASF dual-hosted git repository.
machristie pushed a commit to branch dreg-gateway
in repository https://gitbox.apache.org/repos/asf/airavata-php-gateway.git
commit 3355e295345c31027ad70910afd33a1c7a94af52
Author: root <ro...@dreg-gateway-instance1.jetstreamlocal>
AuthorDate: Mon Jun 25 16:46:28 2018 +0000
changing document
---
public/themes/dreg/assets/img/dreg.exp.summary.png | Bin 52211 -> 31052 bytes
public/themes/dreg/partials/doc.blade.php | 20 ++++++++++++--------
public/themes/dreg/partials/faq.blade.php | 4 ++++
3 files changed, 16 insertions(+), 8 deletions(-)
diff --git a/public/themes/dreg/assets/img/dreg.exp.summary.png b/public/themes/dreg/assets/img/dreg.exp.summary.png
index 183f5c3..28604fe 100755
Binary files a/public/themes/dreg/assets/img/dreg.exp.summary.png and b/public/themes/dreg/assets/img/dreg.exp.summary.png differ
diff --git a/public/themes/dreg/partials/doc.blade.php b/public/themes/dreg/partials/doc.blade.php
index 74c54ce..9859deb 100755
--- a/public/themes/dreg/partials/doc.blade.php
+++ b/public/themes/dreg/partials/doc.blade.php
@@ -54,14 +54,14 @@ The user can check the status of their 'experiment' by clicking the menu 'Saved
<p class="description" style="padding:16px">
7) <b>Check the results</b><br>
-Once a job is completed, the user can click <B>'Download All Results'</B> link in the experiment summary page to download a compressed file described in the <a href="#output" role="tab" data-toggle="tab">'output'</A> sheet in this page, or the user can download any single file from the drop-down list.
+Once a job is completed, the user can select 'Full results' in the drop-down list and then click <B>'Download'</B> link in the experiment summary page to download a compressed file described in the <a href="#output" role="tab" data-toggle="tab">'output'</A> sheet in this page, or the user can download any single file from the drop-down list. The downloaded file with the 'tar.gz' extension can be decompressed by the 'tar' command, the file with the 'gz' extension can be decompressed by th [...]
</p>
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment summary" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.exp.summary.png"></img></div>
<p class="description" style="padding:16px">
8) <b>Switch to Genome Browser</b><br>
-The convenient tool ptovided by the gateway is the user can check the results in the Genome Browser by clicking <b>'Genome Browser'</B> link. </p>
+The convenient tool ptovided by the gateway is the user can check the results in the Genome Browser by clicking <b>'Switch to genome browser'</B> link. </p>
<div style=" display: flex;justify-content: center"><img style="align-self: center;width:70%" alt="dREG experiment summary" src="{{ URL::to('/') }}/themes/{{Session::get('theme')}}/assets/img/dreg.gbview.png"></img></div>
@@ -154,17 +154,21 @@ dREG run generates a compressed file including the dREG and dREG.HD results as f
<th>Description</th>
</tr>
<tr>
- <td>out.dREG.infp.bed.gz</td>
- <td>Informative positions with the scores predicted by the dREG model</td>
+ <td>$PREFIX.dREG.infp.bed.gz</td>
+ <td>Informative positions with the scores predicted by the dREG model. <BR>Decompress it with 'gunzip' in Linux.</td>
</tr>
<tr>
- <td>out.dREG.peak.full.bed.gz</td>
- <td>dREG peaks calling results with score, probability and center position information. </td>
+ <td>$PREFIX.dREG.peak.full.bed.gz</td>
+ <td>dREG peaks calling results with score, probability and center position information. <BR>Decompress it with 'gunzip' in Linux.</td>
</tr>
<tr>
- <td>out.dREG.peak.score.bed.gz</td>
- <td>dREG peaks calling results only with score.</td>
+ <td>$PREFIX.dREG.peak.score.bed.gz</td>
+ <td>dREG peaks calling results only with score. <BR>Decompress it with 'gunzip' in Linux.</td>
</tr>
+ <tr>
+ <td>$PREFIX.tar.gz</td>
+ <td>Including above 3 files, can be decompressed by 'tar -xvzf' in Linux.</td>
+ </tr>
</table>
</div>
diff --git a/public/themes/dreg/partials/faq.blade.php b/public/themes/dreg/partials/faq.blade.php
index ea4b3a9..fd0bb4e 100755
--- a/public/themes/dreg/partials/faq.blade.php
+++ b/public/themes/dreg/partials/faq.blade.php
@@ -5,6 +5,8 @@
<div class="post-entry">
<p>dREG Gateway is online service that supports Web-based science through the execution of online computational experiments and the management of data. The items below are trying to answer qustions from the users</p>
+<p><b>Q: Which browser works well with the dREG gateway?</b></p>
+<p>A: We have tested in the Firefox and Google Chrome so far. In IE (version 10 or 11) or Safari, WashU geneome browser doesn't work.</p>
<p><b>Q: How should I prepare bigWig files for use with the dREG gateway?</b></p>
<p>A: Information about how to prepare files can be found <A href="https://github.com/Danko-Lab/tutorials/blob/master/PRO-seq.md#read-mapping"> here </A>.</p>
@@ -20,6 +22,8 @@
<p>A: Models are currently available only in mammalian organisms. The length and density of genes, which vary considerably between highly divergent species, affects the way that a transcribed promoter or enhancer looks. For this reason, models can only be used in species . We are working to create models in widely-used model organisms, including drosophila and C. elegans. </p>
<p><b>Q: How deeply do I need to sequence PRO-seq libraries?</b></p>
<p>A: Sensitivity is reasonable at ~40 million mapped reads and saturates at ~100 million mapped reads. See our analysis here: <A href="http://www.nature.com/nmeth/journal/v12/n5/fig_tab/nmeth.3329_SF3.html">supplementary figure 3 in dREG paper</A>.</p>
+<p><b>Q: How long do my data and results keep in the dREG gateway?</b></p>
+<p>A: One month.</p>
<p><b>Q: How to I cite the dREG gateway?</b></p>
<p>A: Please cite one of our papers if you use dREG results in your publication:<BR/>
<A target="_blank" href="http://www.nature.com/nmeth/journal/v12/n5/full/nmeth.3329.html">