Merge pull request #79 from croth1/small_ui_updates

Small UI improvements

.env_template

@@ -67,3 +67,6 @@ DEFAULT_SEEDS_FOR_REFINEMENT=2
 
 # 1 will force the server to rebuild the examples
 FORCE_EXAMPLE_CREATION=0
+
+# 1 will add the .zoops_stats file to the downloadable motif zip
+ZIP_INCLUDE_ZOOPS_STATS=0

bammmotif/commands.py

@@ -140,6 +140,9 @@ def get_convert_input_command(job_pk):
     '*.bmscore',
 ]
 
+if settings.ZIP_INCLUDE_ZOOPS_STATS:
+    zip_file_globs.append('*.zoops.stats')
+
 
 def get_compress_command(job):
     job_pk = job.meta_job.pk

bammmotif/templates/home/home.html

@@ -18,7 +18,7 @@
                             </a></center>
 
                         <hr style="border: 1px solid #1f2e2e">
-			<p class="tool_description">Discover motifs enriched in your input sequence set</p>
+			<p class="tool_description"><strong>Discover motifs</strong> enriched in your input sequence set</p>
                         <!--You can either start from a pwm file, known binding sites, or let PengMotif do the work for you...</p>-->
 
                     </font>
@@ -44,7 +44,7 @@
                           </center>
 
                         <hr style="border: 1px solid #1f2e2e">
-			<p class="tool_description"> Scan your input sequence set for matches of an input or database
+			<p class="tool_description"> <strong>Scan your input sequence set</strong> for matches of an input or database
                             motif model</p>
 
                     </font>
@@ -70,7 +70,9 @@
 
                         <center><a class="btn btn-primary btn-lg workflow_button" href='/database/' role="button">Motif database</a></center>
                         <hr style="border: 1px solid #1f2e2e">
-			<p class="tool_description">Search and browse our databases with hundreds of higher-order models learnt on ChIP-seq peaks from GTRD and ReMap.</p>
+			<p class="tool_description"><strong>Search and browse our databases</strong> with hundreds of higher-order models learnt on ChIP-seq peaks from GTRD</a>.
+
+      </p>
                     </font>
                     </div>
                 </div>
@@ -101,7 +103,7 @@
 
 
                         <hr style="border: 1px solid #1f2e2e">
-                        <p class="tool_description">Search with your input model for matching entries in our database</p>
+                        <p class="tool_description"><strong>Search with your input model</strong> for matching entries in our database</p>
 
                     </font>
                     </div>

bammmotif/templates/home/links.html

@@ -6,49 +6,52 @@
   <div class="text_box">
   <h2>Getting help & reporting bugs</h2>
   <hr class="header_line" />
-  <p>If you encounter a bug or have a question that is not yet covered in the <a href="http://bammserver.readthedocs.io/en/latest" target="_blank"> documentation</a>, please open a new issue in our <a href="https://github.com/soedinglab/BaMM_webserver" target="_blank" >github repository</a> or contact us 
+  <p>If you encounter a bug or have a question that is not yet covered in the <a href="http://bammserver.readthedocs.io/en/latest" target="_blank"> documentation</a>, please open a new issue in our <a href="https://github.com/soedinglab/BaMM_webserver" target="_blank" >github repository</a> or contact us
   <!-- http://joemaller.com/js-mailer.shtml -->
   <SCRIPT TYPE="text/javascript">
-  email_adress=('bamm@mpibpc.mpg.de')	
+  email_adress=('bamm@mpibpc.mpg.de')
   document.write(
-    '<a href="mailto:' + email_adress + '">' 
+    '<a href="mailto:' + email_adress + '">'
     + 'directly'+ '</a>'
   )
 </SCRIPT>.
 
   </p>
   </div>
 
-
   <div class="text_box">
-  <h2>Getting the server source code</h2>
+  <h2>Downloading our higher-order motif databases</h2>
   <hr class="header_line" />
   <p>
-  The webserver code is open source and can be found at our <a href="https://github.com/soedinglab/BaMM_webserver" target="_blank" >github repository</a>. For more information on the licensing and how to run the server locally, please refer to the github repository's README file.
+  Our higher-order databases can be downloaded from our <a href="http://wwwuser.gwdg.de/~compbiol/bamm" target="_blank" >data server</a>.
+  We would like to express our gratidute to the <a href="http://gtrd.biouml.org/" target="_blank"> GTRD</a> team for kindly giving us early access to their upcoming ChIP-seq database releases.
   </p>
   </div>
+
+
   <div class="text_box">
-  <h2>Downloading the commandline tools</h2>
+  <h2>Getting the server source code</h2>
   <hr class="header_line" />
   <p>
-  <a href="https://github.com/soedinglab/PEnG-motif" target="_blank">PEnG-motif</a> (seeding stage) and <a href="https://github.com/soedinglab/BaMMmotif2" target="_blank"> BaMMmotif</a> (higher-order refinement) are freely available as command line tools under GPL license.
-  Please refer to the respective README to find out how to use them and how to get help.
+  The webserver code is open source and can be found at our <a href="https://github.com/soedinglab/BaMM_webserver" target="_blank" >github repository</a>.
+  For more information on the licensing and how to run the server locally, please refer to the github repository's <a href="https://github.com/soedinglab/BaMM_webserver/blob/master/README.md" target="_blank">README</a> file.
   </p>
   </div>
-
   <div class="text_box">
-  <h2>Downloading the databases</h2>
+  <h2>Downloading the commandline tools</h2>
   <hr class="header_line" />
   <p>
-  Our higher-order databases can be downloaded from our <a href="http://wwwuser.gwdg.de/~compbiol/bamm" target="_blank" >data server</a>.
+  <a href="https://github.com/soedinglab/PEnG-motif" target="_blank">PEnG-motif</a> (seeding stage) and <a href="https://github.com/soedinglab/BaMMmotif2" target="_blank"> BaMMmotif</a> (higher-order refinement) are freely available as command line tools under GPL license.
+  Please refer to the respective README to find out how to use them and how to get help.
   </p>
   </div>
-
+
+
+
 </div>
 
 
 
 
 
 {% endblock %}
-

docker-compose.yml

@@ -61,6 +61,7 @@ services:
         - MAX_SEEDS_FOR_REFINEMENT=${MAX_SEEDS_FOR_REFINEMENT} 
         - DEFAULT_SEEDS_FOR_REFINEMENT=${DEFAULT_SEEDS_FOR_REFINEMENT}
         - FORCE_EXAMPLE_CREATION=${FORCE_EXAMPLE_CREATION} 
+        - ZIP_INCLUDE_ZOOPS_STATS=${ZIP_INCLUDE_ZOOPS_STATS} 
 
   web:
     build: .

docs/source/results.rst

@@ -299,16 +299,16 @@ How long are the results available?
 ...................................
 .. _How long are the results available:
 
-Currently, the results will be kept for 4 weeks.
+We guarantee that the results will be accessible via job id for at least 3 months.
 
 What is the maximal size of input sequence file that I can upload?
 ..................................................................
 .. _maximal size of input sequence file:
 
-You can upload input sequence file with a maximal size of 40 MB.
+You can upload input sequence file with a maximal size of 50 MB.
 
-For larger sequence files, you can either use our binary tools on the Github repositories, or download this webserver
-and run it locally after changing settings in the .env file.
+For larger sequence files, you can either use our commandline tools, or run the webserver locally after adapting the ``MAX_UPLOAD_FILE_SIZE`` configuration option.
+You can find detailed instructions in the `README <https://github.com/soedinglab/BaMM_webserver/blob/master/README.md>`_ in the webserver's github repository.
 
 Citing and References
 =====================

webserver/settings.py

@@ -267,3 +267,4 @@ def get_from_env(env_variable, converter=str):
 MAX_SEEDS_FOR_REFINEMENT = get_from_env('MAX_SEEDS_FOR_REFINEMENT', converter=int)
 DEFAULT_SEEDS_FOR_REFINEMENT = get_from_env('DEFAULT_SEEDS_FOR_REFINEMENT', converter=int)
 DEFAULT_MOTIF_DB = get_from_env('DEFAULT_MOTIF_DB')
+ZIP_INCLUDE_ZOOPS_STATS = get_from_env('ZIP_INCLUDE_ZOOPS_STATS', converter=lambda x: x == "1")