BIS-1034: removed illumina_ngs from installation options

app-openbis-installer/resource/installer/userInputSpec.xml

@@ -65,9 +65,6 @@
     <field type="check" variable="FLOW">
       <spec txt="Flow Cytometry" true="true" false="false"/>
     </field>
-    <field type="check" variable="ILLUMINA-NGS">
-      <spec txt="Illumina NGS (ETH BSSE Setup)" true="true" false="false"/>
-    </field>
   </panel>
   
   <panel id="UserInputPanel.MISC">

app-openbis-installer/resource/tarball/console.properties

@@ -35,9 +35,6 @@ KEY_STORE_PASSWORD = changeit
 # Password of the key
 KEY_PASSWORD = changeit
 
-# Standard technology ILLUMINA-NGS (ETH BSSE Setup) is disabled by default
-#ILLUMINA-NGS = true
-
 # Standard technology ELN-LIMS is disabled by default
 #ELN-LIMS = true
 

app-openbis-installer/source/java/ch/systemsx/cisd/openbis/installer/izpack/GlobalInstallationContext.java

@@ -43,8 +43,6 @@ public class GlobalInstallationContext
 
     public static final String BACKUP_FOLDER_VARNAME = "BACKUP_FOLDER";
 
-    public static final String TECHNOLOGY_ILLUMINA_NGS = "ILLUMINA-NGS";
-
     public static final String TECHNOLOGY_ELN_LIMS = "ELN-LIMS";
 
     public static final String TECHNOLOGY_ELN_LIMS_TEMPLATE_TYPES = "ELN-LIMS-TEMPLATE-TYPES";
@@ -56,7 +54,7 @@ public class GlobalInstallationContext
     public static final String TECHNOLOGY_SHARED_MICROSCOPY_FLOW_CYTOMETRY = "SHARED";
 
     public static final String[] TECHNOLOGIES =
-            { TECHNOLOGY_ILLUMINA_NGS, TECHNOLOGY_ELN_LIMS, TECHNOLOGY_MICROSCOPY,
+            { TECHNOLOGY_ELN_LIMS, TECHNOLOGY_MICROSCOPY,
                     TECHNOLOGY_FLOW_CYTOMETRY, TECHNOLOGY_ELN_LIMS_TEMPLATE_TYPES };
 
     /**

core-plugin-openbis/dist/tarball/installer/data/doc/getting-started-with-openBIS.html

@@ -71,74 +71,6 @@
 
   <p></p>
 
-  <h4 class="illumina-ngs">Illumina NGS (ETH BSSE Setup)</h4>
-
-  <ol>
-    <li>A flow cell with flow lanes is created reading out two XML files provided by the Illumina sequencer:
-
-      <div class="sourcecode">
-        mkdir -p ${DSS_ROOT_DIR}/create-flowcell-hiseq/120420_SN792_0109_BC0P8LACXX/;<br>
-        cp -R ${DSS_ROOT_DIR}/examples/illumina-ngs/120420_SN792_0109_BC0P8LACXX/*.xml
-        ${DSS_ROOT_DIR}/create-flowcell-hiseq/120420_SN792_0109_BC0P8LACXX;<br>
-        touch ${DSS_ROOT_DIR}/create-flowcell-hiseq/.MARKER_is_finished_120420_SN792_0109_BC0P8LACXX<br>
-      </div>
-    </li>
-
-    <li>A flow cell output from a HiSeq2000 is registered as a data set of the object 120420_SN792_0109_BC0P8LACXX.<br>
-
-      Additionally a data set is registered for each flow lane:
-
-      <div class="sourcecode">
-        rsync -a --exclude=Unaligned* ${DSS_ROOT_DIR}/examples/illumina-ngs/120420_SN792_0109_BC0P8LACXX
-        ${DSS_ROOT_DIR}/register-flowcell-hiseq;<br>
-        touch ${DSS_ROOT_DIR}/register-flowcell-hiseq/.MARKER_is_finished_120420_SN792_0109_BC0P8LACXX;<br>
-      </div>
-    </li>
-
-    <li>The sequencer is finished and we want to track this automatically. Therefore we sync the RTAComplete.txt in a
-    drop box:
-
-      <div class="sourcecode">
-        mkdir -p ${DSS_ROOT_DIR}/read-rta-timestamp/120420_SN792_0109_BC0P8LACXX/; rsync
-        ${DSS_ROOT_DIR}/examples/illumina-ngs/120420_SN792_0109_BC0P8LACXX/RTAComplete.txt
-        ${DSS_ROOT_DIR}/read-rta-timestamp/120420_SN792_0109_BC0P8LACXX/RTAComplete.txt; touch
-        ${DSS_ROOT_DIR}/read-rta-timestamp/.MARKER_is_finished_120420_SN792_0109_BC0P8LACXX
-      </div>
-    </li>
-
-    <li> For creating some objects we use the 'Object Registration'. This is available under the 'Import' menu: <br>    
-      Import -> Object Registration -> Choose object type '(multiple)' and browse to the file:
-      <div class="sourcecode">  ${DSS_ROOT_DIR}/examples/illumina-ngs/tsv-files/example_samples_with_parents.tsv</div>
-      
-      Tick 'Update existing'and press the 'Save' button. <br>
-      This created several objects which can be viewed via Browse -> Objects. You might need to select the Object Type 'all' <br>
-      and the Space 'all'. <br>
-      Note that the objects are in a parent-/child relationship indicated by the objects shown in the 'Parents' column.
-    </li>
-    
-    <br>
-    
-
-    <li>After the demultiplexing using the Illumina 'configureBclToFastq.pl' the FASTQ files are created and also some
-    statistic files are provided.<br>
-      Let's register them as well in openBIS:
-
-      <div class="sourcecode">
-        
-        mkdir ${DSS_ROOT_DIR}/register-unaligned/120420_SN792_0109_BC0P8LACXX; <br>
-        rsync -a ${DSS_ROOT_DIR}/examples/illumina-ngs/120420_SN792_0109_BC0P8LACXX/Unaligned* ${DSS_ROOT_DIR}/register-unaligned/120420_SN792_0109_BC0P8LACXX;<br>
-        touch ${DSS_ROOT_DIR}/register-unaligned/.MARKER_is_finished_120420_SN792_0109_BC0P8LACXX;
-      </div>
-      <br>
-      The demultiplexed FASTQ files are a data set of the objects BSSE-QGF-LIBRARY-1 and BSSE-QGF-LIBRARY-2. Note that lane 1 and two <br>
-      contained both objects which results in two FASTQ data sets for each object.
-      
-    </li>
-  </ol><br>
-  A short description of all drop boxes is also provided here: <a href=
-  "https://wiki-bsse.ethz.ch/display/openBISDoc/openBIS+for+Illumina+NGS" target="_blank">openBIS for Illumina
-  NGS<a><br>
-
  <h4 class="eln-lims">ELN-LIMS</h4>
 
   <p>Here are the steps to create your first experimental step and register an image file as preview into the ELN-LIMS interface.</p>