From 2492881c8c83a0442bb420e08d9c9f60aaaf4db6 Mon Sep 17 00:00:00 2001
From: alaskowski <alaskowski@ethz.ch>
Date: Wed, 17 Apr 2024 16:21:44 +0200
Subject: [PATCH] BIS-1034: removed illumina_ngs from installation options
---
.../resource/installer/userInputSpec.xml | 3 -
.../resource/tarball/console.properties | 3 -
.../izpack/GlobalInstallationContext.java | 4 +-
.../doc/getting-started-with-openBIS.html | 68 -------------------
4 files changed, 1 insertion(+), 77 deletions(-)
diff --git a/app-openbis-installer/resource/installer/userInputSpec.xml b/app-openbis-installer/resource/installer/userInputSpec.xml
index ccd5cfeee48..8b5cb907637 100644
--- a/app-openbis-installer/resource/installer/userInputSpec.xml
+++ b/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">
diff --git a/app-openbis-installer/resource/tarball/console.properties b/app-openbis-installer/resource/tarball/console.properties
index 1376d869be9..cce8ca67137 100644
--- a/app-openbis-installer/resource/tarball/console.properties
+++ b/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
diff --git a/app-openbis-installer/source/java/ch/systemsx/cisd/openbis/installer/izpack/GlobalInstallationContext.java b/app-openbis-installer/source/java/ch/systemsx/cisd/openbis/installer/izpack/GlobalInstallationContext.java
index 67715f30071..af33ae53a1f 100644
--- a/app-openbis-installer/source/java/ch/systemsx/cisd/openbis/installer/izpack/GlobalInstallationContext.java
+++ b/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 };
/**
diff --git a/core-plugin-openbis/dist/tarball/installer/data/doc/getting-started-with-openBIS.html b/core-plugin-openbis/dist/tarball/installer/data/doc/getting-started-with-openBIS.html
index 087d6e1a246..f130820139d 100644
--- a/core-plugin-openbis/dist/tarball/installer/data/doc/getting-started-with-openBIS.html
+++ b/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>
--
GitLab