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molgenis · Jul 26, 2024 · 5464c91 · 5464c91
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diff --git a/.jenkins/build-pod.yaml b/.jenkins/build-pod.yaml
@@ -0,0 +1,17 @@
+apiVersion: v1
+kind: Pod
+metadata:
+  name: jenkins-agent
+spec:
+  containers:
+    - name: jekyll
+      image: molgenis/jekyll:1.1.2
+      imagePullPolicy: IfNotPresent
+      command:
+      - cat
+      tty: true
+      resources:
+        requests:
+          cpu: "1"
+          memory: "1Gi"
+  restartPolicy: Never
diff --git a/CNAME b/CNAME
@@ -0,0 +1 @@
+molgenis.org
diff --git a/MOLGENIS_Privacy_Policy.pdf b/MOLGENIS_Privacy_Policy.pdf
diff --git a/deploy/nginx/redirect.conf b/deploy/nginx/redirect.conf
@@ -11,18 +11,15 @@
 # EXPIRES:      01-01-2019
 # rewrite ^/path https://www.example.com permanent;
 
-
-
-
 # DESCRIPTION:  Download server that provides data for all research we do on GCC
 # MAINTAINER:   ops-team, data-team
 # EXPIRES:      never
-rewrite ^/downloads(.*)        https://molgenis26.gcc.rug.nl/downloads/$1 permanent;
+rewrite ^/downloads(.*)        https://download.molgeniscloud.org/downloads/$1 permanent;
 
 # DESCRIPTION:  Contains the releases for all our customer artifacts
 # MAINTAINER:   ops-team
 # EXPIRES:      never
-rewrite ^/releases              https://molgenis26.gcc.rug.nl/releases permanent;
+rewrite ^/releases              https://download.molgeniscloud.org/releases permanent;
 
 # DESCRIPTION:  This is our system genetics information page
 # MAINTAINER:   Morris Swertz
@@ -42,48 +39,48 @@ rewrite ^/jenkins               http://jenkins.dev.molgenis.org/ permanent;
 # DESCRIPTION:  ?
 # MAINTAINER:   ?
 # EXPIRES:      ?
-rewrite ^/regenotyper           https://molgenis26.gcc.rug.nl/downloads/regenotyper permanent;
+rewrite ^/regenotyper           https://download.molgeniscloud.org/downloads/regenotyper permanent;
 
 # DESCRIPTION:  The documentation of all our processes and workflows.
 #               The ticket system trac is here hosted as well.
 # MAINTAINER:   dev-team, Morris Swertz
 # EXPIRES:      never
-rewrite ^/wiki                  http://wiki.gcc.rug.nl permanent;
+rewrite ^/wiki                  http://trac.molgeniscloud.org permanent;
 
 # DESCRIPTION:  Redirect to reports at trac
 # MAINTAINER:   dev-team, Morris Swertz
 # EXPIRES:      never
-rewrite ^/report                  http://wiki.gcc.rug.nl/report permanent;
+rewrite ^/report                  http://trac.molgeniscloud.org/report permanent;
 
 # DESCRIPTION:  Tickets at trac ticket/xxxx
 # MAINTAINER:   dev-team, Morris Swertz
 # EXPIRES:      never
-rewrite ^/ticket                  http://wiki.gcc.rug.nl/ticket permanent;
+rewrite ^/ticket                  http://trac.molgeniscloud.org/ticket permanent;
 
 # DESCRIPTION:  The research documentation
 # MAINTAINER:   Morris Swertz
 # EXPIRES:      never
-rewrite ^/research              http://wiki.gcc.rug.nl/wiki/research permanent;
+rewrite ^/research              http://trac.molgeniscloud.org/wiki/research permanent;
 
 # DESCRIPTION:  xQTL documentation
 # MAINTAINER:   Joeri van der Velde?
 # EXPIRES:      never
-rewrite ^/xqtl                  http://wiki.gcc.rug.nl/wiki/xQTL permanent;
+rewrite ^/xqtl                  http://trac.molgeniscloud.org/wiki/xQTL permanent;
 
 # DESCRIPTION:  Diagnostic workflow documentation
 # MAINTAINER:   Morris Swertz
 # EXPIRES:      never
-rewrite ^/diagnostic            http://wiki.gcc.rug.nl/wiki/diagnostic permanent;
+rewrite ^/diagnostic            http://trac.molgeniscloud.org/wiki/diagnostic permanent;
 
 # DESCRIPTION:  5GPM
 # MAINTAINER:   Morris Swertz
 # EXPIRES:      never
-rewrite ^/5gpm                  http://wiki.gcc.rug.nl/wiki/5gpm permanent;
+rewrite ^/5gpm                  http://trac.molgeniscloud.org/wiki/5gpm permanent;
 
 # DESCRIPTION:  Genomics documentation
 # MAINTAINER:   Morris Swertz
 # EXPIRES:      never
-rewrite ^/genomics              http://wiki.gcc.rug.nl/wiki/genomics permanent;
+rewrite ^/genomics              http://trac.molgeniscloud.org/wiki/genomics permanent;
 
 # DESCRIPTION:  MOLGENIS server list
 # MAINTAINER:   data-team,
@@ -97,19 +94,19 @@ rewrite ^/molgenis-imputation   https://molgenis.github.io/molgenis-imputation p
 
 # DESCRIPTION:  Genomics documentation
 # MAINTAINER:   Chao Pang
-# EXPIRES:      never
-rewrite ^/connect               https://molgenis17.gcc.rug.nl permanent;
+# EXPIRES:      09-09-2021
+rewrite ^/connect               https://molgenis.org/retired_server_molgenis_connect.html permanent;
 
 # DESCRIPTION:  SORTA annotation tool
 # MAINTAINER:   Chao Pang
 # EXPIRES:      never
-rewrite ^/sorta                 https://molgenis19.gcc.rug.nl permanent;
+rewrite ^/sorta                 https://sorta.molgeniscloud.org permanent;
 
 # Deprecated?
 # DESCRIPTION:  SNP Visualization Diagnostics
-# MAINTAINER:   data-team
+# MAINTAINER:   Connor Stroomberg
 # SINCE:        01-01-2017
-rewrite ^/upd-tool              https://molgenis74.gcc.rug.nl/menu/main/apps/aaaacxzu6j3or6qwhzap6qyaae permanent;
+rewrite ^/upd-tool              https://snptool.molgeniscloud.org permanent;
 
 # DESCRIPTION:  Ase
 # MAINTAINER:   Patrick Deelen
@@ -131,26 +128,16 @@ rewrite ^/capice                 https://capice.molgeniscloud.org permanent;
 # EXPIRES:      ?
 rewrite ^/vkgl                  https://vkgl.molgeniscloud.org permanent;
 
-# DESCRIPTION:  Glia Open Access Database (GOAD)
-# MAINTAINER:   Dennis Hendriksen
-# EXPIRES:      ?
-rewrite ^/goad                  https://molgenis13.gcc.rug.nl permanent;
-
 # DESCRIPTION:  E-rare
-# MAINTAINER:   data-team
+# MAINTAINER:   Marielle v Gijn
 # EXPIRES:      ?
-rewrite ^/said                  https://molgenis77.gcc.rug.nl permanent;
+rewrite ^/said                  https://infevers.umai-montpellier.fr/web/index.php permanent;
 
 # DESCRIPTION:  Global Screening Array
 # MAINTAINER:   Joeri van der Velde
 # EXPIRES:      ?
 rewrite ^/gsa                   https://gsa.molgeniscloud.org permanent;
 
-# DESCRIPTION:  Deconvolution
-# MAINTAINER:   Niek de Klein, Mericko Yang
-# SINCE:        30-11-2018
-rewrite ^/deconvolution         https://molgenis79.gcc.rug.nl/deconvolution permanent;
-
 # DESCRIPTION:  Human Pathway database
 # MAINTAINER:   Miranda
 # EXPIRES:      12-02-2021
@@ -166,25 +153,22 @@ rewrite ^/c2cards               https://molgenis.org/retired_server_c2cards.html
 # EXPIRES:      ?
 rewrite ^/insaid               https://insaid.molgeniscloud.org permanent;
 
-
-
+# DESCRIPTION:  Biobank Universe(mausoleum)
+# MAINTAINER:   Chao Pang
+# EXPIRES:      13-09-2-21
+rewrite ^/biobankuniverse               https://molgenis.org/retired_server_biobank_universe.html permanent;
 
 # DEPRECATED?
 
 # DESCRIPTION:  1000ibd.org
 # MAINTAINER:   Floris Inham
 # EXPIRES:      ?
-rewrite ^/infevers              https://molgenis40.gcc.rug.nl permanent;
+rewrite ^/infevers              https://1000ibd.gcc.rug.nl permanent;
 
 # DESCRIPTION:  BBMRI WP2 Biobank plots
 # MAINTAINER:   data-team
 # EXPIRES:      ?
-rewrite ^/bios                  https://molgenis78.gcc.rug.nl/menu/main/apps/aaaacxuvnfmp76qwh2zcadyaae permanent;
-
-# DESCRIPTION:  Deconvolution 2
-# MAINTAINER:   Mericko Yang
-# EXPIRES:      31-12-2018
-rewrite ^/decon2                https://molgenis04.gcc.rug.nl permanent;
+rewrite ^/bios                  https://omics-explorer.gcc.rug.nl/menu/main/apps/aaaacxuvnfmp76qwh2zcadyaae permanent;
 
 # DESCRIPTION:  Variant Interpretation using Biomedical literature Evidence (VIBE)
 # MAINTAINER:   Dennis Hendriksen

diff --git a/get.md b/get.md
@@ -1,40 +1,57 @@
 ---
 title: GET MOLGENIS
-intro: MOLGENIS is open source and free to download, install and use. There are also hosting services if you don't want to install yourself.
+intro: MOLGENIS is open source and free to download, install and use. There are also hosting services if you don't want to install and maintain yourself.
 layout: blue
 ---
 
-You can freely copy and install MOLGENIS on your own machines (Licence: LGPLv3). See [Releases](https://github.com/molgenis/molgenis/releases) for overview of versions. There are also organisations who can host MOLGENIS for you and provide data management support. And programmers can take MOLGENIS code and customize it. Each option is described below:
+# Data platform
+
+MOLGENIS original product is its FAIR data platform. You can freely copy and install MOLGENIS data platform on your own machines (Licence: LGPLv3). 
+
+The actively developed MOLGENIS is codenamed 'exm2' and you can see [Releases](https://github.com/molgenis/molgenis-emx2/releases) here. It is easier to install as compared to previous version, see README at https://github.com/molgenis/molgenis-emx2. This package also includes pre-packaged the 'catalogue', FAIR genomes and beacon v2 tools.
+
+The previous generation of MOLGENIS is still in maintances and you can see [Releases](https://github.com/molgenis/molgenis/releases) for overview of versions. 
+
+There are also organisations who can host MOLGENIS for you and provide data management support. And programmers can take MOLGENIS code and customize it. Each option is described below.
+
+# Analysis tools
+
+In addition to the data platform quite a range of additional tools have emerged>
+
+*** DataSHIELD armadillo ***
+For federated analysis using the DataSHIELD protocol we have Armadillo. This can be found here https://github.com/molgenis/molgenis-service-armadillo
+
+*** Variant interpretation pipeline (VIP) ***
+For NGS DNA variant analysis we have the VIP toolbox. This can be found here https://github.com/molgenis/vip
+
+*** CAPICE ***
+CAPICE is a modern machine learning based variant pathogenicity classifiction predictor for DNA variants. See https://github.com/molgenis/capice
+
+*** NGS_DNA pipeline ***
+NGS_DNA is a NGS DNA best practice pipeline for Illumina sequencing - alignment, variant calling, annotation and QC. See https://github.com/molgenis/NGS_DNA
+
+*** Compute ***
+Compute is a simple workflow management framework for generating/submitting/monitoring Bash scripts on compute clusters managed by schedulers. eSee https://github.com/molgenis/molgenis-compute
+
+*** TRE/Sandbox for HPC ***
+For setting up trusted research environments for large genome analysis projects (such as Solve-RD) we operate HPC clusters on OpenStack, in close collaboration with University of Groningen center for information technology. See https://docs.gcc.rug.nl/
+
 
 # Hosting and support
-At least two hosting organisations provide MOLGENIS hosting as a service. E.g. for 200 euro/month UMCG hosts 1 MOLGENIS servers and for 250 euro/month 3 MOLGENIS servers. This includes basic data management support with functional application management. In addition, hosting providers can deliver support on a tailor made basis. Please contact one of the support groups below for details and costs regarding tailored support.
+Our team provide MOLGENIS hosting as a service. Please contact us for details and costs regarding tailored support:
 
-**Genomics Coordination Center**  
+**Genomics Coordination Center (GCC)**  
 University Medical Center Groningen  
 email: <molgenis-support@umcg.nl>  
-Example service agreement: [here](/attachments/MOLGENIS_DVO_annex4_20201120.pdf)  
-Acceptable Use policy: [here](/attachements/MOLGENIS_AUP.pdf)
-
-**TraIT service desk, TraIT foundation**   
-Lygature, Utrecht  
-website: <http://www.ctmm-trait.nl/service-desk/>
 
 
-# Install on Linux
+# Install on server for multiple users and data persistence
 
-To install on Linux you need
-* MOLGENIS 'WAR' file (Choose download WAR [here](https://search.maven.org/search?q=g:org.molgenis%20AND%20a:molgenis-app here))
-* Java Platform (JDK)
-* Apache Tomcat
-* PostgreSQL
-* Elasticsearch
-* Optional: OpenCPU (enables R scripting feature)
-* Optional: Python (enables Python scripting feature)
-See for details on versions used the [Manual](https://molgenis.gitbook.io/molgenis/quickstart/guide-tomcat.html).
+If our hosting solution is not suitable and you want to host your own molgenis instance in your own cloud or on your own premise. Please take a look at our [ansible galaxy repo](https://galaxy.ansible.com/molgenis) where the setup and requirements are explained.
 
-# Install using Docker (experimental)
+# Install locally for single user testing with Docker (experimental)
 
-For testing purposes we now use Docker. We have the ambition to also use it for production but then you need to configure data persistence. However feel free to use our docker as a starting point. Get [Docker Images](https://github.com/molgenis/docker)
+For local testing purposes we provide a Docker image.  Get [Docker Images](https://github.com/molgenis/docker)
 
 # For programmers
 The complete source code of MOLGENIS is open source available at [Github](http://github.com/molgenis/molgenis)

diff --git a/images/retired/biobank_universe/Figure1_overall.jpg b/images/retired/biobank_universe/Figure1_overall.jpg
diff --git a/images/retired/biobank_universe/example_1.png b/images/retired/biobank_universe/example_1.png
diff --git a/images/retired/biobank_universe/example_2.png b/images/retired/biobank_universe/example_2.png
diff --git a/images/retired/biobank_universe/example_3.png b/images/retired/biobank_universe/example_3.png
diff --git a/images/retired/molgenis_connect/example_2.png b/images/retired/molgenis_connect/example_2.png
diff --git a/images/retired/molgenis_connect/example_3.png b/images/retired/molgenis_connect/example_3.png
diff --git a/images/retired/molgenis_connect/example_4.png b/images/retired/molgenis_connect/example_4.png
diff --git a/retired_server_biobank_universe.md b/retired_server_biobank_universe.md
@@ -0,0 +1,46 @@
+---
+title: BiobankUniverse
+intro: BiobankUniverse is archived on the 22th of September 2021.
+layout: blue
+---
+
+
+# **Project is archived** - Welcome to BiobankUniverse
+
+
+## Introduction
+Welcome to BiobankUniverse. The demonstration website has been archived on the 13th of September 2021. Below for your convenience an overview of what you would have found. The features of BiobankUniverse have been merged with the MOLGENIS 'mapping service'.
+
+BiobankUniverse was a data discovery and matching system for biobanks built in ([MOLGENIS](https://github.com/molgenis/molgenis)) that could automatically tag biobank attributes (metadata) with ontology terms from Unified Medical Language System (UMLS) and based on which generate candidate attribute matches between biobanks. In addition, BiobankUniverse could calculate the overall similarities between biobanks so that users can quickly get an approximation of how close/far the biobanks are to each other. Please note that this server is shelved, for the greatest and latest features of MOLGENIS look ([here](https://www.molgenis.org)).
+
+The instruction on how to deploy it in tomcat 7 can be found ([here](http://www.molgenis.org/wiki/Molgenis-connect)). The source code is avaiable on ([GitHub](https://github.com/chaopang/molgenis/tree/feature/biobankuniverse)). 
+
+---
+
+## Discover biobanks
+
+The circle represents a biobank and the larger a biobank, the larger the circle. The line represents the distance between the biobanks, the longer the line, the less similar the connected biobanks are to each other. There are two types of universes, one is generated based on the overall similarity of the automatically tagged ontology terms, the other one is generated based on the number of candidate matches.
+
+![Example 1](images/retired/biobank_universe/example_1.png)
+
+For example, see image below. When clicked on the button 'Number of matches', typed in 'Beer' in the search box and selected 'C0004922:Beer' and then hit the 'Search' button, only the candidate matches related to 'Beer' are retrieved and universe will reduce in size. The search box was configured with typeahead function to provide ontology terms. See the image 'Example 2' below.
+
+![Example 2](images/retired/biobank_universe/example_2.png)
+
+---
+
+## Curate attribute matches
+
+We had pre-generated the candidate attribute matches between the biobanks including Finrisk2002, Finrisk2007, Lifelines, Prevend, Mitchelstown and HOP. The matches generated where pairwise so users needed to choose a leading 'target' data schema to generate the match table, in which they can curate the candidate matches. An example can be seen in 'Example 3' with the term 'hop'.
+
+![Example 3](images/retired/biobank_universe/example_3.png)
+
+---
+
+## Technical design
+
+![Technical design](images/retired/biobank_universe/Figure1_overall.jpg)
+
+---
+
+# If you want to use molgenis with new features, visit [molgenis.org](https://molgenis.org)