From e8898da5a848d267f96f913d57cf1727dabf15cc Mon Sep 17 00:00:00 2001
From: ritamtbsilva <ritamtbsilva@gmail.com>
Date: Thu, 29 May 2025 16:48:08 +0100
Subject: [PATCH 1/3] update gitignore to not ignore application.yml

---
 .gitignore | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 7a71ed3..ab8be6a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,5 +5,4 @@
 **.bkp
 
 shinyproxy/shiny-apps
-shinyproxy/application.yml
 nginx/nginx.conf

From 48bc130e2940e61ca255ae5b98539cfc7f6e3661 Mon Sep 17 00:00:00 2001
From: ritamtbsilva <ritamtbsilva@gmail.com>
Date: Thu, 29 May 2025 16:53:21 +0100
Subject: [PATCH 2/3] update index.html with new apps

---
 nginx/location_apps.conf        |  6 +++++
 shinyproxy/templates/index.html | 46 ++++++++++++++++++++++++++-------
 2 files changed, 42 insertions(+), 10 deletions(-)

diff --git a/nginx/location_apps.conf b/nginx/location_apps.conf
index e1f473f..00ddbc2 100644
--- a/nginx/location_apps.conf
+++ b/nginx/location_apps.conf
@@ -11,3 +11,9 @@ location = /cTRAP      { return 307 /app/cTRAP; }
 location = /ctrap      { return 307 /app/cTRAP; }
 location = /voyAGEr    { return 307 /app/voyAGEr; }
 location = /voyager    { return 307 /app/voyAGEr; }
+location = /betas      { return 307 /app/betAS; }
+location = /betAS      { return 307 /app/betAS; }
+
+# redirect to external links
+location = /betas/tutorial { return 307 https://www.youtube.com/watch?v=h6Xj1eIO5OU; }
+location = /betAS/tutorial { return 307 https://www.youtube.com/watch?v=h6Xj1eIO5OU; }
diff --git a/shinyproxy/templates/index.html b/shinyproxy/templates/index.html
index 3756849..33f508d 100644
--- a/shinyproxy/templates/index.html
+++ b/shinyproxy/templates/index.html
@@ -137,7 +137,7 @@ <h1><b>
                  <!-- Examples of App Impact -->
                  <p style="color: grey; ">  
                      Impact (examples):
-                      <a href="https://www.nature.com/articles/s41467-019-14020-5#Sec11" style="margin-left:1em">Neurobiology</a>
+                      <a href="https://www.nature.com/articles/s41467-019-14020-5" style="margin-left:1em">Neurobiology</a>
                       <a href="https://www.sciencedirect.com/science/article/pii/S0092867418316246" >  Splicing Regulation</a> 
                      <a href="https://elifesciences.org/articles/47678">Cancer</a> 
                      
@@ -202,7 +202,7 @@ <h1> <b>
                  <p style="color: grey;">  
                      Impact (examples):
                      <br> 
-                     <a href="https://pubmed.ncbi.nlm.nih.gov/30856170/">Cancer</a> 
+                     <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006832">Cancer</a> 
                  
                 </p>
             </div>
@@ -220,7 +220,9 @@ <h1> <b>
 
                 <!-- App Resources -->
                  <p> 
-                    <a href="assets/tutorial_voyAGEr.pdf">Tutorial</a>  
+                    <a href="https://doi.org/10.7554/eLife.88623.3">Paper</a> 
+                    <a href="https://github.com/DiseaseTranscriptomicsLab/voyAGEr">GitHub</a> 
+                    <a href="https://diseasetranscriptomicslab.github.io/voyAGEr/www/voyAGEr-WebAppTutorial.html">Tutorial</a>  
                   </p> 
 
                 <!-- App Description -->
@@ -233,7 +235,6 @@ <h1> <b>
             </div>
          </div>
 
-
          <!-- ------ betAS ------ -->
          <div class="card reveal">
             <div>
@@ -248,8 +249,12 @@ <h1> <b>
                 </b> </h1> 
                 <!-- App Resources -->
                 <p> 
-                    <a href=""> </a>
-                     
+                	<a href="https://rnajournal.cshlp.org/content/30/4/337.abstract">Paper</a> 
+                    <a href="https://github.com/DiseaseTranscriptomicsLab/betAS/tree/dev">GitHub</a> 
+         
+                     Tutorial
+                        <a style="margin-right: 0em;" href="https://compbio.imm.medicina.ulisboa.pt/betas/tutorial">[1]</a>
+                        <a href="https://diseasetranscriptomicslab.github.io/betAS/inst/betAS_tutorial.html">[2]</a>
                  </p>
 
                 <!-- App Description -->
@@ -265,8 +270,8 @@ <h1> <b>
                      Impact (examples):
                      <br> 
                      Alternative Splicing    
-                        <a style="margin-right: 0em;" href="https://pubmed.ncbi.nlm.nih.gov/32963109/">[1]</a> 
-                        <a href="https://pubmed.ncbi.nlm.nih.gov/34039990/">[2]</a>  
+                        <a style="margin-right: 0em;" href="https://rnajournal.cshlp.org/content/26/12/1935.long">[1]</a> 
+                        <a href="https://www.nature.com/articles/s41467-021-23505-1">[2]</a>  
                  
                 </p>
 
@@ -306,10 +311,30 @@ <h1> <b>
             </div>
          </div>
 
-         <!-- ------ missing card ------ 
+         <!-- ------ markeR ------ -->
+         <div class="card ">
+            <div>
+                <h1> <b> 
+                    <!-- Icon App -->
+                    <i class="fa-solid fa-align-left"></i> 
+                    <!-- Name App --> 
+                    markeR 
+                </b></h1>  
+
+                <!-- App Resources -->
+                 <p>  
+                    <a href="https://github.com/DiseaseTranscriptomicsLab/markeR/">GitHub</a> 
+                 </p>
+
+                 <!-- App Description -->
+                 <p style="font-family: Syne Mono;"> Toolkit for Evaluating Gene Signatures as Phenotype Markers in R  </p>
+            </div>
+         </div>
+
+         <!-- ------ missing card ------ --> 
          <div class="missing_card reveal">
              
-         </div> -->
+         </div> 
 
          <!-- ------ missing card ------ 
          <div class="missing_card reveal">
@@ -551,3 +576,4 @@ <h5><b> <a href = "https://hub.docker.com/r/nunoagostinho/rsem">rsem</a>  </b></
 </body>
 
 </html>
+

From c47349868f2659427f6f4af1956cd97b200a3097 Mon Sep 17 00:00:00 2001
From: ritamtbsilva <ritamtbsilva@gmail.com>
Date: Fri, 30 May 2025 09:38:10 +0100
Subject: [PATCH 3/3] update application.yml

---
 shinyproxy/.gitignore      |   1 -
 shinyproxy/application.yml | 156 +++++++++++++++++++++++++++++++++++++
 2 files changed, 156 insertions(+), 1 deletion(-)
 create mode 100644 shinyproxy/application.yml

diff --git a/shinyproxy/.gitignore b/shinyproxy/.gitignore
index e699518..d392f0e 100644
--- a/shinyproxy/.gitignore
+++ b/shinyproxy/.gitignore
@@ -1,2 +1 @@
 *.jar
-application.yml
diff --git a/shinyproxy/application.yml b/shinyproxy/application.yml
new file mode 100644
index 0000000..a080d0b
--- /dev/null
+++ b/shinyproxy/application.yml
@@ -0,0 +1,156 @@
+# more info at https://shinyproxy.io/documentation/configuration
+
+spring.application.name: NMorais Lab - Bioinformatic Apps
+spring:
+  servlet:
+    multipart:
+      max-file-size: 200MB
+      max-request-size: 200MB
+
+proxy: 
+  title: NMorais Lab - Bioinformatic Apps
+  port: 8080
+  # bind-address: 127.0.0.1
+  hide-navbar: false
+  template-path: /opt/shinyproxy/templates
+  container-wait-time: 30000
+  container-log-path: /container-logs
+  usage-stats-url: micrometer
+
+  # app recovery enabled
+  stop-proxies-on-shutdown: false
+  recover-running-proxies: true
+
+  docker:
+    internal-networking: true
+    container-network: shiny-net
+  specs:
+  - id: psichomics
+    description: Alternative splicing quantification, visualisation and analysis
+    container-image: nunoagostinho/psichomics:1.28.1
+    container-cmd: ["R", "-e", "psichomics::psichomics(host='0.0.0.0', port=3838, shinyproxy=TRUE, cache='~/Downloads/AnnotationHub')"]
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/psichomics/data:/root/Downloads" ]
+    template-properties:
+      startup-time: 20s
+      listed: true
+  - id: voyAGEr
+    description: Analysis of age-related gene expression changes in human
+    container-image: diseasetranscriptomicslab/voyager:v2.0.2
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/voyAGEr/data:/home/app/data" ]
+    template-properties:
+      listed: true
+  - id: cTRAP
+    description: Identifying candidate causal perturbations from differential gene expression data
+    container-image: nunoagostinho/ctrap:1.14.1
+    container-network: "${proxy.docker.container-network}"
+    container-cmd: ["R", "-e", "cTRAP::cTRAP(host='0.0.0.0', port=3838, expire=30, flowerURL='http://flower:5555/flower')"]
+    container-volumes: [ "/srv/apps/cTRAP/sessions:/data" ]
+    template-properties:
+      startup-time: 15s
+      listed: true
+  - id: scStudio_MCT
+    container-image: genomeptimm/scstudio_mct:1.6
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio_MCT/datasets:/home/app/datasets" ]
+    template-properties:
+      listed: true
+  - id: scStudio
+    container-image: martabica/scstudio-home:1.2
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio/tokens:/home/app/tokens", "/srv/apps/scStudio/public_datasets:/home/app/public_datasets", "/srv/apps/scStudio/session_data:/home/app/session_data" ]
+    template-properties:
+      listed: true
+  - id: scStudio_DATA
+    container-image: martabica/scstudio-selectdata:1.1
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio/tokens:/home/app/tokens", "/srv/apps/scStudio/public_datasets:/home/app/public_datasets", "/srv/apps/scStudio/session_data:/home/app/session_data" ]
+    template-properties:
+      listed: true
+  - id: scStudio_QC
+    container-image: martabica/scstudio-qc:1.1
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio/tokens:/home/app/tokens", "/srv/apps/scStudio/public_datasets:/home/app/public_datasets", "/srv/apps/scStudio/session_data:/home/app/session_data" ]
+    template-properties:
+      listed: true
+  - id: scStudio_NORM
+    container-image: martabica/scstudio-normalization:1.1
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio/tokens:/home/app/tokens", "/srv/apps/scStudio/public_datasets:/home/app/public_datasets", "/srv/apps/scStudio/session_data:/home/app/session_data" ]
+    template-properties:
+      listed: true
+  - id: scStudio_DIMRED
+    container-image: martabica/scstudio-dimred:1.1
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio/tokens:/home/app/tokens", "/srv/apps/scStudio/public_datasets:/home/app/public_datasets", "/srv/apps/scStudio/session_data:/home/app/session_data" ]
+    template-properties:
+      listed: true
+  - id: scStudio_CLUSTER
+    container-image: martabica/scstudio-clustering:1.1
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio/tokens:/home/app/tokens", "/srv/apps/scStudio/public_datasets:/home/app/public_datasets", "/srv/apps/scStudio/session_data:/home/app/session_data" ]
+    template-properties:
+      listed: true
+  - id: scStudio_DEA
+    container-image: martabica/scstudio-dea:1.5
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio/tokens:/home/app/tokens", "/srv/apps/scStudio/public_datasets:/home/app/public_datasets", "/srv/apps/scStudio/session_data:/home/app/session_data" ]
+    template-properties:
+      listed: true
+  - id: scStudio_GSEA
+    container-image: martabica/scstudio-fea:1.3
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio/tokens:/home/app/tokens", "/srv/apps/scStudio/public_datasets:/home/app/public_datasets", "/srv/apps/scStudio/session_data:/home/app/session_data" ]
+    template-properties:
+      listed: true
+  - id: scStudio_FEATPLOT
+    container-image: martabica/scstudio-featureplots:1.1
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio/tokens:/home/app/tokens", "/srv/apps/scStudio/public_datasets:/home/app/public_datasets", "/srv/apps/scStudio/session_data:/home/app/session_data" ]
+    template-properties:
+      listed: true
+  - id: scStudio_SETTINGS
+    container-image: martabica/scstudio-settings:1.1
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio/tokens:/home/app/tokens", "/srv/apps/scStudio/public_datasets:/home/app/public_datasets", "/srv/apps/scStudio/session_data:/home/app/session_data" ]
+    template-properties:
+      listed: true
+  - id: scStudio_REPORT
+    container-image: martabica/scstudio-report:1.1
+    container-network: "${proxy.docker.container-network}"
+    container-volumes: [ "/srv/apps/scStudio/tokens:/home/app/tokens", "/srv/apps/scStudio/public_datasets:/home/app/public_datasets", "/srv/apps/scStudio/session_data:/home/app/session_data" ]
+    template-properties:
+      listed: true      
+  - id: splicingSenescenceDashboard
+    display-name: Splicing in senescence
+    description: Splicing in senescence (dashboard)
+    container-image: marianaferreira/splicing-senescence-dasboard
+    container-network: "${proxy.docker.container-network}"
+    template-properties:
+      startup-time: 20s
+      listed: false
+  - id: betAS
+    description: Intuitive differential alternative splicing analysis
+    container-image: marianaferreira/betas:v1.2.1
+    container-cmd: ["R", "-e", "betAS::betASapp(host='0.0.0.0', port=3838)"]
+    container-network: "${proxy.docker.container-network}"
+    template-properties:
+      startup-time: 5s
+      listed: true
+
+logging:
+  file:
+    name: /log/shinyproxy.log
+
+management:
+  metrics:
+    export:
+      prometheus:
+        enabled: true
+
+server:
+  secure-cookies: true
+  forward-headers-strategy: native
+  frame-options: sameorigin
+