Bump packages and update to .NET 8.0

Author: Maozi Chen

slim/Dockerfile

@@ -2,17 +2,15 @@ FROM python:3-slim
 
 WORKDIR /root
 
-# Install .net 6.0 runtime
+# Install .NET 8.0 runtime
 RUN file=packages-microsoft-prod.deb; \
     apt update && \
     apt install -y wget && \
-    wget -q https://packages.microsoft.com/config/debian/11/$file -O $file && \
+    wget -q https://packages.microsoft.com/config/debian/12/$file -O $file && \
     dpkg -i $file && \
     rm -f $file && \
     apt update && \
-    apt install -y apt-transport-https && \
-    apt update && \
-    apt install -y dotnet-runtime-6.0
+    apt install -y dotnet-runtime-8.0
 
 # Install PROPKA
 RUN pip install propka
@@ -22,7 +20,7 @@ RUN apt install -y openbabel
 
 # Install Vega CLI
 # Delete libssl.so and libcrypto.so because the system ships with newer version
-RUN file=Vega_3.2.1.33_Linux_x86-x64-ARM.tar.gz; \
+RUN file=Vega_3.2.3.28_Linux_x86-x64-ARM.tar.gz; \
     wget -q https://www.ddl.unimi.it/vega/packages/$file && \
     tar -zxf $file -C / && \
     chmod -R 755 /Vega/Bin/* && \
@@ -35,7 +33,7 @@ ENV PATH=$VEGADIR/Bin/Linux_x64:$PATH
 # Install chimera
 # Please read the official licensing document before installing:
 # https://www.cgl.ucsf.edu/chimera/docs/licensing.html
-RUN file=chimera-1.16-linux_x86_64.bin; \
+RUN file=chimera-1.17.3-linux_x86_64.bin; \
     wget -q https://www.cgl.ucsf.edu$(wget -q -O - --post-data "file=linux_x86_64%2F$file&choice=Accept" https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py | awk -v 'RS=http-equiv="[rR]efresh" *content="[0-9 ;]*[uU][rR][lL]=' -F '"' '/^\//{print $1;exit}') -O $file && \
     chmod +x $file && \
     echo /chimera | ./$file && \
@@ -47,10 +45,10 @@ ENV PATH=/chimera/bin:$PATH
 # Install MCCS toolchain - jdock, mccsx, gpcrn, pdbm, pdbget, pdbqtf, pdbrn
 RUN cd /usr/local/bin && \
     wget -q https://github.com/stcmz/jdock/releases/download/v2.2.3c/jdock_linux_x64 -O jdock && \
-    wget -q https://github.com/stcmz/mccsx/releases/download/v1.4.2/mccsx_linux_x64 -O mccsx && \
+    wget -q https://github.com/stcmz/mccsx/releases/download/v1.5.1/mccsx_linux_x64 -O mccsx && \
     wget -q https://github.com/stcmz/gpcrn/releases/download/v1.0.8/gpcrn_linux_x64 -O gpcrn && \
     wget -q https://github.com/stcmz/pdbm/releases/download/v1.1.0/pdbm_linux_x64 -O pdbm && \
-    wget -q https://github.com/stcmz/pdbget/releases/download/v1.0.3/pdbget_linux_x64 -O pdbget && \
+    wget -q https://github.com/stcmz/pdbget/releases/download/v1.2.4/pdbget_linux_x64 -O pdbget && \
     wget -q https://github.com/stcmz/pdbqtf/releases/download/v1.1/pdbqtf_linux_x64 -O pdbqtf && \
     wget -q https://github.com/stcmz/pdbrn/releases/download/v1.0.1/pdbrn_linux_x64 -O pdbrn && \
     chmod +x jdock mccsx gpcrn pdbm pdbget pdbqtf pdbrn && \