Install ViennaRNA on Mac ARM64

saltstack/pillar/common/mac.sls

@@ -11,17 +11,18 @@ machine:
       hdf5: https://mac.r-project.org/bin/darwin20/arm64/hdf5-1.12.1-darwin.20-arm64.tar.xz
       java: https://download.java.net/java/GA/jdk18.0.1.1/65ae32619e2f40f3a9af3af1851d6e19/2/GPL/openjdk-18.0.1.1_macos-aarch64_bin.tar.gz
       netcdf: https://mac.r-project.org/bin/darwin20/arm64/netcdf-4.8.1-darwin.20-arm64.tar.xz
+      viennarna: https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_6_x/ViennaRNA-2.6.3.tar.gz
     intel:
       dotnet: https://download.visualstudio.microsoft.com/download/pr/2ef12357-499b-4a5b-a488-da45a5f310e6/fbe35c354bfb50934a976fc91c6d8d81/dotnet-runtime-6.0.13-osx-x64.pkg
       gsl: https://mac.r-project.org/bin/darwin17/x86_64/gsl-2.7-darwin.17-x86_64.tar.xz
       hdf5: https://mac.r-project.org/bin/darwin17/x86_64/hdf5-1.12.1-darwin.17-x86_64.tar.xz
       java: https://download.java.net/java/GA/jdk18.0.1.1/65ae32619e2f40f3a9af3af1851d6e19/2/GPL/openjdk-18.0.1.1_macos-x64_bin.tar.gz
       netcdf: https://mac.r-project.org/bin/darwin17/x86_64/netcdf-4.8.1-darwin.17-x86_64.tar.xz
+      viennarna: https://www.tbi.univie.ac.at/RNA/download/osx/macosx/ViennaRNA-2.5.0-MacOSX.dmg
     clustal_omega: http://www.clustal.org/omega/clustal-omega-1.2.3-macosx
     cmake: https://github.com/Kitware/CMake/releases/download/v3.23.0/cmake-3.23.0-macos-universal.dmg
     jags: https://cfhcable.dl.sourceforge.net/project/mcmc-jags/JAGS/4.x/Mac%20OS%20X/JAGS-4.3.1.pkg
     macfuse: https://github.com/osxfuse/osxfuse/releases/download/macfuse-4.2.4/macfuse-4.2.4.dmg
-    viennarna: https://www.tbi.univie.ac.at/RNA/download/osx/macosx/ViennaRNA-2.5.0-MacOSX.dmg
     glpk: https://mac.r-project.org/bin/darwin20/x86_64/glpk-5.0-darwin.20-x86_64.tar.xz
   downloads:                {# For BBS #}
     intel:
@@ -31,6 +32,11 @@ machine:
     openssl: https://mac.r-project.org/bin/darwin20/arm64/openssl-1.1.1t-darwin.20-arm64.tar.xz
     pkgconfig: https://mac.r-project.org/bin/darwin20/x86_64/pkgconfig-0.29.2-darwin.20-x86_64.tar.xz
     xquartz: https://github.com/XQuartz/XQuartz/releases/download/XQuartz-2.8.5/XQuartz-2.8.5.pkg
+  deployment_target: 11.0
+  sdk:
+    path: /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk
+    target: MacOSX11.3.sdk
+
 r:
   cran:
     - rgl

saltstack/salt/dependencies/viennarna/init.sls

@@ -1,32 +1,47 @@
 # Needed by BioC GeneGA
+# Mac Only
 
 {% set machine = salt["pillar.get"]("machine") %}
-{% set download = machine.dependencies.viennarna.split("/")[-1] %}
-{% set viennarna_version = download[10:-11] %}
 {%- if machine.r_path is defined %}
 {% set r_path = machine.r_path %}
 {% else %}
-{% set r_path = '' %}
+{% set r_path = "" %}
 {%- endif %}
 
-{%- if grains['os'] == 'Ubuntu' %}
-install_libgsl:
-  pkg.installed:
-    - pkgs:
-      - libgsl23
-      - libgslcblas0
-
-install_viennarna:
-  cmd.run:
-    - name: wget {{ machine.dependencies.viennarna }} && dpkg -i {{ download }} 
+{%- if grains["osarch"] == "arm64" %}
+{% set download_url = machine.dependencies.arm64.viennarna %}
+{% else %}
+{% set download_url = machine.dependencies.intel.viennarna %}
+{%- endif %}
+{% set download = download_url.split("/")[-1] %}
 
-{%- elif grains['os'] == 'MacOS' %}
 download_viennarna:
   cmd.run:
-    - name: curl -LO {{ machine.dependencies.viennarna }} 
+    - name: curl -LO {{ download_url }}
     - cwd: {{ machine.user.home }}/biocbuild/Downloads
     - runas: biocbuild
 
+{%- if grains["osarch"] == "arm64" %}
+untar_viennarna:
+  cmd.run:
+    - name: tar xvfJ {{ machine.user.home }}/biocbuild/Downloads/{{ download }}
+    - cwd: {{ machine.user.home }}/biocbuild/Downloads
+    - require:
+      - cmd: download_viennarna
+
+configure_compile_install_viennarna:
+  cmd.run:
+    - name: |
+        version=$(perl -v | grep version | awk -F'[ ,]' '{print $4 "." $7}')
+        export CPATH={{ machine.sdk.path }}/System/Library/Perl/$version/darwin-thread-multi-2level/CORE/EXTERN.h && ./configure
+        export CPATH={{ machine.sdk.path }}/System/Library/Perl/$version/darwin-thread-multi-2level/CORE/EXTERN.h make
+        export CPATH={{ machine.sdk.path }}/System/Library/Perl/$version/darwin-thread-multi-2level/CORE/EXTERN.h make install
+    - cwd: {{ machine.user.home }}/biocbuild/Downloads/{{ download[:-7] }}
+    - require:
+      - cmd: untar_viennarna
+{%- else %}
+{% set viennarna_version = download[10:-11] %}
+
 install_viennarna:
   cmd.run:
     - name: |

saltstack/salt/rlang/mac.sls

@@ -133,24 +133,24 @@ download_minimum_supported_macossdk:
 untar_macossdk:
   cmd.run:
     - name: tar -xf {{ machine.user.home }}/biocbuild/Downloads/MacOSX11.3.sdk.tar.xz
-    - cwd: /Library/Developer/CommandLineTools/SDKs 
+    - cwd: /Library/Developer/CommandLineTools/SDKs
     - group: wheel
     - require:
       - cmd: download_minimum_supported_macossdk
 
 symlink_minor_to_major_version:
   file.symlink:
-    - name: /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk
-    - target: MacOSX11.3.sdk
-    - cwd: /Library/Developer/CommandLineTools/SDKs 
+    - name: {{ machine.sdk.path }}
+    - target: {{ machine.sdk.target }}
+    - cwd: /Library/Developer/CommandLineTools/SDKs
     - group: wheel 
     - require:
       - cmd: untar_macossdk
 
 fix_gfortran_sdk_symlink:
   file.symlink:
     - name: /opt/gfortrant/SDK 
-    - target: /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk
+    - target: {{ machine.sdk.path }}
     - cwd: /opt/gfortran 
     - group: admin
     - require:
@@ -160,7 +160,7 @@ export_minimum_build_in_profile:
   file.append:
     - name: /etc/profile
     - text: |
-        export SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk
-        export MACOSX_DEPLOYMENT_TARGET=11.0
+        export SDKROOT={{ machine.sdk.path }}
+        export MACOSX_DEPLOYMENT_TARGET={{ machine.deployment_target }}
     - require:
       - file: fix_gfortran_sdk_symlink