Add dependency quarto (Bioconductor#132)

jwokaty · Nov 14, 2023 · 17d6079 · 17d6079
1 parent 61b0b0b
commit 17d6079
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diff --git a/saltstack/pillar/common/linux.sls b/saltstack/pillar/common/linux.sls
@@ -5,4 +5,5 @@ build:
 machine:
   dependencies:
     dotnet: https://packages.microsoft.com/config/ubuntu/22.04/packages-microsoft-prod.deb
+    quarto: https://github.com/quarto-dev/quarto-cli/releases/download/v1.3.450/quarto-1.3.450-linux-amd64.deb
     viennarna: https://www.tbi.univie.ac.at/RNA/download/ubuntu/ubuntu_20_04/viennarna_2.4.17-1_amd64.deb
diff --git a/saltstack/pillar/common/mac.sls b/saltstack/pillar/common/mac.sls
@@ -21,6 +21,7 @@ machine:
     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-4.5.0/macfuse-4.5.0.dmg
+    quarto: https://github.com/quarto-dev/quarto-cli/releases/download/v1.3.450/quarto-1.3.450-macos.pkg
     viennarna: https://www.tbi.univie.ac.at/RNA/download/osx/macosx/ViennaRNA-2.5.0-MacOSX.dmg
   downloads:                {# For BBS #}
     intel:

diff --git a/saltstack/salt/dependencies/quarto/init.sls b/saltstack/salt/dependencies/quarto/init.sls
@@ -0,0 +1,38 @@
+# Needed for quarto
+
+{% set machine = salt["pillar.get"]("machine") %}
+{% set download = machine.dependencies.quarto.split("/")[-1] %}
+{% set quarto = download[:-4] %}
+
+download_quarto:
+  cmd.run:
+    - name: curl -LO {{ machine.dependencies.quarto }}
+    - cwd: /tmp
+    - user: {{ machine.user.name }}
+
+{%- if grains['os'] == 'Ubuntu' %}
+install_quarto:
+  cmd.run:
+    - name: dpkg -i {{ quarto }}.deb
+    - require:
+      - cmd: download_quarto
+{% else %}
+install_quarto:
+  cmd.run:
+    - name: installer -pkg /tmp/{{ quarto }}.pkg -target /
+    - require:
+      - cmd: download_quarto
+
+fix_/usr/local_permissions_quarto:
+  cmd.run:
+    - name: |
+        chown -R {{ machine.user.name }}:admin /usr/local/*
+        chown -R root:wheel /usr/local/texlive
+    - require:
+      - cmd: install_quarto
+{% endif %}
+
+test_quarto_install:
+  cmd.run:
+    - name: Rscript -e 'install.packages("quarto", type="source", repos="https://cran.r-project.org")'
+    - runas: {{ machine.user.name }}
diff --git a/saltstack/salt/top.sls b/saltstack/salt/top.sls
@@ -35,3 +35,4 @@ base:
     - dependencies.ensemblvep                   # BioC ensemblVEP, MMAPPR2
     - dependencies.immunespace                  # BioC ImmuneSpaceR
     - dependencies.reticulate_python            # Bioc seqArchR
+    - dependencies.quarto                       # Bioc BiocBook