diff --git a/saltstack/pillar/common/linux.sls b/saltstack/pillar/common/linux.sls index 4f9732c..bf58519 100644 --- 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 index d7575f8..0fbfc96 100644 --- 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 new file mode 100644 index 0000000..7d2b378 --- /dev/null +++ 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 index 96e0965..f8eaf28 100644 --- 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