├── .gitignore ├── .travis.yml ├── LICENSE ├── README.docker.md ├── README.md ├── add-key.yml ├── all.yml ├── bio.yml ├── common.yml ├── docker ├── Dockerfile-baseimage ├── Dockerfile-bio-tags ├── Dockerfile-local ├── Dockerfile-repo ├── Dockerfile-rnasik ├── host_vars │ └── localhost └── rnasik_wrapper.sh ├── group_vars └── all ├── hosts ├── interactive.yml ├── meta └── main.yml ├── roles ├── R │ ├── defaults │ │ └── main.yml │ ├── tasks │ │ ├── main.yml │ │ ├── r_base.yml │ │ ├── r_extras.yml │ │ └── r_java.yml │ └── templates │ │ ├── bioconductor.R │ │ ├── cran.R │ │ ├── renv.R │ │ └── sw-module.lua.j2 ├── add-public-key │ └── tasks │ │ ├── main.yml │ │ └── set-authorized-key.yml ├── apache │ ├── defaults │ │ └── main.yml │ ├── handlers │ │ └── main.yml │ ├── tasks │ │ ├── apache-config.yml │ │ ├── apache-install.yml │ │ └── main.yml │ └── templates │ │ └── 000-default.conf.j2 ├── bds │ ├── defaults │ │ └── main.yml │ ├── tasks │ │ ├── bds.yml │ │ └── main.yml │ └── templates │ │ ├── bds.config-slurm.j2 │ │ ├── bds.config.j2 │ │ ├── clusterGenericSLURM │ │ ├── kill.sh │ │ ├── postMortemInfo.sh │ │ ├── run.pl │ │ ├── run.sh │ │ └── stat.sh │ │ └── sw-module.lua.j2 ├── bio_tools │ ├── defaults │ │ └── main.yml │ ├── tasks │ │ ├── bcftools.yml │ │ ├── bcl2fastq2.yml │ │ ├── bedtools.yml │ │ ├── bioperl.yml │ │ ├── biotradis.yml │ │ ├── blast-src.yml │ │ ├── bowtie2.yml │ │ ├── bwa.yml │ │ ├── cdhit.yml │ │ ├── cellranger.yml │ │ ├── conda-package.yml │ │ ├── conda.yml │ │ ├── cutadapt.yml │ │ ├── emboss.yml │ │ ├── fastqc.yml │ │ ├── freebayes.yml │ │ ├── gatk.yml │ │ ├── hifive.yml │ │ ├── htslib.yml │ │ ├── igv.yml │ │ ├── igv_github.yml │ │ ├── infernal.yml │ │ ├── macs2.yml │ │ ├── macs3.yml │ │ ├── main.yml │ │ ├── mimodd.yml │ │ ├── minimap2.yml │ │ ├── mothur.yml │ │ ├── multiqc.yml │ │ ├── muscle.yml │ │ ├── picard.yml │ │ ├── qiime2.yml │ │ ├── qualimap.yml │ │ ├── raxml.yml │ │ ├── rnasik-pipe.yml │ │ ├── sabre.yml │ │ ├── samtools.yml │ │ ├── seqtk.yml │ │ ├── skewer.yml │ │ ├── smalt.yml │ │ ├── snpeff.yml │ │ ├── spades.yml │ │ ├── sratoolkit.yml │ │ ├── star.yml │ │ ├── subread.yml │ │ ├── tools-conda.yml │ │ ├── tools.yml │ │ ├── trimmomatic.yml │ │ ├── vcflib.yml │ │ ├── vcftools.yml │ │ └── vsearch.yml │ └── templates │ │ ├── igv │ │ ├── igvtools │ │ ├── java-wrapper.sh.j2 │ │ ├── mimodd.config │ │ ├── qiime-module.lua.j2 │ │ ├── sik.config │ │ └── sw-module.lua.j2 ├── common │ ├── defaults │ │ └── main.yml │ ├── handlers │ │ └── main.yml │ ├── tasks │ │ ├── apt.yml │ │ ├── basemount.yml │ │ ├── config.yml │ │ ├── duck.yml │ │ ├── email_setup.yml │ │ ├── extra-debs.yml │ │ ├── gdal_ppa.yml │ │ ├── java-adoptium.yml │ │ ├── lua.yml │ │ ├── main.yml │ │ ├── motd.yml │ │ ├── python.yml │ │ ├── r_java.yml │ │ ├── r_repo.yml │ │ ├── sh_is_bash.yml │ │ ├── singularity-apt.yml │ │ ├── timezone.yml │ │ ├── ubuntu-20.yml │ │ └── ubuntu-22.yml │ └── templates │ │ ├── 60-lmod-recent │ │ ├── mailname │ │ └── main.cf ├── conda │ ├── defaults │ │ └── main.yml │ ├── tasks │ │ ├── conda-apt.yml │ │ ├── condarc.yml │ │ └── main.yml │ └── templates │ │ └── condarc.j2 ├── extra_modules │ ├── defaults │ │ └── main.yml │ ├── tasks │ │ ├── ant.yml │ │ ├── conda-package.yml │ │ ├── environment-script.yml │ │ ├── golang.yml │ │ ├── main.yml │ │ ├── maven.yml │ │ ├── nodejs.yml │ │ ├── rclone-conda.yml │ │ └── stack.yml │ └── templates │ │ ├── bioansible_env.sh.j2 │ │ └── sw-module.lua.j2 ├── jupyterhub │ ├── defaults │ │ └── main.yml │ ├── tasks │ │ ├── conda-env-add-packages.yml │ │ ├── conda-package.yml │ │ ├── jupyter.yml │ │ ├── jupyterhub-service.yml │ │ └── main.yml │ └── templates │ │ ├── jupyter-config.py.j2 │ │ ├── jupyter.bash.j2 │ │ ├── jupyterhub.service.j2 │ │ └── sw-module.lua.j2 ├── lmod │ ├── defaults │ │ └── main.yml │ ├── tasks │ │ ├── lmod.yml │ │ ├── lmod_stdenv.yml │ │ └── main.yml │ └── templates │ │ ├── RNAseqSuite.lua │ │ ├── StdEnv.lua │ │ └── VariantCallingSuite.lua ├── lmod_etc │ ├── defaults │ │ └── main.yml │ └── tasks │ │ ├── lmod_etc.yml │ │ ├── lmod_stdenv.yml │ │ └── main.yml ├── make_dirs │ └── tasks │ │ └── main.yml ├── make_sw_guy │ ├── defaults │ │ └── main.yml │ └── tasks │ │ └── main.yml ├── nginx │ ├── defaults │ │ └── main.yml │ ├── tasks │ │ └── main.yml │ └── templates │ │ └── bio_ansible_nginx.conf ├── podman │ ├── defaults │ │ └── main.yml │ └── tasks │ │ └── main.yml ├── rstudio_server │ ├── defaults │ │ └── main.yml │ ├── tasks │ │ ├── main.yml │ │ ├── rstudio-config.yml │ │ ├── rstudio-deps.yml │ │ ├── rstudio-server-pro.yml │ │ └── rstudio-server.yml │ └── templates │ │ └── sw-module.lua.j2 ├── shiny_server │ ├── defaults │ │ └── main.yml │ ├── tasks │ │ ├── main.yml │ │ └── shiny-server.yml │ └── templates │ │ ├── shiny-server.conf │ │ └── shiny-server.service.j2 ├── shpc │ ├── defaults │ │ └── main.yml │ ├── tasks │ │ ├── find-mamba.yml │ │ ├── install-modules.yml │ │ ├── main.yml │ │ ├── shpc-install.yml │ │ └── system-wide-config.yml │ └── templates │ │ ├── settings.yml.j2 │ │ └── shpc-lmod.sh.j2 ├── sshd │ └── tasks │ │ └── main.yml └── vnc │ └── tasks │ └── main.yml ├── scripts ├── bash │ ├── link_R_data.bash │ └── mkuser.bash └── other │ ├── brew2lmod.rb │ ├── download-gencode.sh │ ├── download-igenomes.sh │ ├── download-rseqc-ref.py │ ├── download-uniprot.sh │ ├── find-jvms │ ├── rseqc-ref-files.xml │ └── useradd.sh ├── sshd.yml ├── supplementary ├── RNAsik.md ├── TODO.md ├── dependencies.md ├── list_of_tags.md ├── notes.md ├── pip_packages.md └── playbook_breakdown.md ├── tarballs ├── README.md └── download_oracle_java.sh └── templates ├── conda-module.lua.j2 └── lmod ├── lmod.profile.sh.j2 └── z00_StdEnv.sh /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MonashBioinformaticsPlatform/bio-ansible/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: 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