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diff --git a/communities/all/labs/genome b/communities/all/labs/genome
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+../../genome/lab/
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diff --git a/communities/all/labs/proteomics b/communities/all/labs/proteomics
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+../../proteomics/lab/
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diff --git a/communities/all/labs/single-cell b/communities/all/labs/single-cell
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+../../spoc/lab/
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diff --git a/communities/all/labs/spoc b/communities/all/labs/spoc
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+../../spoc/lab/
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diff --git a/communities/genome/lab/CONTRIBUTORS b/communities/genome/lab/CONTRIBUTORS
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--- /dev/null
+++ b/communities/genome/lab/CONTRIBUTORS
@@ -0,0 +1,3 @@
+# If GitHub username, name and avatar will be fetched and displayed
+AnnaSyme
+neoformit
diff --git a/communities/genome/lab/annotation.yml b/communities/genome/lab/annotation.yml
new file mode 100644
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+++ b/communities/genome/lab/annotation.yml
@@ -0,0 +1,361 @@
+id: annotation
+title: Genome annotation
+tabs:
+ - id: tools
+ title: Tools
+ heading_md: >
+ Common tools are listed here, or search for more in the full tool panel to the left.
+ content:
+ - title_md: MAKER - genome annotation pipeline
+ description_md: >
+
+ MAKER is able to annotate both prokaryotes and eukaryotes. It works by aligning as many evidences as possible along the genome sequence, and then reconciling all these signals to determine probable gene structures.
+
The evidences can be transcript or protein sequences from the same (or closely related) organism. These sequences can come from public databases (like NR or GenBank) or from your own experimental data (transcriptome assembly from an RNASeq experiment for example). MAKER is also able to take into account repeated elements.
+
+ Funannotate predict performs a comprehensive whole genome gene prediction. Uses AUGUSTUS, GeneMark, Snap, GlimmerHMM, BUSCO, EVidence Modeler, tbl2asn, tRNAScan-SE, Exonerate, minimap2. This approach differs from Maker as it does not need to train ab initio predictors.
+
+ inputs:
+ - datatypes:
+ - fasta
+ label: Genome assembly (soft-masked)
+ - datatypes:
+ - bam
+ label: Mapped RNA evidence (optional)
+ - datatypes:
+ - fasta
+ label: Protein evidence (optional)
+ button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffunannotate_predict%2Ffunannotate_predict"
+ - title_md: RepeatMasker - screen DNA sequences for interspersed repeats and low complexity regions
+ description_md: >
+
+ RepeatMasker is a program that screens DNA for repeated elements such as tandem repeats, transposons, SINEs and LINEs. Galaxy AU has installed the full and curated DFam screening databases, or a custom database can be provided in fasta format. Additional reference data can be downloaded from RepBase.
+
+ Interproscan is a batch tool to query the InterPro database. It provides annotations based on multiple searches of profile and other functional databases.
+
+ Funannotate compare compares several annotations and outputs a GFF3 file with the best gene models. It can be used to compare the results of different gene predictors, or to compare the results of a gene predictor with a reference annotation.
+
+ Annotate an assembled genome and output a GFF3 file. There are several modules that do different things - search for FGENESH in the tool panel to see them.
+
+ inputs:
+ - datatypes:
+ - fasta
+ label: Genome assembly
+ - datatypes:
+ - fasta
+ label: Repeat-masked (hard) genome assembly
+ button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=fgenesh_annotate&version=latest"
+
+ - id: workflows
+ title: Workflows
+ heading_md: >
+ A workflow is a series of Galaxy tools that have been linked together to perform a specific analysis. You can use and customize the example workflows below.
+ Learn more.
+ content:
+ subsections:
+ - id: general
+ title: General use
+ content:
+ - title_md: Annotation with Maker
+ description_md: >
+
+ Annotates a genome using multiple rounds of Maker, including gene prediction using SNAP and Augustus.
Tools: makersnapaugustusbuscojbrowse
+
+ inputs:
+ - label: Genome assembly
+ datatypes:
+ - fasta
+ - label: RNAseq Illumina reads
+ datatypes:
+ - fastq
+ - label: Proteins
+ datatypes:
+ - fasta
+ button_link: "{{ galaxy_base_url }}/u/anna/w/genome-annotation-with-maker"
+ view_link: ''
+ view_tip: ''
+ button_tip: Run in Galaxy AU
+ - title_md: Annotation with Funannotate
+ description_md: >
+
+ Annotates a genome using Funannotate, includes RNAseq data with RNAstar, and protein predictions from EggNOG.
+ This How-to-Guide will describe the steps required to align transcript data to your genome on the Galaxy Australia platform, using multiple workflows. The outputs from these workflows can then be used as inputs into the next annotation workflow using FgenesH++.
+
+ inputs:
+ - datatypes:
+ - fasta
+ label: Assembled genome
+ - datatypes:
+ - fasta
+ label: Masked genome
+ - datatypes:
+ - fasta
+ label: >
+ Outputs from TSI convert formats workflow
+ (*.cdna,
+ *.pro,
+ *.dat)
+ button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=881"
+ view_link: https://workflowhub.eu/workflows/881
+ view_tip: View in WorkflowHub
+ button_tip: Import to Galaxy Australia
+
+ - id: help
+ title: Help
+ content:
+ - title_md: What is genome annotation?
+ description_md: >
+
+ These slides from the Galaxy training network explain the process of genome annotation in detail. You can use the ← and → keys to navigate through the slides.
+
+ The flowchart below shows how you might use your input data (in green) with different Galaxy tools (in blue) to annotate a genome assembly. For example, one pathway would be taking an assembled genome, plus information about repeats, and data from RNA-seq, to run in the Maker pipeline. The annotatations can then be viewed in JBrowse.
+
+
+
+ A graphical representation of genome annotation
+
+ - title_md: Can I use Fgenesh++ for annotation?
+ description_md: >
+
+ Fgenesh++ is a bioinformatics pipeline for automatic prediction of genes in eukaryotic genomes. It is presently not installed in Galaxy Australia, but the Australian Biocommons and partners have licensed the software and made it available via commandline. Australian researchers can apply for access through the Australian BioCommons.
+
+ button_md: Apply
+ button_link: https://www.biocommons.org.au/fgenesh-plus-plus
+ button_tip: Apply for access to Fgenesh++
+ - title_md: Can I use Apollo to share and edit the annotated genome?
+ description_md: >
+
+ Apollo is web-browser accessible system that lets you conduct real-time collaborative curation and editing of genome annotations.
+
+
+ The Australian BioCommons and our partners at QCIF and Pawsey provide a hosted Apollo Portal service where your genome assembly and supporting evidence files can be hosted. All system administration is taken care of, so you and your team can focus on the annotation curation itself.
+
+
+ This Galaxy tutorial provides a complete walkthrough of the process of refining eukaryotic genome annotations with Apollo.
+
+ button_md: More info
+ button_link: https://support.biocommons.org.au/support/solutions/articles/6000244843-apollo-for-collaborative-curation-and-editing
+ - title_md: Tutorials
+ description_md: >
+
+ Genome annotation with Maker
+
+
+ Genome annotation of eukaryotes is a little more complicated than for prokaryotes: eukaryotic genomes are usually larger than prokaryotes, with more genes. The sequences determining the beginning and the end of a gene are generally less conserved than the prokaryotic ones. Many genes also contain introns, and the limits of these introns (acceptor and donor sites) are not highly conserved. This Galaxy tutorial uses MAKER to annotate the genome of a small eukaryote: Schizosaccharomyces pombe (a yeast).
+
+
+
+ Genome annotation with Funannotate
+
+
+ This Galaxy tutorial provides a complete walkthrough of the process of annotation with Funannotate, including the preparation of RNAseq data, structural annotation, functional annotation, visualisation, and comparing annotations.
+
+ - title_md: Galaxy Australia support
+ description_md: >
+
+ Any user of Galaxy Australia can request support through an online form.
+
+ button_md: Request support
+ button_link: /request/support
diff --git a/communities/genome/lab/assembly.yml b/communities/genome/lab/assembly.yml
new file mode 100644
index 00000000..fcd13631
--- /dev/null
+++ b/communities/genome/lab/assembly.yml
@@ -0,0 +1,375 @@
+id: assembly
+title: Genome assembly
+tabs:
+ - id: tools
+ title: Tools
+ heading_md: >
+ Common tools are listed here, or search for more in the full tool panel to the left.
+ content:
+ - title_md: Hifiasm - assembly with PacBio HiFi data
+ description_md: >
+ A haplotype-resolved assembler for PacBio HiFi reads.
+ inputs:
+ - datatypes:
+ - fasta
+ button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhifiasm%2Fhifiasm"
+ - title_md: Flye - assembly with PacBio or Nanopore data
+ description_md: >
+ de novo assembly of single-molecule sequencing reads, designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies.
+ inputs:
+ - datatypes:
+ - fasta
+ - fastq
+ button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fflye%2Fflye"
+ - title_md: Unicycler - assembly with Illumina, PacBio or Nanopore data - bacteria only
+ description_md: >
+ Hybrid assembly pipeline for bacterial genomes, uses both Illumina reads and long reads (PacBio or Nanopore).
+ inputs:
+ - datatypes:
+ - fastq
+ button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Funicycler%2Funicycler"
+ - title_md: YAHS - scaffold assembly with HiC data
+ description_md: >
+ YAHS is a scaffolding tool based on a computational method that exploits the genomic proximity information in Hi-C data sets for long-range scaffolding of de novo genome assemblies. Inputs are the primary assembly (or haplotype 1), and HiC reads mapped to the assembly. See this tutorial to learn how to create a suitable BAM file.
+ inputs:
+ - label: Primary assembly or Haplotype 1 genome.fasta
+ datatypes:
+ - fasta
+ - label: HiC reads mapped to assembly mapped_reads.bam
+ datatypes:
+ - bam
+ button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2yahs"
+ - title_md: Quast - assess genome assembly quality
+ description_md: >
+ QUAST = QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics. If you have one or multiple genome assemblies, you can assess their quality with Quast. It works with or without reference genome.
+ inputs:
+ - datatypes:
+ - fasta
+ button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fquast%2Fquast"
+ - title_md: Busco - assess genome assembly quality
+ description_md: >
+ BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs. The tool attempts to provide a quantitative assessment of the completeness in terms of the expected gene content of a genome assembly, transcriptome, or annotated gene set.
+ inputs:
+ - datatypes:
+ - fasta
+ button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbusco%2Fbusco"
+ - title_md: MitoHiFi - assemble mitochondrial genomes
+ description_md: >
+ Assemble mitochondrial genomes from PacBio HiFi reads. Run first to find a related mitogenome, then run to assemble the genome. Inputs are PacBio HiFi reads in fasta or fastq format, and a related mitogenome in both fasta and genbank formats.
+ inputs:
+ - datatypes:
+ - fasta
+ - fastq
+ - genbank
+ button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fmitohifi%2Fmitohfi"
+
+ - id: workflows
+ title: Workflows
+ heading_md: >
+ A workflow is a series of Galaxy tools that have been linked together to perform a specific analysis. You can use and customize the example workflows below.
+ Learn more.
+ content:
+ subsections:
+ - id: pacbio
+ title: TSI assembly workflows - PacBio HiFi or Nanopore data
+ content:
+ - title_md: About these workflows
+ description_md: >
+ This How-to-Guide will describe the steps required to assemble your genome on the Galaxy Australia platform, using multiple workflows. There is also a guide about the Genome Assessment workflow, and the HiC Scaffolding workflow.
+ - title_md: BAM to FASTQ + QC v1.0
+ description_md: >
+ Convert a BAM file to FASTQ format to perform QC analysis (required if your data is in BAM format).
+ inputs:
+ - datatypes:
+ - bam
+ label: PacBio subreads.bam
+ button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=220"
+ view_link: https://workflowhub.eu/workflows/220
+ view_tip: View in WorkflowHub
+ button_tip: Import to Galaxy Australia
+ - title_md: PacBio HiFi genome assembly using hifiasm v2.1
+ description_md: >
+ Assemble a genome using PacBio HiFi reads.
+ inputs:
+ - datatypes:
+ - fastqsanger
+ label: HiFi reads
+ button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=221"
+ view_link: https://workflowhub.eu/workflows/221
+ view_tip: View in WorkflowHub
+ button_tip: Import to Galaxy Australia
+ - title_md: Purge duplicates from hifiasm assembly v1.0
+ description_md: >
+ Optional workflow to purge duplicates from the contig assembly.
+ inputs:
+ - datatypes:
+ - fastqsanger
+ label: HiFi reads
+ - datatypes:
+ - fasta
+ label: Primary assembly contigs
+ button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=237"
+ view_link: https://workflowhub.eu/workflows/237
+ view_tip: View in WorkflowHub
+ button_tip: Import to Galaxy Australia
+ - title_md: Nanopore genome assembly using Flye
+ description_md: >
+ Assemble a genome using Nanopore reads.
+ inputs:
+ - datatypes:
+ - fastqsanger
+ - fastq
+ label: Nanopore reads
+ button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1114"
+ view_link: https://workflowhub.eu/workflows/1114
+ view_tip: View in WorkflowHub
+ button_tip: Import to Galaxy Australia
+ - title_md: Genome assessment post-assembly
+ description_md: >
+ Evaluate the quality of your genome assembly with a comprehensive report including FASTA stats, BUSCO, QUAST, Meryl and Merqury.
+ inputs:
+ - datatypes:
+ - fasta
+ label: Primary assembly contigs
+ button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=403"
+ view_link: https://workflowhub.eu/workflows/403
+ view_tip: View in WorkflowHub
+ button_tip: Import to Galaxy Australia
+ - title_md: Optional HiC scaffolding workflow
+ description_md: >
+ If you have HiC data, scaffold your assembly using YAHS.
+ inputs:
+ - datatypes:
+ - fasta
+ label: Primary or Hap1 assembly
+ - datatypes:
+ - fastqsanger.gz
+ label: HiC forward reads, HiC reverse reads
+ button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1054"
+ view_link: https://workflowhub.eu/workflows/1054
+ view_tip: View in WorkflowHub
+ button_tip: Import to Galaxy Australia
+
+ - id: nanopore
+ title: General assembly workflows - Nanopore and Illumina data
+ content:
+ - title_md: About these workflows
+ description_md: >
+ This tutorial describes the steps required to assemble a genome on Galaxy with Nanopore and Illumina data.
+ - title_md: Flye assembly with Nanopore data
+ description_md: >
+ Assemble Nanopore long reads. This workflow can be run alone or as part of a combined workflow for large genome assembly.
+ inputs:
+ - datatypes:
+ - fastqsanger
+ label: Long reads (may be raw, filtered and/or corrected)
+ button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=225"
+ view_link: https://workflowhub.eu/workflows/225
+ view_tip: View in WorkflowHub
+ button_tip: Import to Galaxy Australia
+ - title_md: Assembly polishing
+ description_md: >
+ Polishes (corrects) an assembly, using long reads (Racon and Medaka) and short reads (Racon).
+ inputs:
+ - datatypes:
+ - fasta
+ label: Assembly to polish
+ - datatypes:
+ - fastq
+ label: Long reads (those used in assembly)
+ - datatypes:
+ - fastq
+ label: Short reads to be used for polishing (R1 only)
+ button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=226"
+ view_link: https://workflowhub.eu/workflows/226
+ view_tip: View in WorkflowHub
+ button_tip: Import to Galaxy Australia
+ - title_md: Assess genome quality
+ description_md: >
+ Assesses the quality of the genome assembly. Generates statistics, determines if expected genes are present and align contigs to a reference genome.
+ inputs:
+ - datatypes:
+ - fasta
+ label: Polished assembly
+ - datatypes:
+ - fasta
+ label: Reference genome assembly (e.g. related species)
+ button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=229"
+ view_link: https://workflowhub.eu/workflows/229
+ view_tip: View in WorkflowHub
+ button_tip: Import to Galaxy Australia
+ - id: hic
+ title: VGP assembly workflows - PacBio HiFi and (optional) HiC data
+ content:
+ - title_md: About these workflows
+ description_md: >
+ These workflows have been developed as part of the global Vertebrate Genome Project (VGP). A guide to using these in Galaxy Australia can be found here. A complete guide to the individual workflows and sample results can be found here. There are many different ways that these workflows can be used in practice - for a comprehensive example, check out this Galaxy tutorial.
+ - title_md: Kmer profiling
+ description_md: >
+ This workflow produces a Meryl database and Genomescope outputs that will be used to determine parameters for following workflows, and assess the quality of genome assemblies. Specifically, it provides information about the genomic complexity, such as the genome size and levels of heterozygosity and repeat content, as well about the data quality.
+ inputs:
+ - datatypes:
+ - fastq
+ label: PacBio HiFi reads
+ button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=dockstore.org&trs_id=%23workflow/github.com/iwc-workflows/kmer-profiling-hifi-VGP1/main"
+ view_link: https://dockstore.org/workflows/github.com/iwc-workflows/kmer-profiling-hifi-VGP1/main:main
+ view_tip: View in WorkflowHub
+ button_tip: Import to Galaxy Australia
+ - title_md: Hifi assembly and HiC phasing
+ description_md: >
+
+ This workflow uses hifiasm (HiC mode) to generate HiC-phased haplotypes (hap1 and hap2). This is in contrast to its default mode, which generates primary and alternate pseudohaplotype assemblies. This workflow includes three tools for evaluating assembly quality: gfastats, BUSCO and Merqury.
+
+
+ Note: if you have multiple input files for each HiC set, they need to be concatenated. The forward set needs to be concatenated in the same order as reverse set.
+
+ inputs:
+ - datatypes:
+ - fasta
+ label: PacBio HiFi reads
+ - datatypes:
+ - fastq
+ label: PacBio HiC reads (forward)
+ - datatypes:
+ - fastq
+ label: PacBio HiC reads (reverse)
+ - datatypes:
+ - meryldb
+ label: Meryl kmer database
+ - datatypes:
+ - txt
+ label: GenomeScope genome profile summary
+ button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=dockstore.org&trs_id=%23workflow/github.com/iwc-workflows/Assembly-Hifi-HiC-phasing-VGP4/main"
+ view_link: https://dockstore.org/workflows/github.com/iwc-workflows/Assembly-Hifi-HiC-phasing-VGP4/main:main
+ view_tip: View in WorkflowHub
+ button_tip: Import to Galaxy Australia
+
+ - title_md: Hifi assembly without HiC data
+ description_md: >
+ This workflow uses hifiasm to generate primary and alternate pseudohaplotype assemblies. This workflow includes three tools for evaluating assembly quality: gfastats, BUSCO and Merqury.
+ inputs:
+ - datatypes:
+ - fasta
+ label: PacBio HiFi reads
+ - datatypes:
+ - meryldb
+ label: Meryl kmer database
+ - datatypes:
+ - txt
+ label: GenomeScope genome profile summary
+ button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=dockstore.org&trs_id=%23workflow/github.com/iwc-workflows/Assembly-Hifi-only-VGP3/main"
+ view_link: https://dockstore.org/workflows/github.com/iwc-workflows/Assembly-Hifi-only-VGP3/main:main
+ view_tip: View in Dockstore
+ button_tip: Import to Galaxy Australia
+
+ - title_md: HiC scaffolding
+ description_md: >
+ This workflow scaffolds the assembly contigs using information from HiC data.
+ inputs:
+ - datatypes:
+ - gfa
+ label: Assembly of haplotype 1
+ - datatypes:
+ - fastq
+ label: HiC forward reads
+ - datatypes:
+ - fastq
+ label: HiC reverse reads
+ button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=dockstore.org&trs_id=%23workflow/github.com/iwc-workflows/Scaffolding-HiC-VGP8/main"
+ view_link: https://dockstore.org/workflows/github.com/iwc-workflows/Scaffolding-HiC-VGP8/main:main
+ view_tip: View in WorkflowHub
+ button_tip: Import to Galaxy Australia
+ - title_md: Decontamination
+ description_md: >
+ This workflow identifies and removes contaminants from the assembly.
+ inputs:
+ - datatypes:
+ - fasta
+ label: Assembly
+ button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=dockstore.org&trs_id=%23workflow/github.com/iwc-workflows/Assembly-decontamination-VGP9/main:v0.1"
+ view_link: https://dockstore.org/workflows/github.com/iwc-workflows/Assembly-decontamination-VGP9/main:v0.1
+ view_tip: View in WorkflowHub
+ button_tip: Import to Galaxy Australia
+
+ - id: help
+ title: Help
+ content:
+ - title_md: Can I use Galaxy Australia to assemble a large genome?
+ description_md: >
+
+ Yes. Galaxy Australia has assembly tools for small prokaryote genomes as well as larger eukaryote genomes. We are continually adding new tools and optimising them for large genome assemblies - this means adding enough computer processing power to run data-intensive tools, as well as configuring aspects such as parallelisation.
+
+
+ Please contact us if:
+
+
+
you need to increase your data storage limit
+
there is a tool you wish to request
+
a tool appears to be broken or running slowly
+
+ button_md: Request support
+ button_link: /request
+ - title_md: How can I learn about genome assembly?
+ description_md: >
+
+
See the tutorials in this Help section. They cover different approaches to genome assembly.
+
Read the methods in scientific papers about genome assembly, particularly those about genomes with similar characteristics to those in your project
+
See the Workflows section for examples of different approaches to genome assembly - these cover different sequencing data types, and a variety of tools.
+ Genome assembly can be a very involved process. A typical genome assembly procedure might look like:
+
+
+
Data QC - check the quality and characteristics of your sequencing reads.
+
Kmer counting - to determine genome characteristics such as ploidy and size.
+
Data preparation - trimming and filtering sequencing reads if required.
+
Assembly - for large genomes, this is usually done with long sequencing reads from PacBio or Nanopore.
+
Polishing - the assembly may be polished (corrected) with long and/or short (Illumina) reads.
+
Scaffolding - the assembly contigs may be joined together with other sequencing data such as HiC.
+
Assessment - at any stage, the assembly can be assessed for number of contigs, number of base pairs, whether expected genes are present, and many other metrics.
+
Annotation - identify features on the genome assembly such as gene names and locations.
+
+
+
+ A graphical representation of genome assembly
+
+ - title_md: Which tools should I use?
+ description_md: >
+
+ There is no best set of tools to recommend - new tools are developed constantly, sequencing technology improves rapidly, and many genomes have never been sequenced before and thus their characteristics and quirks are unknown. The "Tools" tab in this section includes a list of commonly-used tools that could be a good starting point. You will find other tools in recent publications or used in workflows.
+
+
+ You can also search for tools in Galaxy's tool panel. If they aren't installed on Galaxy Australia, you can request installation of a tool.
+
+
+ We recommend testing a tool on a small data set first and seeing if the results make sense, before running on your full data set.
+
+ - title_md: How can I assess the quality of my genome assembly?
+ description_md: >
+ Once a genome has been assembled, it is important to assess the quality of the assembly, and in the first instance, this quality control (QC) can be achieved using the workflow described here.
+ button_md: Workflow tutorial
+ button_link: https://australianbiocommons.github.io/how-to-guides/genome_assembly/assembly_qc
+ - title_md: Galaxy Australia support
+ description_md: >
+ Any user of Galaxy Australia can request support through an online form.
+ button_md: Request support
+ button_link: /request/support
diff --git a/communities/genome/lab/base.yml b/communities/genome/lab/base.yml
new file mode 100644
index 00000000..48383389
--- /dev/null
+++ b/communities/genome/lab/base.yml
@@ -0,0 +1,33 @@
+# Request this on site.usegalaxy.org.au with:
+# https://site.usegalaxy.org.au/lab/export?content_root=https://github.com/galaxyproject/galaxy_codex/blob/main/subdomains/genome/base.yml
+
+# Check out the documentation for building exported labs:
+# https://site.usegalaxy.org.au/lab/export
+
+# Use these variables in HTML templates like:
+# "Welcome to the Galaxy {{ site_name }} {{ lab_name }}"
+# To make the content more generic and reusable across sites
+site_name: ""
+lab_name: Genome Lab
+nationality: ""
+galaxy_base_url: https://genome.usegalaxy.org # Use for rendering tool/workflow URLs. Trailing '/' will be removed.
+subdomain: genome
+root_domain: usegalaxy.org
+# feedback_email: help@mygalaxy.org # set to enable feedback form
+
+# Custom content relative to this file URL
+header_logo: static/logo.png
+custom_css: static/custom.css
+intro_md: templates/intro.html
+conclusion_md: templates/conclusion.html
+footer_md: templates/footer.html
+
+
+# Data (Tools, Workflows etc.) to be rendered into sections/tabs/accordion elements.
+# Either:
+# 1. Relative to this file URL
+# 2. Full URL to fetch content from a different remote location
+sections:
+ - data.yml
+ - assembly.yml
+ - annotation.yml
diff --git a/communities/genome/lab/data.yml b/communities/genome/lab/data.yml
new file mode 100644
index 00000000..7ffbc0f7
--- /dev/null
+++ b/communities/genome/lab/data.yml
@@ -0,0 +1,164 @@
+id: data
+title: Data import and preparation
+tabs:
+ - id: help
+ title: Overview
+ heading_md: >
+ If you are new to galaxy, uploading your data is a good place to start!
+
+ Check out the Tools and Workflows tabs for different approaches to uploading data.
+ content:
+ - title_md: How can I import my genomics data?
+ description_md: >
+
+ You can upload your data to Galaxy using the Upload tool from anywhere in Galaxy. Just look for the "Upload data" button at the top of the tool panel.
+
+ button_md: More info
+ button_link: https://training.galaxyproject.org/training-material/topics/galaxy-interface/
+ - title_md: How can I subsample my data?
+ description_md: >
+
+ We recommend subsampling large data sets to test tools and workflows. A useful tool is seqtk_seq, setting the parameter at "Sample fraction of sequences".
+
+ - title_md: How can I import data from the BPA portal?
+ description_md: >
+
+ BioPlatforms Australia allows data downloads via URL. Once you have generated one of these URLs in the BPA portal, you can import it into Galaxy using the "Fetch data" feature of the Upload tool.
+
+ button_md: More info
+ button_link: https://australianbiocommons.github.io/how-to-guides/genome_assembly/hifi_assembly#in-depth-workflow-guide
+ - title_md: Can I upload sensitive data?
+ description_md: >
+
+ No, do not upload personal or sensitive, such as human health or clinical data. Please see our Data Privacy page for definitions of sensitive and health-related information.
+
+
+ Please also make sure you have read our Terms of Service, which covers hosting and analysis of research data.
+
+ - title_md: Is my data private?
+ description_md: >
+
+ Please read our Privacy Policy for information on your personal data and any data that you upload.
+
+ - title_md: How can I increase my storage quota?
+ description_md: >
+
+ Please submit a quota request if your Galaxy Australia account reaches its data storage limit. Requests are usually provisioned quickly if you provide a reasonable use case for your request.
+
+ Quality control and data cleaning is an essential first step in any NGS analysis. This tutorial will show you how to use and interpret results from FastQC, NanoPlot and PycoQC.
+
+ button_md: Tutorial
+ button_link: https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html
+ - title_md: "Tutorial: introduction to Genomics and Galaxy"
+ description_md: >
+
+ This practical aims to familiarize you with the Galaxy user interface. It will teach you how to perform basic tasks such as importing data, running tools, working with histories, creating workflows, and sharing your work.
+
+ button_md: Tutorial
+ button_link: https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-strands/tutorial.html
+ - title_md: Galaxy Australia support
+ description_md: >
+
+ Any user of Galaxy Australia can request support through an online form.
+
+ button_md: Request support
+ button_link: /request/support
+ - id: tools
+ title: Tools
+ heading_md: >
+ Common tools are listed here, or search for more in the full tool panel to the left.
+ content:
+ - title_md: Import data to Galaxy
+ description_md: >
+ Standard upload of data to Galaxy, from your computer or from the web.
+ button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=upload1"
+ - title_md: FastQC - sequence quality reports
+ description_md: >
+
+ Before using your sequencing data, it's important to ensure that
+ the data quality is sufficient for your analysis.
+
+ Prepare kmer count histogram for input to GenomeScope.
+
+ inputs:
+ - datatypes:
+ - fastq
+ - fasta
+ button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmeryl%2Fmeryl"
+ - id: workflows
+ title: Workflows
+ heading_md: >
+ A workflow is a series of Galaxy tools that have been linked together to perform a specific analysis. You can use and customize the example workflows below.
+ Learn more.
+ content:
+ - title_md: Data QC
+ description_md: >
+
+ Report statistics from sequencing reads.
Tools: nanoplotfastqcmultiqc
+
+ button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=222"
+ view_link: https://workflowhub.eu/workflows/222
+ view_tip: View in WorkflowHub
+ button_tip: Import to Galaxy AU
+ - title_md: Kmer counting to estimate genome size
+ description_md: >
+
+ Estimates genome size and heterozygosity based on counts of kmers.
Tools: merylgenomescope
+
+ button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=223"
+ view_link: https://workflowhub.eu/workflows/223
+ view_tip: View in WorkflowHub
+ button_tip: Import to Galaxy AU
+ - title_md: Trim and filter reads
+ description_md: >
+
+ Trims and filters raw sequence reads according to specified settings.
Tools: fastp
+
+ button_link: "{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=224"
+ view_link: https://workflowhub.eu/workflows/224
+ view_tip: View in WorkflowHub
+ button_tip: Import to Galaxy AU
diff --git a/communities/genome/lab/static/annotation-overview.png b/communities/genome/lab/static/annotation-overview.png
new file mode 100644
index 00000000..0bdeaa80
Binary files /dev/null and b/communities/genome/lab/static/annotation-overview.png differ
diff --git a/communities/genome/lab/static/assembly-overview.png b/communities/genome/lab/static/assembly-overview.png
new file mode 100644
index 00000000..61cf705c
Binary files /dev/null and b/communities/genome/lab/static/assembly-overview.png differ
diff --git a/communities/spoc/subdomain/static/custom.css b/communities/genome/lab/static/custom.css
similarity index 100%
rename from communities/spoc/subdomain/static/custom.css
rename to communities/genome/lab/static/custom.css
diff --git a/communities/genome/lab/static/logo.png b/communities/genome/lab/static/logo.png
new file mode 100644
index 00000000..ea8b9ffa
Binary files /dev/null and b/communities/genome/lab/static/logo.png differ
diff --git a/communities/spoc/subdomain/templates/footer.html b/communities/genome/lab/templates/conclusion.html
similarity index 100%
rename from communities/spoc/subdomain/templates/footer.html
rename to communities/genome/lab/templates/conclusion.html
diff --git a/communities/genome/lab/templates/footer.html b/communities/genome/lab/templates/footer.html
new file mode 100644
index 00000000..e69de29b
diff --git a/communities/genome/lab/templates/intro.html b/communities/genome/lab/templates/intro.html
new file mode 100644
index 00000000..9460cb1b
--- /dev/null
+++ b/communities/genome/lab/templates/intro.html
@@ -0,0 +1,40 @@
+
+
+ Welcome to the Galaxy {{ site_name }} {{ lab_name }}. Get quick access to tools, workflows and tutorials for genome assembly and annotation.
+
+
+ What is this page?
+
+
+
+
+
+
+
+
Galaxy {{ site_name }}
+
+
+
+
+ This site {{ subdomain }}.{{ root_domain }} is connected to the same server as {{ root_domain }}, but with an interface dedicated to helping our {{ nationality }} researchers. Your history, jobs and data quota are shared with the "Base" website.
+
+
+
+ Switch between sites quickly using the dropdown in Galaxy {{ site_name }}'s main navigation bar (note, if your Galaxy server does not have this, please request that they install the "Site Switcher" plugin from Galaxy Australia):
+
+
+
diff --git a/communities/genome/lab/usegalaxy.org.au.yml b/communities/genome/lab/usegalaxy.org.au.yml
new file mode 100644
index 00000000..a47dea03
--- /dev/null
+++ b/communities/genome/lab/usegalaxy.org.au.yml
@@ -0,0 +1,22 @@
+# This content extends base.yml
+
+# Request this on site.usegalaxy.org.au with:
+# https://site.usegalaxy.org.au/lab/export?content_root=https://github.com/galaxyproject/galaxy_codex/blob/main/subdomains/genome/usegalaxy.org.au.yml
+
+# Check out the documentation for building exported labs:
+# https://site.usegalaxy.org.au/lab/export
+
+# Use these variables in HTML templates like:
+# "Welcome to the Galaxy {{ site_name }} {{ lab_name }}"
+# To make the content more generic and reusable across sites
+site_name: Australia
+lab_name: Genome Lab
+nationality: Australian
+galaxy_base_url: https://genome.usegalaxy.org.au # Use for rendering tool/workflow URLs. Trailing '/' will be removed.
+subdomain: genome
+root_domain: usegalaxy.org.au
+feedback_email: help@genome.edu.au
+
+# Custom content relative to this file URL
+conclusion_md: usegalaxy.org.au/templates/conclusion.html
+footer_md: usegalaxy.org.au/templates/footer.html
diff --git a/communities/genome/lab/usegalaxy.org.au/templates/conclusion.html b/communities/genome/lab/usegalaxy.org.au/templates/conclusion.html
new file mode 100644
index 00000000..13e7d771
--- /dev/null
+++ b/communities/genome/lab/usegalaxy.org.au/templates/conclusion.html
@@ -0,0 +1,163 @@
+
+
What's happening in {{ nationality }} genomics research?
+ Welcome to the Galaxy {{ site_name }} {{ lab_name }}. Get quick access to tools, workflows and tutorials for genome assembly and annotation.
+
+
+ What is this page?
+
+
+
+
+
+
+
+
Galaxy {{ site_name }}
+
+
+
+
+ This site {{ subdomain }}.{{ root_domain }} is connected to the same server as {{ root_domain }}, but with an interface dedicated to helping our {{ nationality }} researchers. Your history, jobs and data quota are shared with the "Base" website.
+
+
+
+ Switch between sites quickly using the dropdown in Galaxy {{ site_name }}'s main navigation bar:
+
+
+
diff --git a/communities/proteomics/lab/CONTRIBUTORS b/communities/proteomics/lab/CONTRIBUTORS
new file mode 100644
index 00000000..a690e999
--- /dev/null
+++ b/communities/proteomics/lab/CONTRIBUTORS
@@ -0,0 +1,3 @@
+# If GitHub username, name and avatar will be fetched and displayed
+supernord
+neoformit
diff --git a/communities/proteomics/lab/base.yml b/communities/proteomics/lab/base.yml
new file mode 100644
index 00000000..eb32af5a
--- /dev/null
+++ b/communities/proteomics/lab/base.yml
@@ -0,0 +1,47 @@
+# Request this on site.usegalaxy.org.au with:
+# https://site.usegalaxy.org.au/lab/export?content_root=https://github.com/galaxyproject/galaxy_codex/blob/main/subdomains/proteomics/base.yml
+
+# Check out the documentation for building exported labs:
+# https://site.usegalaxy.org.au/lab/export
+
+# Use these variables in HTML templates like:
+# "Welcome to the Galaxy {{ site_name }} {{ lab_name }}"
+# To make the content more generic and reusable across sites.
+site_name: ""
+lab_name: Proteomics Lab
+nationality: ""
+galaxy_base_url: https://usegalaxy.org # Use for rendering tool/workflow URLs. Trailing '/' will be removed.
+subdomain: proteomics
+root_domain: usegalaxy.org
+# feedback_email: help@mygalaxy.org # Set to enable feedback form
+
+# Custom content relative to this file URL
+header_logo: static/logo.png
+custom_css: static/custom.css
+intro_md: templates/intro.html
+conclusion_md: templates/conclusion.html
+footer_md: templates/footer.html
+
+# Data (Tools, Workflows etc.) to be rendered into sections/tabs/accordion elements.
+# Either:
+# 1. Relative to this file URL
+# 2. Full URL to fetch content from a different remote location
+sections:
+ - sections/data.yml
+ - sections/conversion_modification.yml
+ - sections/database_searching.yml
+ - sections/dda_standardised_tools.yml
+ - sections/dia_standardised_tools.yml
+ - sections/dda_tmt.yml
+
+# Histories listed here will be shown in a table
+# An empty list will remove this feature from the page
+shared_histories:
+ - url: https://usegalaxy.org.au/u/mike/h/lfq-and-tmt
+ label_html: >
+ Demo data for LFQanalyst and TMTanalyst.
+ - url: https://usegalaxy.org.au/u/johan/h/maxquant-and-msstats-for-the-analysis-of-label-free-data-1
+ label_html: >
+ Example data provided for the "MaxQuant and MSstats for the analysis of
+ label-free data" Galaxy Training Network (GTN) tutorial, which is available
+ here.
diff --git a/communities/proteomics/lab/sections/conversion_modification.yml b/communities/proteomics/lab/sections/conversion_modification.yml
new file mode 100644
index 00000000..6a074920
--- /dev/null
+++ b/communities/proteomics/lab/sections/conversion_modification.yml
@@ -0,0 +1,49 @@
+id: conversion_modification
+title: MS file conversion
+tabs:
+ - id: tools
+ title: Tools
+ heading_md: >
+ Some example tools are listed here: you can also search for more in the full tool panel to the left.
+ content:
+ - title_md: "msconvert"
+ description_md: >
+
+ Convert and/or filter mass spectrometry files.
+
+ inputs:
+ - datatypes:
+ - thermo.raw
+ label: Thermo RAW file
+ button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/thermo_raw_file_converter/thermo_raw_file_converter/"
+ # - id: help
+ # title: Help
+ # content: []
diff --git a/communities/proteomics/lab/sections/data.yml b/communities/proteomics/lab/sections/data.yml
new file mode 100644
index 00000000..b162e648
--- /dev/null
+++ b/communities/proteomics/lab/sections/data.yml
@@ -0,0 +1,55 @@
+id: data
+title: Data import
+tabs:
+ - id: tools
+ title: Tools
+ heading_md: "Some example tools are listed here: you can also search for more in the full tool panel to the left."
+ content:
+ - title_md: "Import data to Galaxy"
+ description_md: "
Standard upload of data to Galaxy, from your computer or from the web.
"
+ button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=upload1"
+ - id: help
+ title: Help
+ content:
+ - title_md: "Can I upload sensitive data?"
+ description_md: |
+
+ No, do not upload personal or sensitive, such as human health or clinical data.
+ Please see our
+ Data Privacy
+ page for definitions of sensitive and health-related information.
+
+
+ Please also make sure you have read our
+ Terms of Service,
+ which covers hosting and analysis of research data.
+
+ - title_md: "Is my data private?"
+ description_md: |
+
+ Please read our
+ Privacy Policy
+ for information on your personal data and any data that you upload.
+
+ - title_md: "How can I increase my storage quota?"
+ description_md: |
+
+ Please submit a quota request if your Galaxy Australia account reaches its data storage limit. Requests are usually provisioned quickly if you provide a reasonable use case for your request.
+
+ button_link: "/request/quota"
+ button_md: "Request"
+ - title_md: "Tutorial: Introduction to proteomics, protein identification, quantification and statistical modelling"
+ description_md: |
+
+ This practical aims to familiarize you with Galaxy for Proteomics, including theory, methods and software examples.
+
+ Any user of Galaxy Australia can request support through an
+ online form.
+
+ button_link: "/request/support"
+ button_md: "Request support"
diff --git a/communities/proteomics/lab/sections/database_searching.yml b/communities/proteomics/lab/sections/database_searching.yml
new file mode 100644
index 00000000..fb36ab0c
--- /dev/null
+++ b/communities/proteomics/lab/sections/database_searching.yml
@@ -0,0 +1,78 @@
+id: database_searching
+title: Database searching
+tabs:
+ - id: tools
+ title: Tools
+ heading_md: >
+ Some example tools are listed here: you can also search for more in the full tool panel to the left.
+ content:
+ - title_md: "DecoyDatabase"
+ description_md: >
+
+ Create decoy sequence database from forward sequence database.
+
+ inputs:
+ - datatypes:
+ - fasta
+ label: Input FASTA file(s), each containing a database
+ button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decoydatabase/DecoyDatabase/"
+ - title_md: "MaxQuant"
+ description_md: >
+
+ MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.
+
+ Database search algorithm for high-resolution tandem mass spectra.
+
+ inputs:
+ - datatypes:
+ - mzML
+ label: Indexed mzML
+ - datatypes:
+ - fasta
+ - uniprotxml
+ label: "MS Protein Search Database: UniProt Xml or Fasta"
+ button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/morpheus/morpheus/"
+ - id: help
+ title: Help
+ content:
+ - title_md: "Introduction to proteomics, protein identification, quantification and statistical modelling"
+ description_md: >
+
+ Start here if you are new to proteomic analysis in Galaxy.
+
+ button_link: "https://usegalaxy.org.au/training-material/topics/proteomics/tutorials/introduction/slides.html"
+ button_md: "Tutorial"
+ - title_md: "Label-free data analysis using MaxQuant"
+ description_md: >
+
+ Learn how to use MaxQuant for the analysis of label-free shotgun (DDA) data.
+
+ button_link: "https://proteomics.usegalaxy.org.au/training-material/topics/proteomics/tutorials/maxquant-label-free/tutorial.html"
+ button_md: "Tutorial"
+ - title_md: "Peptide and Protein ID using OpenMS tools"
+ description_md: >
+
+ Learn how to identify proteins from LC-MS/MS raw files.
+
+ Any user of Galaxy Australia can request support through an online form.
+
+ button_link: "/request/support"
+ button_md: "Request support"
\ No newline at end of file
diff --git a/communities/proteomics/lab/sections/dda_standardised_tools.yml b/communities/proteomics/lab/sections/dda_standardised_tools.yml
new file mode 100644
index 00000000..d66139c7
--- /dev/null
+++ b/communities/proteomics/lab/sections/dda_standardised_tools.yml
@@ -0,0 +1,71 @@
+id: dda_standardised_tools
+title: DDA Standardised Tools
+tabs:
+ - id: tools
+ title: Tools
+ heading_md: >
+ Some example tools are listed here: you can also search for more in the full tool panel to the left.
+ content:
+ - title_md: "MaxQuant"
+ description_md: >
+
+ MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.
+
+ Any user of Galaxy Australia can request support through an online form.
+
+ button_link: "/request/support"
+ button_md: "Request support"
diff --git a/communities/proteomics/lab/sections/dda_tmt.yml b/communities/proteomics/lab/sections/dda_tmt.yml
new file mode 100644
index 00000000..ae8bd0b8
--- /dev/null
+++ b/communities/proteomics/lab/sections/dda_tmt.yml
@@ -0,0 +1,60 @@
+id: dda_tmt
+title: DDA TMT
+tabs:
+ - id: tools
+ title: Tools
+ heading_md: >
+ Some example tools are listed here: you can also search for more in the full tool panel to the left.
+ content:
+ - title_md: "MaxQuant"
+ description_md: >
+
+ MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.
+
+ Any user of Galaxy Australia can request support through an online form.
+
+ button_link: "/request/support"
+ button_md: "Request support"
diff --git a/communities/proteomics/lab/sections/dia_standardised_tools.yml b/communities/proteomics/lab/sections/dia_standardised_tools.yml
new file mode 100644
index 00000000..825e07f5
--- /dev/null
+++ b/communities/proteomics/lab/sections/dia_standardised_tools.yml
@@ -0,0 +1,43 @@
+id: dia_standardised_tools
+title: DIA Standardised Tools
+tabs:
+ - id: tools
+ title: Tools
+ heading_md: >
+ Some example tools are listed here: you can also search for more in the full tool panel to the left.
+ content:
+ - title_md: "MSstats"
+ description_md: >
+
+ Statistical relative protein significance analysis in DDA, SRM and DIA Mass Spectrometry.
+
+ inputs:
+ - datatypes:
+ - tabular
+ - csv
+ label: Either the 10-column MSstats format or the outputs of spectral processing tools such as MaxQuant, OpenSWATH.
+ button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/"
+ - id: help
+ title: Help
+ content:
+ - title_md: "Galaxy Australia support"
+ description_md: >
+
+ Any user of Galaxy Australia can request support through an online form.
+
+ Learn how to analyse HEK-Ecoli spike-in DIA data in Galaxy, understand DIA data principles and characteristics, and use OpenSwathworkflow to analyze HEK-Ecoli spike-in DIA data.
+
+ button_link: "https://usegalaxy.org.au/training-material/topics/proteomics/tutorials/DIA_Analysis_OSW/tutorial.html"
+ button_md: "Tutorial"
+ - title_md: "Library Generation for DIA Analysis"
+ description_md: >
+
+ Learn how to generate a spectral library from data dependent acquisition (DDA) MS data, understand DIA data principles and characteristics, and optimize and refine a spectral library for the analysis of DIA data.
+
+ Welcome to the {{ site_name }} {{ lab_name }}. Get quick access to the
+ tools, workflows and tutorials you need to get started with proteomics on
+ Galaxy.
+
+ The Galaxy {{ site_name }} {{ lab_name }} is your one-stop-shop for everything proteomics! From proteomics data conversion, database searching, identification, quantitation, all the way to visualisation.
+
+
+
+ This site provides a "skin" over Galaxy {{ site_name }}, pointing you towards useful tools, workflows and resources for proteomics. The underlying Galaxy server is identical to
+ {{ root_domain }}.
+ You can run all the same tools. Your jobs go into the same history. Your data is shared and uses the same quota.
+
+
+
+ If you feel restricted by the Proteomics tool panel, you can quickly switch back to the full tool panel using the dropdown at the top of the tool panel.
+
+
+
+ Switching between the "Base site"
+ ({{ root_domain }})
+ and {{ lab_name }}
+ ({{ subdomain }}.{{ root_domain }})
+ is easy - look for the icon in the top navigation bar to switch between sites:
+
+
+
+ {% if site_name == 'Australia' %}
+
+ Please note: unfortunately, AAF login is not configured for Galaxy Labs, but we are working on fixing this.
+
+ This set of proteomics-specific shared histories contain test or demo data for software available on {{ lab_name }}. You can copy these histories directly to your account on Galaxy, making it faster to get started!
+
diff --git a/communities/proteomics/lab/usegalaxy.org.au.yml b/communities/proteomics/lab/usegalaxy.org.au.yml
new file mode 100644
index 00000000..d6922c65
--- /dev/null
+++ b/communities/proteomics/lab/usegalaxy.org.au.yml
@@ -0,0 +1,32 @@
+# This content extends base.yml
+
+# Request this on site.usegalaxy.org.au with:
+# https://site.usegalaxy.org.au/lab/export?content_root=https://github.com/galaxyproject/galaxy_codex/blob/main/subdomains/proteomics/usegalaxy.org.au.yml
+
+# Check out the documentation for building exported labs:
+# https://site.usegalaxy.org.au/lab/export
+
+# Use these variables in HTML templates like:
+# "Welcome to the Galaxy {{ site_name }} {{ lab_name }}"
+# To make the content more generic and reusable across sites
+site_name: Australia
+lab_name: Proteomics Lab
+nationality: Australian
+galaxy_base_url: https://proteomics.usegalaxy.org.au # Use for rendering tool/workflow URLs. Trailing '/' will be removed.
+subdomain: proteomics
+root_domain: usegalaxy.org.au
+feedback_email: help@genome.edu.au
+
+# Custom content relative to this file URL
+conclusion_md: usegalaxy.org.au/templates/conclusion.html
+footer_md: usegalaxy.org.au/templates/footer.html
+
+shared_histories:
+ - url: https://usegalaxy.org.au/u/mike/h/lfq-and-tmt
+ label_html: >
+ Demo data for LFQanalyst and TMTanalyst.
+ - url: https://usegalaxy.org.au/u/johan/h/maxquant-and-msstats-for-the-analysis-of-label-free-data-1
+ label_html: >
+ Example data provided for the "MaxQuant and MSstats for the analysis of
+ label-free data" Galaxy Training Network (GTN) tutorial, which is available
+ here.
\ No newline at end of file
diff --git a/communities/proteomics/lab/usegalaxy.org.au/templates/conclusion.html b/communities/proteomics/lab/usegalaxy.org.au/templates/conclusion.html
new file mode 100644
index 00000000..c097223b
--- /dev/null
+++ b/communities/proteomics/lab/usegalaxy.org.au/templates/conclusion.html
@@ -0,0 +1 @@
+{% include 'home/snippets/header-cards.html' %}
diff --git a/communities/proteomics/lab/usegalaxy.org.au/templates/footer.html b/communities/proteomics/lab/usegalaxy.org.au/templates/footer.html
new file mode 100644
index 00000000..259d18e6
--- /dev/null
+++ b/communities/proteomics/lab/usegalaxy.org.au/templates/footer.html
@@ -0,0 +1,9 @@
+
+
diff --git a/communities/spoc/subdomain/CONTRIBUTORS b/communities/spoc/lab/CONTRIBUTORS
similarity index 100%
rename from communities/spoc/subdomain/CONTRIBUTORS
rename to communities/spoc/lab/CONTRIBUTORS
diff --git a/communities/spoc/subdomain/LICENSE b/communities/spoc/lab/LICENSE
similarity index 100%
rename from communities/spoc/subdomain/LICENSE
rename to communities/spoc/lab/LICENSE
diff --git a/communities/spoc/lab/README.md b/communities/spoc/lab/README.md
new file mode 100644
index 00000000..a067b8eb
--- /dev/null
+++ b/communities/spoc/lab/README.md
@@ -0,0 +1,13 @@
+# Single Cell Lab
+
+This Galaxy Lab was developed by Wendi Bacon (@nomadscientist) and Cameron Hyde
+(@neoformit).
+
+Render this Galaxy Lab webpage:
+
+https://labs.usegalaxy.org.au/?content_root=https://raw.githubusercontent.com/galaxyproject/galaxy_codex/refs/heads/main/communities/spoc/lab/base.yml
+
+
+Render the EU version of Galaxy Lab webpage:
+
+https://labs.usegalaxy.org.au/?content_root=https://raw.githubusercontent.com/galaxyproject/galaxy_codex/refs/heads/main/communities/spoc/lab/usegalaxy.eu.yml
diff --git a/communities/spoc/subdomain/base.yml b/communities/spoc/lab/base.yml
similarity index 97%
rename from communities/spoc/subdomain/base.yml
rename to communities/spoc/lab/base.yml
index cb34d2c6..8fd77d1b 100644
--- a/communities/spoc/subdomain/base.yml
+++ b/communities/spoc/lab/base.yml
@@ -59,7 +59,7 @@ footer_md: templates/footer.html
# Data (Tools, Workflows etc.) to be rendered into sections/tabs/accordion elements.
# Either:
# 1. Relative to this file URL
-# 2. Full URL to fetch globally centralized content
+# 2. Full URL to fetch content from a different remote location
sections:
- sections/1_beginner.yml
- sections/3_advanced.yml
diff --git a/communities/spoc/subdomain/sections/1_beginner.yml b/communities/spoc/lab/sections/1_beginner.yml
similarity index 100%
rename from communities/spoc/subdomain/sections/1_beginner.yml
rename to communities/spoc/lab/sections/1_beginner.yml
diff --git a/communities/spoc/subdomain/sections/2_intermediate.yml b/communities/spoc/lab/sections/2_intermediate.yml
similarity index 100%
rename from communities/spoc/subdomain/sections/2_intermediate.yml
rename to communities/spoc/lab/sections/2_intermediate.yml
diff --git a/communities/spoc/subdomain/sections/3_advanced.yml b/communities/spoc/lab/sections/3_advanced.yml
similarity index 100%
rename from communities/spoc/subdomain/sections/3_advanced.yml
rename to communities/spoc/lab/sections/3_advanced.yml
diff --git a/communities/spoc/subdomain/sections/4_community.yml b/communities/spoc/lab/sections/4_community.yml
similarity index 100%
rename from communities/spoc/subdomain/sections/4_community.yml
rename to communities/spoc/lab/sections/4_community.yml
diff --git a/communities/spoc/lab/static/custom.css b/communities/spoc/lab/static/custom.css
new file mode 100644
index 00000000..e69de29b
diff --git a/communities/spoc/subdomain/static/logo_single_cell.svg b/communities/spoc/lab/static/logo_single_cell.svg
similarity index 100%
rename from communities/spoc/subdomain/static/logo_single_cell.svg
rename to communities/spoc/lab/static/logo_single_cell.svg
diff --git a/communities/spoc/subdomain/templates/conclusion.html b/communities/spoc/lab/templates/conclusion.html
similarity index 85%
rename from communities/spoc/subdomain/templates/conclusion.html
rename to communities/spoc/lab/templates/conclusion.html
index b751908f..486a59f8 100644
--- a/communities/spoc/subdomain/templates/conclusion.html
+++ b/communities/spoc/lab/templates/conclusion.html
@@ -18,10 +18,10 @@
News and Events
-
+
-
+
diff --git a/communities/spoc/lab/templates/footer.html b/communities/spoc/lab/templates/footer.html
new file mode 100644
index 00000000..e69de29b
diff --git a/communities/spoc/subdomain/templates/intro.html b/communities/spoc/lab/templates/intro.html
similarity index 100%
rename from communities/spoc/subdomain/templates/intro.html
rename to communities/spoc/lab/templates/intro.html
diff --git a/communities/spoc/subdomain/tool_panel/hca-scanpy.yml b/communities/spoc/lab/tool_panel/hca-scanpy.yml
similarity index 100%
rename from communities/spoc/subdomain/tool_panel/hca-scanpy.yml
rename to communities/spoc/lab/tool_panel/hca-scanpy.yml
diff --git a/communities/spoc/subdomain/tool_panel/hca-scanpy.yml.lock b/communities/spoc/lab/tool_panel/hca-scanpy.yml.lock
similarity index 100%
rename from communities/spoc/subdomain/tool_panel/hca-scanpy.yml.lock
rename to communities/spoc/lab/tool_panel/hca-scanpy.yml.lock
diff --git a/communities/spoc/subdomain/tool_panel/hicexplorer.yml b/communities/spoc/lab/tool_panel/hicexplorer.yml
similarity index 100%
rename from communities/spoc/subdomain/tool_panel/hicexplorer.yml
rename to communities/spoc/lab/tool_panel/hicexplorer.yml
diff --git a/communities/spoc/subdomain/tool_panel/hicexplorer.yml.lock b/communities/spoc/lab/tool_panel/hicexplorer.yml.lock
similarity index 100%
rename from communities/spoc/subdomain/tool_panel/hicexplorer.yml.lock
rename to communities/spoc/lab/tool_panel/hicexplorer.yml.lock
diff --git a/communities/spoc/subdomain/tool_panel/import.yml b/communities/spoc/lab/tool_panel/import.yml
similarity index 100%
rename from communities/spoc/subdomain/tool_panel/import.yml
rename to communities/spoc/lab/tool_panel/import.yml
diff --git a/communities/spoc/subdomain/tool_panel/import.yml.lock b/communities/spoc/lab/tool_panel/import.yml.lock
similarity index 100%
rename from communities/spoc/subdomain/tool_panel/import.yml.lock
rename to communities/spoc/lab/tool_panel/import.yml.lock
diff --git a/communities/spoc/subdomain/tool_panel/multiomics.yml b/communities/spoc/lab/tool_panel/multiomics.yml
similarity index 100%
rename from communities/spoc/subdomain/tool_panel/multiomics.yml
rename to communities/spoc/lab/tool_panel/multiomics.yml
diff --git a/communities/spoc/subdomain/tool_panel/multiomics.yml.lock b/communities/spoc/lab/tool_panel/multiomics.yml.lock
similarity index 100%
rename from communities/spoc/subdomain/tool_panel/multiomics.yml.lock
rename to communities/spoc/lab/tool_panel/multiomics.yml.lock
diff --git a/communities/spoc/subdomain/tool_panel/sccaf.yml b/communities/spoc/lab/tool_panel/sccaf.yml
similarity index 100%
rename from communities/spoc/subdomain/tool_panel/sccaf.yml
rename to communities/spoc/lab/tool_panel/sccaf.yml
diff --git a/communities/spoc/subdomain/tool_panel/sccaf.yml.lock b/communities/spoc/lab/tool_panel/sccaf.yml.lock
similarity index 100%
rename from communities/spoc/subdomain/tool_panel/sccaf.yml.lock
rename to communities/spoc/lab/tool_panel/sccaf.yml.lock
diff --git a/communities/spoc/subdomain/tool_panel/seurat.yml b/communities/spoc/lab/tool_panel/seurat.yml
similarity index 100%
rename from communities/spoc/subdomain/tool_panel/seurat.yml
rename to communities/spoc/lab/tool_panel/seurat.yml
diff --git a/communities/spoc/subdomain/tool_panel/seurat.yml.lock b/communities/spoc/lab/tool_panel/seurat.yml.lock
similarity index 100%
rename from communities/spoc/subdomain/tool_panel/seurat.yml.lock
rename to communities/spoc/lab/tool_panel/seurat.yml.lock
diff --git a/communities/spoc/subdomain/tool_panel/single_cell.yml b/communities/spoc/lab/tool_panel/single_cell.yml
similarity index 100%
rename from communities/spoc/subdomain/tool_panel/single_cell.yml
rename to communities/spoc/lab/tool_panel/single_cell.yml
diff --git a/communities/spoc/subdomain/tool_panel/single_cell.yml.lock b/communities/spoc/lab/tool_panel/single_cell.yml.lock
similarity index 100%
rename from communities/spoc/subdomain/tool_panel/single_cell.yml.lock
rename to communities/spoc/lab/tool_panel/single_cell.yml.lock
diff --git a/communities/spoc/subdomain/tool_panel/spatial.yml b/communities/spoc/lab/tool_panel/spatial.yml
similarity index 100%
rename from communities/spoc/subdomain/tool_panel/spatial.yml
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similarity index 100%
rename from communities/spoc/subdomain/tool_panel/spatial.yml.lock
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diff --git a/communities/spoc/subdomain/tool_panel/tool_panel_view.yml b/communities/spoc/lab/tool_panel/tool_panel_view.yml
similarity index 100%
rename from communities/spoc/subdomain/tool_panel/tool_panel_view.yml
rename to communities/spoc/lab/tool_panel/tool_panel_view.yml
diff --git a/communities/spoc/subdomain/tool_panel/usegalaxy.org.au.yml b/communities/spoc/lab/tool_panel/usegalaxy.org.au.yml
similarity index 100%
rename from communities/spoc/subdomain/tool_panel/usegalaxy.org.au.yml
rename to communities/spoc/lab/tool_panel/usegalaxy.org.au.yml
diff --git a/communities/spoc/subdomain/usegalaxy.eu.yml b/communities/spoc/lab/usegalaxy.eu.yml
similarity index 100%
rename from communities/spoc/subdomain/usegalaxy.eu.yml
rename to communities/spoc/lab/usegalaxy.eu.yml
diff --git a/communities/spoc/subdomain/usegalaxy.eu/static/custom.css b/communities/spoc/lab/usegalaxy.eu/static/custom.css
similarity index 100%
rename from communities/spoc/subdomain/usegalaxy.eu/static/custom.css
rename to communities/spoc/lab/usegalaxy.eu/static/custom.css
diff --git a/communities/spoc/subdomain/usegalaxy.eu/templates/footer.html b/communities/spoc/lab/usegalaxy.eu/templates/footer.html
similarity index 100%
rename from communities/spoc/subdomain/usegalaxy.eu/templates/footer.html
rename to communities/spoc/lab/usegalaxy.eu/templates/footer.html
diff --git a/communities/spoc/subdomain/usegalaxy.org.au.yml b/communities/spoc/lab/usegalaxy.org.au.yml
similarity index 100%
rename from communities/spoc/subdomain/usegalaxy.org.au.yml
rename to communities/spoc/lab/usegalaxy.org.au.yml
diff --git a/communities/spoc/subdomain/usegalaxy.org.au/templates/footer.html b/communities/spoc/lab/usegalaxy.org.au/templates/footer.html
similarity index 100%
rename from communities/spoc/subdomain/usegalaxy.org.au/templates/footer.html
rename to communities/spoc/lab/usegalaxy.org.au/templates/footer.html
diff --git a/communities/spoc/subdomain/usegalaxy.org.yml b/communities/spoc/lab/usegalaxy.org.yml
similarity index 100%
rename from communities/spoc/subdomain/usegalaxy.org.yml
rename to communities/spoc/lab/usegalaxy.org.yml
diff --git a/communities/spoc/subdomain/README.md b/communities/spoc/subdomain/README.md
deleted file mode 100644
index 0c71ba4d..00000000
--- a/communities/spoc/subdomain/README.md
+++ /dev/null
@@ -1,2 +0,0 @@
-# Lab_testing
-Testing of configurations of Galaxy Lab yamls
+ 
+ 
+ 
+