diff --git a/README.md b/README.md index 0c71ba4..a3cb4e9 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,3 @@ -# Lab_testing -Testing of configurations of Galaxy Lab yamls +# SIG Lab Template +Template for Galaxy Community SIGs Lab building. +Intended to be served live diff --git a/lab_test.yml b/SIG-LAB-temp.yml similarity index 79% rename from lab_test.yml rename to SIG-LAB-temp.yml index b612ccf..b554895 100644 --- a/lab_test.yml +++ b/SIG-LAB-temp.yml @@ -7,15 +7,15 @@ # 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: Wendi and Gareth take over Galaxy Labs -nationality: Australian +site_name: Galaxy CoDex +lab_name: Galaxy Community Hub - Special Interest Groups - Galaxy Lab Template +nationality: Global galaxy_base_url: https://genome.usegalaxy.org.au # Use for rendering tool/workflow URLs. Trailing '/' will be removed. -subdomain: genome +subdomain: template root_domain: usegalaxy.org.au # Custom content relative to this file URL -header_logo: static/logo_single_cell.svg +header_logo: static/your-logo-here-placeholder-symbol-vector.png custom_css: static/custom.css intro_html: templates/intro.html conclusion_html: templates/conclusion.html @@ -27,6 +27,6 @@ footer_html: templates/footer.html # 1. Relative to this file URL # 2. Full URL to fetch globally centralized content sections: - - data.yml - - count.yml - - annotation.yml + - section2.yml + - section1.yml + - section3.yml diff --git a/count.yml b/count.yml deleted file mode 100644 index 600b66d..0000000 --- a/count.yml +++ /dev/null @@ -1,358 +0,0 @@ -id: assembly -title: Count and Normalisation -tabs: - - id: tools - title: Tools - heading_html: > - Common tools are listed here, or search for more in the full tool panel to the left. - content: - - title_html: RaceID - Initial processing using RaceID - description_html: > -

- Performs filtering, normalisation, and confounder removal to generate a normalised and filtered count matrix of single-cell RNA data. -

- inputs: - - datatypes: - - count_matrix - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fraceid_filtnormconf%2Fraceid_filtnormconf%2F0.2.3+galaxy3" - - title_html: Flye - assembly with PacBio or Nanopore data - description_html: > -

- 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_html: Unicycler - assembly with Illumina, PacBio or Nanopore data - bacteria only - description_html: > -

- 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_html: Salsa - scaffold assembly with HiC data - description_html: > -

- Salsa 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: - - datatypes: - - fasta - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsalsa%2Fsalsa" - - title_html: Quast - assess genome assembly quality - description_html: > -

- 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_html: Busco - assess genome assembly quality - description_html: > -

- 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" - - - id: workflows - title: Workflows - heading_html: > - 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: Assembly with PacBio HiFi data - content: - - title_html: About these workflows - description_html: > -

- This How-to-Guide will describe the steps required to assemble your genome on the Galaxy Australia platform, using multiple workflows. -

- - title_html: BAM to FASTQ + QC v1.0 - description_html: > -

- 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_html: PacBio HiFi genome assembly using hifiasm v2.1 - description_html: > -

- 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_html: Purge duplicates from hifiasm assembly v1.0 - description_html: > -

- 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_html: Genome assessment post-assembly - description_html: > -

- 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 - - id: nanopore - title: Assembly with Nanopore data and polishing with Illumina data - content: - - title_html: About these workflows - description_html: > -

- This tutorial describes the steps required to assemble a genome on Galaxy with Nanopore and Illumina data. -

- - title_html: Flye assembly with Nanopore data - description_html: > -

- 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_html: Assembly polishing - description_html: > -

- 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_html: Assess genome quality - description_html: > -

- 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: Assembly with PacBio HiFi and HiC data - content: - - title_html: About these workflows - description_html: > -

- 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_html: Kmer profiling - description_html: > -

- 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_html: Hifi assembly and HiC phasing - description_html: > -

- 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_html: HiC scaffolding - description_html: > -

- 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_html: Decontamination - description_html: > -

- 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_html: Can I use Galaxy Australia to assemble a large genome? - description_html: > -

- 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: -

- - button_html: Request support - button_link: /request - - title_html: How can I learn about genome assembly? - description_html: > - - - title_html: Genome assembly overview - description_html: > -

- Genome assembly can be a very involved process. A typical genome assembly procedure might look like: -

- - Genome assembly flowchart -

- A graphical representation of genome assembly -

- - title_html: Which tools should I use? - description_html: > -

- 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_html: Tutorials - description_html: > -

- Find 15+ Galaxy training tutorials here. -

-

- Introduction to genome assembly and annotation (slides) -

-

- Vertebrate genome assembly pipeline (tutorial) -

-

- Nanopore and illumina genome assembly (tutorial) -

-

- Share workflows and results with workflow reports (tutorial) -

- - title_html: How can I assess the quality of my genome assembly? - description_html: > -

- 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_html: Workflow tutorial - button_link: https://australianbiocommons.github.io/how-to-guides/genome_assembly/assembly_qc - - title_html: Galaxy Australia support - description_html: > -

- Any user of Galaxy Australia can request support through an online form. -

- button_html: Request support - button_link: /request/support diff --git a/data.yml b/data.yml deleted file mode 100644 index f405000..0000000 --- a/data.yml +++ /dev/null @@ -1,110 +0,0 @@ -id: data -title: Data import and preparation -tabs: - - id: tools - title: Tools - heading_html: > - Common tools are listed here, or search for more in the full tool panel to the left. - content: - - title_html: Import data to Galaxy - description_html: > -

- Standard upload of data to Galaxy, from your computer or from the web. -

- button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=upload1" - - title_html: FastQC - sequence quality reports - description_html: > -

- Before using your sequencing data, it's important first ensure that the data quality is sufficient for your analysis. -

- inputs: - - datatypes: - - fastq - - bam - - sam - button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastqc%2Ffastqc" - - title_html: FastP - sequence quality reports, trimming & filtering - description_html: > -

- Faster run than FastQC, this tool can also trim reads and filter by quality. -

- - id: workflows - title: Workflows - heading_html: > - 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_html: Data QC - description_html: > -

- Report statistics from sequencing reads.

Tools: nanoplot fastqc multiqc -

- 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_html: Trim and filter reads - description_html: > -

- 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 - - id: help - title: Help - content: - - title_html: How can I import my Single Cell data? - description_html: > -

- 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_html: More info - button_link: https://training.galaxyproject.org/training-material/topics/galaxy-interface/ - - title_html: How can I subsample my data? - description_html: > -

- 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_html: Can I upload sensitive data? - description_html: > -

- 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_html: Is my data private? - description_html: > -

- Please read our Privacy Policy for information on your personal data and any data that you upload. -

- - title_html: How can I increase my storage quota? - description_html: > -

- 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_html: Request - button_link: /request/quota - - title_html: "Tutorial: Quality Control" - description_html: > -

- 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_html: Tutorial - button_link: https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html - - title_html: "Tutorial: introduction to Genomics and Galaxy" - description_html: > -

- 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_html: Tutorial - button_link: https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-strands/tutorial.html - - title_html: Galaxy Australia support - description_html: > -

- Any user of Galaxy Australia can request support through an online form. -

- button_html: Request support - button_link: /request/support diff --git a/section1.yml b/section1.yml new file mode 100644 index 0000000..cf80b15 --- /dev/null +++ b/section1.yml @@ -0,0 +1,50 @@ +id: section +title: 3 menu section +tabs: + - id: tools + title: Tools + heading_html: > + Common tools are listed here, or can be search for more in the full tool panel to the left. + content: + - title_html: Tool1 - tool 1 + description_html: > +

+ Text explaining tool 1. +

+ inputs: + - datatypes: + - example1 + - example2 + # button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastqc%2Ffastqc" + - title_html: Tool2 - tool 2 + description_html: > +

+ Text explaining tool 2. +

+ - id: workflows + title: Workflows + heading_html: > + 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_html: Sub-section1 + description_html: > +

+ Sub-section1.

Tools: 1st tool 2nd tool 3rd and more +

+ # 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 + + - id: help + title: Help + content: + - title_html: How can I do my analysis in Galaxy? + description_html: > +

+ You do analysis by the following X, Y and Z. +

+ button_html: More info + button_link: https://training.galaxyproject.org/training-material/topics/galaxy-interface/ + \ No newline at end of file diff --git a/section2.yml b/section2.yml new file mode 100644 index 0000000..581a015 --- /dev/null +++ b/section2.yml @@ -0,0 +1,15 @@ +id: section2 +title: Simple section +tabs: + - id: section2 + title: Simple + heading_html: > + Introduction text goes here. + content: + - title_html: Simple explanation + description_html: > +

+ This is text, button, tool link, URL or widget. +

+ + \ No newline at end of file diff --git a/annotation.yml b/section3.yml similarity index 99% rename from annotation.yml rename to section3.yml index 696df37..c928ab3 100644 --- a/annotation.yml +++ b/section3.yml @@ -1,5 +1,5 @@ id: annotation -title: Genome annotation +title: Complex section - TBD tabs: - id: tools title: Tools diff --git a/static/Evil_scientist.jpeg b/static/Evil_scientist.jpeg deleted file mode 100644 index 2d79357..0000000 Binary files a/static/Evil_scientist.jpeg and /dev/null differ diff --git a/static/annotation-overview.png b/static/annotation-overview.png deleted file mode 100644 index 0bdeaa8..0000000 Binary files a/static/annotation-overview.png and /dev/null differ diff --git a/static/assembly-overview.png b/static/assembly-overview.png deleted file mode 100644 index 61cf705..0000000 Binary files a/static/assembly-overview.png and /dev/null differ diff --git a/static/logo.png b/static/logo.png deleted file mode 100644 index ea8b9ff..0000000 Binary files a/static/logo.png and /dev/null differ diff --git a/static/logo_single_cell.svg b/static/logo_single_cell.svg deleted file mode 100644 index 43540c2..0000000 --- a/static/logo_single_cell.svg +++ /dev/null @@ -1,276 +0,0 @@ - - - - - - - - - - - - - - - - image/svg+xml - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/static/test b/static/test deleted file mode 100644 index a2eed70..0000000 --- a/static/test +++ /dev/null @@ -1 +0,0 @@ -test of "/" for folder diff --git a/static/your-logo-here-placeholder-symbol-vector.png b/static/your-logo-here-placeholder-symbol-vector.png new file mode 100644 index 0000000..24b9335 Binary files /dev/null and b/static/your-logo-here-placeholder-symbol-vector.png differ diff --git a/templates/conclusion.html b/templates/conclusion.html index f2a0c34..694620c 100644 --- a/templates/conclusion.html +++ b/templates/conclusion.html @@ -1,5 +1,5 @@
-

What's happening in {{ nationality }} Single Cell and Spatial Omics research?

+

What's happening in {{ nationality }} my Special Interest Group?



-

What do you think of the {{ site_name }}?

+

What do you think of the Site Name - eg: {{ site_name }}?