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Merge pull request #2689 from galaxyproject/sars-cov-2-variant-discovery
[Variant analysis] New tutorial - "Identification of allelic variants in SARS-CoV-2 from deep sequencing reads"
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‎faqs/galaxy/datasets_upload.md‎

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---
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title: Upload few files (1-10)
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area: datasets
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box_type: tip
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layout: faq
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---
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1. Click on **Upload Data** on the top of the left panel
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2. Click on **Choose local file** and select the files or drop the files in the **Drop files here** part
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3. Click on **Start**
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4. Click on **Close**

‎faqs/galaxy/datasets_upload_ftp.md‎

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---
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title: Upload many files (>10) via FTP
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area: datasets
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box_type: tip
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layout: faq
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---
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1. Make sure to have an FTP client installed
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There are many options. We can recommend [FileZilla](https://filezilla-project.org/), a free FTP client that is available on Windows, MacOS, and Linux.
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2. Establish FTP connection to the Galaxy server
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1. Provide the Galaxy server's FTP server name (e.g. `usegalaxy.org`, `ftp.usegalaxy.eu`)
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2. Provide the **username** (usually the email address) and the **password** on the Galaxy server
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3. Connect
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3. Add the files to the FTP server by dragging/dropping them or right clicking on them and uploading them
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The FTP transfer will start. We need to wait until they are done.
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4. Open the Upload menu on the Galaxy server
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5. Click on **Choose FTP file** on the bottom
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6. Select files to import into the history
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7. Click on **Start**

‎faqs/galaxy/histories_import.md‎

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---
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title: Import an history
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area: histories
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box_type: tip
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layout: faq
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---
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1. Open the link to the shared history
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2. Click on the {% icon new-history %} *Import history* button on the top right
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3. Enter a title for the new history
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4. Click on **Import**

‎faqs/galaxy/workflows_import_search.md‎

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---
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title: Importing a workflow using the search
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area: workflows
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box_type: tip
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layout: faq
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---
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- Click on *Workflow* on the top menu bar of Galaxy. You will see a list of all your workflows.
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- Click on the {% icon galaxy-upload %} **Import** icon at the top-right of the screen
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- Click on **search form** in **Import a Workflow from Configured GA4GH Tool Registry Servers (e.g. Dockstore)**
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{% if include.trs_server %}
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- Select *"TRS Server"*: `{{ include.trs_server }}`
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{% else %}
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- Select the relevant TRS Server
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{% endif %}
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{% if include.search_query %}
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- Type `{{ include.search_query }}` in the search query
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{% else %}
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- Type the query
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{% endif %}
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{% if include.workflow_name %}
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- Expand the workflow named `{{ include.workflow_name }}`
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{% else %}
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- Expand the correct workflow
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{% endif %}
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- Click on the wanted version
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The workflow will be imported in your workflows

‎topics/variant-analysis/images/sars-cov-2-variant-discovery/ncov_clades.png‎

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‎topics/variant-analysis/images/sars-cov-2-variant-discovery/schema.png‎

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‎topics/variant-analysis/images/sars-cov-2-variant-discovery/variant-frequency.svg‎

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‎topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/data-library.yaml‎

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---
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destination:
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type: library
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name: GTN - Material
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description: Galaxy Training Network Material
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synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
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items:
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- name: Variant Analysis
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description: Summary
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items:
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- name: Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data
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‎topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.bib‎

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@article{li_2010,
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journal = {Bioinformatics},
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doi = {10.1093/bioinformatics/btp698},
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number = {5},
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publisher = {Oxford University Press (OUP)},
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title = {Fast and accurate long-read alignment with Burrows–Wheeler transform},
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url = {https://doi.org/10.1093%2Fbioinformatics%2Fbtp698},
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volume = {26},
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author = {Li, Heng and Durbin, Richard},
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pages = {589--595},
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date = {2010-01},
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year = {2010},
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month = {1},
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}
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@article{li_2018,
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title={Minimap2: pairwise alignment for nucleotide sequences},
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author={Li, Heng},
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journal={Bioinformatics},
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volume={34},
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number={18},
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pages={3094--3100},
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year={2018},
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publisher={Oxford University Press}
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}
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@article{langmead_2012,
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journal = {Nature Methods},
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doi = {10.1038/nmeth.1923},
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number = {4},
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publisher = {Springer Science and Business Media LLC},
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title = {Fast gapped-read alignment with Bowtie 2},
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url = {https://doi.org/10.1038%2Fnmeth.1923},
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volume = {9},
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author = {Langmead, Ben and Salzberg, Steven L},
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pages = {357--359},
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date = {2012-03},
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year = {2012},
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month = {3},
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}
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@article{wilm_2012,
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journal = {Nucleic Acids Research},
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doi = {10.1093/nar/gks918},
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number = {22},
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publisher = {Oxford University Press (OUP)},
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title = {{LoFreq}: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets},
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url = {https://doi.org/10.1093%2Fnar%2Fgks918},
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volume = {40},
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author = {Wilm, Andreas and Aw, Pauline Poh Kim and Bertrand, Denis and Yeo, Grace Hui Ting and Ong, Swee Hoe and Wong, Chang Hua and Khor, Chiea Chuen and Petric, Rosemary and Hibberd, Martin Lloyd and Nagarajan, Niranjan},
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pages = {11189--11201},
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date = {2012-10},
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year = {2012},
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month = {10},
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}
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