Training Sanger sequences CHD8

sequence-analysis-Manage_AB1_Sanger/training-sanger-sequences-chd8

Author(s)
Coline Royaux
version Version
1
last_modification Last updated
Jan 8, 2024
license License
MIT
galaxy-tags Tags

Features

Tutorial
hands_on Clean and manage Sanger sequences from raw files to aligned consensus
workflow Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00179
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
output
output
output
unzipped
output
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output
output
out_fasta
out_file1
unzipped
out_file1
output_discarded
output_filtered
output_filtered
output
output
default
default
output_file
output
output
output
default
output_file
output_file
output
aligned_sequences
output
output
output
out_fasta
output
out_file1
out_file1
ℹ️ Input Dataset
AOPEP_and_CHD8_sequences_20220907.zip?download=1
ℹ️ Input Dataset
Prim
Unzip
Filter FASTA
Filter FASTA
Extract element identifiers
Degap.seqs
Degap.seqs
Regex Find And Replace
Regex Find And Replace
Reverse-Complement
Filter collection
Filter collection
ab1 to FASTQ converter
ab1 to FASTQ converter
seqtk_trimfq
seqtk_trimfq
FASTQ Groomer
Sort collection
Sort collection
Reverse-Complement
seqtk_mergepe
FASTQ Groomer
FASTQ to Tabular
Tabular-to-FASTA
Align sequences
Consensus sequence from aligned FASTA
Merge.files
Merge.files
Regex Find And Replace
Align sequences
NCBI BLAST+ blastn

Inputs

Input Label
Input dataset AOPEP_and_CHD8_sequences_20220907.zip?download=1
Input dataset Prim

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0 Reverse-Complement

Tools

Tool Links
__FILTER_FROM_FILE__
__SORTLIST__
toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.5 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ecology/ab1_fastq_converter/ab1_fastq_converter/1.20.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ecology/aligned_to_consensus/aligned_to_consensus/1.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/6.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_degap_seqs/mothur_degap_seqs/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergepe/1.3.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands On: Importing a workflow
  1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on galaxy-upload Import at the top-right of the screen
  3. Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  4. Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
2 9b2a39983 2024-01-02 11:11:58 Update workflow
1 1d51e2dc3 2023-12-19 13:35:27 Move files from ecology to sequence analysis

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Training-Sanger-sequences-CHD8.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows