Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)

epigenetics-tal1-binding-site-identification/tal1-binding-site-identification-workflow

Author(s)

Version
1
Last updated
Oct 7, 2020
License
None Specified, defaults to CC-BY-4.0
Tags

epigenetics

Features

Tutorial
Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)

Workflow Testing
Tests: ✅
Results: Not yet automated

FAIRness PURL
https://gxy.io/GTN:W00071

Download Workflow RO-Crate

View on (Dev) WorkflowHub

Launch in Tutorial Mode
Download

Inputs

Input	Label
G1E_input_R1_downsampled_SRR507859.fastqsanger	G1E_input_R1_downsampled_SRR507859.fastqsanger
G1E_input_R2_downsampled_SRR507860.fastqsanger	G1E_input_R2_downsampled_SRR507860.fastqsanger
G1E_Tal1_R1_downsampled_SRR492444.fastqsanger	G1E_Tal1_R1_downsampled_SRR492444.fastqsanger
G1E_Tal1_R2_downsampled_SRR492445.fastqsanger	G1E_Tal1_R2_downsampled_SRR492445.fastqsanger
Megakaryocyte_input_R1_downsampled_SRR492453.fastqsanger	Megakaryocyte_input_R1_downsampled_SRR492453.fastqsanger
Megakaryocyte_input_R2_downsampled_SRR492454.fastqsanger	Megakaryocyte_input_R2_downsampled_SRR492454.fastqsanger
Megakaryocyte_Tal1_R1_downsampled_SRR549006.fastqsanger	Megakaryocyte_Tal1_R1_downsampled_SRR549006.fastqsanger
Megakaryocytes_Tal1_R2_downsampled_SRR549007.fastqsanger	Megakaryocytes_Tal1_R2_downsampled_SRR549007.fastqsanger
RefSeq_gene_annotations_mm10.bed	RefSeq_gene_annotations_mm10.bed

Outputs

From	Output	Label
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0	bedtools Intersect intervals
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0	bedtools Intersect intervals
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0	bedtools Intersect intervals

Tools

Tool	Links
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.3.2.0.0	View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0	View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.3.2.0.0	View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.3.2.0.0	View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.3.2.0.0	View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.2.0.1	View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4	View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1	View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3	View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0	View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6	View in ToolShed
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0	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

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

Click on galaxy-upload Import at the top-right of the screen

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”

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
5	818f00219	2020-10-06 20:46:16	Fixed JSON format.
4	473da245d	2020-10-06 20:22:32	Updated outputs in workflow and test.yml.
3	3bee4c537	2020-10-06 19:28:34	Updated inputs in workflow and test.yml.
2	e9f2fa109	2020-10-06 10:48:12	Updated workflow with tags.
1	7fe3ca36a	2020-10-05 19:06:49	Added workflow.

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/tal1-binding-site-identification/workflows/tal1-binding-site-identification-workflow.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