Proteomics: database handling

proteomics-database-handling/wf-database-handling

Author(s)

Version
5
Last updated
Nov 1, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
proteomics

Features
Tutorial
Protein FASTA Database Handling
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00153
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["Protein Database Downloader"];
  1["Protein Database Downloader"];
  2["FASTA-to-Tabular"];
  0 -->|output_database| 2;
  3["Add column"];
  2 -->|output| 3;
  4["Tabular-to-FASTA"];
  3 -->|out_file1| 4;
  5["FASTA Merge Files and Filter Unique Sequences"];
  4 -->|output| 5;
  1 -->|output_database| 5;
  6["DecoyDatabase"];
  5 -->|output| 6;

Inputs

Input Label

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1 Protein Database Downloader
toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.1 Protein Database Downloader
toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 FASTA-to-Tabular
addValue Add column
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 Tabular-to-FASTA
toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0 FASTA Merge Files and Filter Unique Sequences
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decoydatabase/DecoyDatabase/2.6+galaxy0 DecoyDatabase

Tools

Tool Links
addValue
toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 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/galaxyp/dbbuilder/dbbuilder/0.3.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decoydatabase/DecoyDatabase/2.6+galaxy0 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 Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on 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
6 54b4d9fcc 2020-11-01 09:56:40 Adding tags to workflows
5 ca84d7395 2020-10-31 20:41:54 Updating Tutorials to OpenMS 2.6, adjusting of parameters and tools, adding tool versions
4 667ff3de9 2020-01-22 10:59:29 annotation
3 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
2 7da80b341 2020-01-10 14:56:15 Workflows fix
1 2c1271b67 2017-05-23 13:07:42 Restructure proteomics

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/database-handling/workflows/wf_database-handling.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