https://github.com/naturalis/galaxy-tool-taxonmatcher

Find for your input taxonomy the taxonomy from an other database
https://github.com/naturalis/galaxy-tool-taxonmatcher

Last synced: about 2 months ago
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Find for your input taxonomy the taxonomy from an other database

• Host: GitHub
• URL: https://github.com/naturalis/galaxy-tool-taxonmatcher
• Owner: naturalis
• Created: 2018-09-20T12:44:45.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2024-01-31T13:18:50.000Z (11 months ago)
• Last Synced: 2024-08-04T03:11:08.178Z (5 months ago)
• Language: Python
• Size: 45.9 KB
• Stars: 3
• Watchers: 12
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

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README

        
# galaxy-tool-taxonmatcher

Find for your input taxonomy the taxonomy from an other database, currently GBIF and The Dutch species register.  

## Installation

### Manual

Clone this repo in your Galaxy ***Tools*** directory:  

`git clone https://github.com/naturalis/galaxy-tool-taxonmatcher`  

Make the python script executable:  

`chmod 755 galaxy-tool-taxonmatcher/taxonmatcher.sh`  

`chmod 755 galaxy-tool-taxonmatcher/taxonmatcher.py` 

Append the file ***tool_conf.xml***:    

``  

### Ansible

Depending on your setup the [ansible.builtin.git](https://docs.ansible.com/ansible/latest/collections/ansible/builtin/git_module.html) module could be used.  

[Install the tool](https://docs.ansible.com/ansible/latest/collections/ansible/builtin/git_module.html#examples) 

by including the following in your dedicated ***.yml** file:  

`  - repo: https://github.com/naturalis/galaxy-tool-taxonmatcher`  

  `file: taxonmatcher.xml`  

  `version: master`  

### Note

The instructions above assume python3 and gcc compiler are installed.  

## Create reference databases  

The steps below shoud be executed from the galaxy-tool-taxonmatcher folder  

in your Galaxy ***Tools*** directory.  

### Creating the reference database for GBIF

Download the taxonomy backbone  

`wget https://hosted-datasets.gbif.org/datasets/backbone/current/backbone.zip`  

unzip  

`unzip -p backbone.zip Taxon.tsv > Taxon.tsv`  

Taxon.tsv should be in path/to/galaxy-tool-taxonmatcher/  

Create the database (currently the path to Taxon.tsv is hardcoded)  

`python3 utilities/make_gbif_database.py`  

The output file is **gbif_taxonmatcher**  

### Creating the reference database for The Dutch species register  

Download the taxonomy backbone  

`wget http://api.biodiversitydata.nl/v2/taxon/dwca/getDataSet/nsr`  

unzip  

`unzip -p nsr Taxa.txt > Taxa.txt`  

Taxa.txt should be in path/to/galaxy-tool-taxonmatcher/  

Create the database (currently the path to Taxon.txt is hardcoded)  

`python3 utilities/make_nsr_database.py`  

The output file is **nsr_taxonmatcher**  

### Specify database file location  

Move the database files (gbif_taxonmatcher and nsr_taxonmatcher) to the desired location  

(in our case: /data/blast_databases/taxonomy/). Make sure the path in **taxonmatcher.sh**  

corresponds to this location.