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Galaxy toolshed installation of the tool

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asmariyaz23 edited this page Jul 18, 2018 · 6 revisions
  1. Git clone Galaxy by following instructions here.
  2. cd </path/to/galaxy>
  3. Configure Galaxy (config/galaxy.yml) with settings below:
    1. admin_users:
    2. conda_prefix: </valid/path/>
    3. conda_auto_install: true
    4. conda_auto_init: true
  4. Run Galaxy: sh run.sh
  5. Register and login with your admin email id used in config/galaxy.yml as below: Register
  6. Go to the Admin tab on the top panel
  7. Select Install new tools and select Galaxy Tool Shed New_tools
  8. Search for ctat_metagenomics and install it install
  9. Similarly install ctat_centrifuge_indexes_data_manager install_dm
  10. Next download to ctat_metagenomics data resource on your server/machine, click on Local Data (under Admin Tab). Under Data Manager Tools select CTAT metagenomics annotations Data Manager and fill the form as below (this may take a while): dm
  11. If install and download was a success then upload fasta/fastq files using the Get Data tool. Some test data is available here.
  12. Run the ctat-metagenomics tool, leave all settings to default and select required genome.

Kim, D., Song, L., Breitwieser, F. P., & Salzberg, S. L. (2016). Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Research, 26(12), 1721–1729. https://doi.org/10.1101/gr.210641.116

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