Mercurial > repos > computationaltranscriptomics > glassgo

Configuration of Galaxy to run GLASSgo via Docker
=================================================

Prerequisites
-------------

1) configure Galaxy to run tools in Docker as described at https://galaxyproject.org/admin/tools/docker/.
   In addition, GLASSgo requires the current BLAST nucleotide database. For that, the `tool-data/blastdb.loc`
   has to be configured accordingly as the GLASSgo wrapper reads this information as options when laying out
   the user interface. We use Docker volumes to do so (Docker CLI option -v). For that, we add Docker volumes
   to the (id=`docker_local`) Docker destination

   `<param id="docker_volumes">$defaults,/Volumes/TC1/nt:/Volumes/TC1/nt/</param>`

   More information can be found in the ./config/job_conf.xml.sample_advanced (https://github.com/galaxyproject/galaxy/blob/release_18.09/config/job_conf.xml.sample_advanced#L378) of any Galaxy instance. Obviously, the exposed folder needs to be identical with the path specified in `tool-data/blastdb.loc`. Here the local folder `Volumes/TC1/nt` contains the BLAST database and is exposed to the Docker container. In this case, the folder is bound to the same location in the container. This allows to execute the GLASSgo call in the tool XML file directly with the selected option.

2) Install GLASSgo from the Galaxy Toolshed (https://toolshed.g2.bx.psu.edu/view/computationaltranscriptomics/glassgo).
   Afterwards, the Galaxy instance needs to be configured such that it is aware of the accession lists. This can be done either
   manually or using a custom script.

   - manually
        download the accession lists from Zenodo (https://zenodo.org/record/1320180) and add the corresponding paths to the file
        glassgo_accession_list.txt Afterwards, copy the file into the folder tool-data of Galaxy (e.g., /galaxy/tool-data/) or
   - using the script
        use the config_lookup script that downloads the lookup tables and creates glassgo_accession_list.txt in tool-data of the Galaxy instance.

Restart Galaxy.


config_lookup
-------------
We provide the source file config_lookup.py as well as a one-file bundled executable config_lookup
`
usage: config_lookup [-h] --galaxy GALAXY [--acclinks ACCLINKS --acclists ACCLISTS]

incorporate the accession lists in GLASSgo/Galaxy to enable clade-specific searches

optional arguments:
  -h, --help           show this help message and exit
  --galaxy GALAXY      (absolute) path to the root directory of the Galaxy instance
  --acclinks ACCLINKS  (absolute) path to file containing URLs to the accession lists
  --acclists ACCLISTS  (absolute) path to directory to save the accession lists to
`
author	computationaltranscriptomics
date	Thu, 16 Jan 2020 02:34:33 -0500
parents	acbcdd5b4c60
children