ggd uninstall

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ggd uninstall is used to uninstall ggd package(s) from your local conda environment that has been installed by ggd. It ensures a correct uninstall of the data package along with removal of additional files created during installation.

Note

Running conda uninstall <package> will work, however, it will only uninstall the package and will not provide file and system management. Please use ggd uninstall <package> when uninstalling a ggd data package.

Using ggd uninstall

Use ggd uninstall to uninstall a ggd data package previously installed using ggd install. Running ggd uninstall -h will give you the following message:

Uninstall arguments:

ggd uninstall	Use ggd to uninstall a ggd data package installed in the current conda environment
-h, --help	show this help message and exit
names	the name(s) of the ggd package(s) to uninstall
-c, --channel	(Optional) The ggd channel the desired recipe is stored in.(Default = genomics)

Additional argument explanation:

Required arguments:

• names: The names is the name or names of the ggd data package(s) to uninstall.

Optional arguments:

• -c: The -c flag represents the ggd channel. The default channel is genomics. If the data package you want to uninstall is in a different ggd channel you will need to supply the channel name using this flag.

  Note

  You need to be in the conda environment/prefix in which the data has been installed in order to uninstall it. If the data packages you are trying to uninstall is not in the current/active conda environment it will not be uninstalled, or it will uninstall the package that is in that environment which would not be the intent.

Examples

1. Failed uninstall example:

$ ggd uninstall hg19-ga

  :ggd:uninstall: Checking for installation of hg19-ga

  :ggd:uninstall: hg19-ga is not in the ggd-genomics channel

  :ggd:uninstall: Unable to find any package similar to the package entered. Use 'ggd search' or 'conda find' to identify the right package

  :ggd:uninstall: This package may not be installed on your system

2. Successful uninstall example:

$ ggd uninstall hg19-gaps-ucsc-v1

  :ggd:uninstall: Checking for installation of hg19-gaps-ucsc-v1

  :ggd:uninstall: hg19-gaps-ucsc-v1 is installed by conda on your system

  :ggd:uninstall: Uninstalling hg19-gaps-ucsc-v1
  Collecting package metadata (repodata.json): done
  Solving environment: done

  ## Package Plan ##

    environment location: <env>

    removed specs:
      - hg19-gaps-ucsc-v1


  The following packages will be REMOVED:

    hg19-gaps-ucsc-v1-1-1


  Preparing transaction: done
  Verifying transaction: done
  Executing transaction: done

  :ggd:uninstall: Removing hg19-gaps-ucsc-v1 version 1 file(s) from ggd recipe storage

  :ggd:uninstall: Deleting 9 items of hg19-gaps-ucsc-v1 version 1 from your conda root

  :ggd:env: Removing the ggd_hg19_gaps_ucsc_v1_dir environment variable

  :ggd:env: Removing the ggd_hg19_gaps_ucsc_v1_file environment variable

  :ggd:uninstall: Updating installed package list

  :ggd:uninstall: DONE