ggd list

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The ggd list command is used to list the installed ggd data packages in a specific conda environment. This command is similar to conda list, but is specific for ggd data packages.

Using ggd list

Use ggd list to list ggd data package installed in the current or specific conda environment. Running ggd list -h will give you the following message:

List arguments:

ggd list	Get a list of ggd data packages installed in the current or specified conda prefix/environment.
-h, --help	show this help message and exit
-p, --pattern	(Optional) pattern to match the name of the ggd data package.
--prefix	(Optional) The name or the full directory path to a conda environment where a ggd recipe is stored. (Only needed if listing data files not in the current environment)

Additional argument explanation:

Optional arguments:

• -p: The -p flag is used to list a specific installed data package. If -p is not used, all installed data packages will be displayed.

• –prefix: --prefix flag is used to list the installed data packages for a specific conda environment/prefix. If not set the data packages for the current environment will be listed

Examples

1. List all installed data packages:

$ ggd list

  # Packages in environment: <env>
  #
  ------------------------------------------------------------------------------------------------------------------------
      Name                                Pkg-Version Pkg-Build   Channel         Environment-Variables
  ------------------------------------------------------------------------------------------------------------------------
  -> grch37-haploinsufficient-genes-clingen-v1    1         1   ggd-genomics     $ggd_grch37_haploinsufficient_genes_clingen_v1_dir

  -> hg19-chromsizes-ggd-v1                       1         1    ggd-genomics    $ggd_hg19_chromsizes_ggd_v1_dir, $ggd_hg19_chromsizes_ggd_v1_file

  -> hg19-gaps-ucsc-v1                            1         1    ggd-genomics    $ggd_hg19_gaps_ucsc_v1_dir, $ggd_hg19_gaps_ucsc_v1_file

  ...

  # To use the environment variables run `source activate base`
  # You can see the available ggd data package environment variables by running `ggd show-env`

2. List a specific installed data package using a pattern:

$ ggd list -p chromsizes

  # Packages in environment: <env>
  #
  ------------------------------------------------------------------------------------------------------------------------
      Name                                Pkg-Version Pkg-Build   Channel         Environment-Variables
  ------------------------------------------------------------------------------------------------------------------------
  -> hg19-chromsizes-ggd-v1                      1         1   ggd-genomics $ggd_hg19_chromsizes_ggd_v1_dir, $ggd_hg19_chromsizes_ggd_v1_file

  # To use the environment variables run `source activate base`
  # You can see the available ggd data package environment variables by running `ggd show-env`

3. List installed packages in a different prefix:

$ ggd list --prefix data

  # Packages in environment: <data environment>
  #
  ------------------------------------------------------------------------------------------------------------------------
      Name                                Pkg-Version Pkg-Build   Channel         Environment-Variables
  ------------------------------------------------------------------------------------------------------------------------
  -> grch37-chromsizes-ggd-v1                    1         1   ggd-genomics        $ggd_grch37_chromsizes_ggd_v1_dir, $ggd_grch37_chromsizes_ggd_v1_file

  -> grch37-eiee-genes-ostrander-v1              1         1   ggd-genomics        $ggd_grch37_eiee_genes_ostrander_v1_dir

  -> grch37-microsatellites-ucsc-v1              1         1   ggd-genomics        $ggd_grch37_microsatellites_ucsc_v1_dir, $ggd_grch37_microsatellites_ucsc_v1_file

  ...

  # The environment variables are only available when you are using the '<data environment>' conda environment.