ggd install

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ggd install is used to install a ggd package from the Anaconda cloud. ggd install determines your file system and ensures a proper install. If the package fails to install for some reason it will clean up the failed install.

ggd provide functionality to install multiple packages at the same time by appending data package names as positional arguments during the install command, and/or using the --file flag.

ggd also provides functionality to install and use data packages into a different conda environment then the one you are currently in using the --prefix flag.

Examples are available at the bottom of this page that highlight the functionality of ggd install

Note

Running conda install <package> will NOT work!! There are specific steps that GGD takes in order to install a data package that conda does not. Please use ggd install <package> when installing a ggd data package.

Using ggd install

Use ggd install to install a data package hosted by ggd. Running ggd install -h will give you the following message:

Install arguments:

ggd install

Install a ggd data package into the current or specified conda environment

-h, --help

show this help message and exit

name

Required The data package name to install. Can use more than once (e.g. ggd install <pkg 1> <pkg 2> <pkg 3> ) (NOTE: No need to designate version as it is implicated in the package name)

-c, --channel

(Optional) The ggd channel the desired recipe is stored in.(Default = genomics)

-d, --debug

(Optional) When the -d flag is set debug output will be printed to stdout.

--file

A file with a list of ggd data packages to install. One package per line. Can use more than one (e.g. ggd install –file <file_1> –file <file_2> )

--prefix

(Optional) The name or the full directory path to an existing conda environment where you want to install a ggd data package. (Only needed if you want to install the data package into a different conda environment then the one you are currently in)

--id, (meta-recipe ID)

The ID to use for the meta recipe being installed. For example, if installing the GEO meta-recipe for GEO Accession ID GSE123, use –id GSE123 NOTE: GGD will NOT try to correct the ID. The ID must be accurately entered with case sensitive alphanumeric order

Additional argument explanation:

Required arguments:

  • name: The name represents the name(s) of the ggd package(s) to download and is required. If the name provided is not in the ggd channel it will not be downloaded, and the user will be informed. At least one package name is required, but multiple names can be supplied

Optional arguments:

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

    For example, if the data was located in the ‘proteomics’ channel, you would use:

    ggd install <package> -c proteomics

  • –file: The --file flag is used to install data packages listed in a file. It requires that the each package in the file be separated by a new line, that is, one package name per line. This is similar to a requirements.txt file used for installing software packages from conda. (See example 4 below.

  • –prefix: The --prefix flag is used to install a data package into a different conda environment/prefix then the current one you are in. This flag is commonly used when a environment has been created to store data packages without having duplicate copies of a package in different environments. You can store all data packages in a single environment and access them from any other environment using the --prefix flag available in other ggd tools

Required if meta-recipe:

  • id: The --id parameter is used to designate the ID to use when installing a meta-recipe. This ID is required in order

    to install the meta-recipe. The ID represents a unique identifier that the meta-recipe can used to download data from the database the meta-recipe is created for. For example, if you are using the GEO meta-recipe and want to install the data for the GEO accession ID GSE123, you would add --id GSE123 to the end of your install command. The ID entered is based on an ID that can be used by the specific meta-recipe being installed. The meta-recipe should have a description of what IDs can be entered and what they should be. NOTE: GGD does not try to fix IDs. They must be entered correctly including being case sensitive with proper alphanumeric order.

    Note

    Installing a meta-recipe takes slightly longer then a normal recipe because the ID specific meta-recipe is build locally prior to installation

Note

During the installation you will see a multiple progress spinners. The time it takes to install the data package(s) is dependent on how big the data package is being installed as well as the internet bandwidth you have. When you see: Executing Transaction |- you are in the final stages of installation, however, this stage takes the longest. Please be patient as the package is being installed, processed, and curated.

Note

Environment variable(s) are created for each data package installed for easy access and use. Most of the time these environment variables need to be activated. After the installation is complete, run the following command to activate: source activate base

Examples

1. Failed install example:

$ ggd install hg19-ga

  :ggd:install: Looking for hg19-ga in the 'ggd-genomics' channel

  :ggd:install: 'hg19-ga' was not found in ggd-genomics
  :ggd:install:  You can search for recipes using the ggd search tool:
      'ggd search hg19-ga'

2. Successful install example:

$ ggd install hg19-gaps-ucsc-v1


  :ggd:install: Looking for hg19-gaps-ucsc-v1 in the 'ggd-genomics' channel

  :ggd:install: hg19-gaps-ucsc-v1 exists in the ggd-genomics channel

  :ggd:install: hg19-gaps-ucsc-v1 version 1 is not installed on your system

  :ggd:install: hg19-gaps-ucsc-v1 has not been installed by conda

  :ggd:install: The hg19-gaps-ucsc-v1 package is uploaded to an aws S3 bucket. To reduce processing time the package will be downloaded from an aws S3 bucket


  :ggd:install:   Attempting to install the following cached package(s):
    hg19-gaps-ucsc-v1


  :ggd:utils:bypass: Installing hg19-gaps-ucsc-v1 from the ggd-genomics conda channel

  Collecting package metadata: done
  Processing data: done

  ## Package Plan ##

    environment location: <env>

    added / updated specs:
      - hg19-gaps-ucsc-v1


  The following packages will be downloaded:

      package                    |            build
      ---------------------------|-----------------
      hg19-gaps-ucsc-v1-1        |                1           6 KB  ggd-genomics
      ------------------------------------------------------------
                                             Total:           6 KB

  The following NEW packages will be INSTALLED:

    hg19-gaps-ucsc-v1  ggd-genomics/noarch::hg19-gaps-ucsc-v1-1-1



  Downloading and Extracting Packages
  hg19-gaps-ucsc-v1-1  | 6 KB      | ############################################################################ | 100%
  Preparing transaction: done
  Verifying transaction: done
  Executing transaction: done

  :ggd:install: Updating installed package list

  :ggd:install: Initiating data file content validation using checksum

  :ggd:install: Checksum for hg19-gaps-ucsc-v1

  :ggd:install: ** Successful Checksum **

  :ggd:install: Install Complete


  :ggd:install: Installed file locations
  ======================================================================================================================

           GGD Package                                     Environment Variable(s)
       ----------------------------------------------------------------------------------------------------
  ->  hg19-gaps-ucsc-v1                              $ggd_hg19_gaps_ucsc_v1_dir
                                                     $ggd_hg19_gaps_ucsc_v1_file


  Install Path: <conda root>/share/ggd/Homo_sapiens/hg19/hg19-gaps-ucsc-v1/1


       ----------------------------------------------------------------------------------------------------

  :ggd:install: To activate environment variables run `source activate base` in the environment the packages were installed in

  :ggd:install: NOTE: These environment variables are specific to the <env> conda environment and can only be accessed from within that environment
  ======================================================================================================================




  :ggd:install: Environment Variables
  *****************************

  Inactive or out-of-date environment variables:
  > $ggd_hg19_gaps_ucsc_v1_dir
  > $ggd_hg19_gaps_ucsc_v1_file

  To activate inactive or out-of-date vars, run:
  source activate base

  *****************************


  :ggd:install: DONE

Note

To activate environment variables run: source activate base

3. Successful install with multiple packages:

You can install multiple data packages at the same time. You simply append the name of each data package after the ggd install command. The example below shows the install for two data packages, but there is no limit to the number of data packages to install at the same time.

Note

The more data packages you append to the install command the longer it will take to install them.

Note

If one of the data packages doesn’t install correctly, doesn’t exists as a data package in ggd, or has some problem during installation, the installation process will not finish and the process will be rolled back. That is, NO data packages will be installed

$ ggd install grch37-haploinsufficient-genes-clingen-v1 grch37-microsatellites-ucsc-v1


  :ggd:install: Looking for grch37-haploinsufficient-genes-clingen-v1 in the 'ggd-genomics' channel

  :ggd:install: grch37-haploinsufficient-genes-clingen-v1 exists in the ggd-genomics channel

  :ggd:install: grch37-haploinsufficient-genes-clingen-v1 version 1 is not installed on your system

  :ggd:install: grch37-haploinsufficient-genes-clingen-v1 has not been installed by conda


  :ggd:install: Looking for grch37-microsatellites-ucsc-v1 in the 'ggd-genomics' channel

  :ggd:install: grch37-microsatellites-ucsc-v1 exists in the ggd-genomics channel

  :ggd:install: grch37-microsatellites-ucsc-v1 version 1 is not installed on your system

  :ggd:install: grch37-microsatellites-ucsc-v1 has not been installed by conda

  :ggd:install: The grch37-haploinsufficient-genes-clingen-v1 package is uploaded to an aws S3 bucket. To reduce processing time the package will be downloaded from an aws S3 bucket

  :ggd:install: The grch37-microsatellites-ucsc-v1 package is uploaded to an aws S3 bucket. To reduce processing time the package will be downloaded from an aws S3 bucket


  :ggd:install:   Attempting to install the following cached package(s):
    grch37-haploinsufficient-genes-clingen-v1
    grch37-microsatellites-ucsc-v1


  :ggd:utils:bypass: Installing grch37-haploinsufficient-genes-clingen-v1, grch37-microsatellites-ucsc-v1 from the ggd-genomics conda channel

  Collecting package metadata: done
  Processing data: done

  ## Package Plan ##

    environment location: <envs>

    added / updated specs:
      - grch37-haploinsufficient-genes-clingen-v1
      - grch37-microsatellites-ucsc-v1


  The following packages will be downloaded:

      package                    |            build
      ---------------------------|-----------------
      grch37-haploinsufficient-genes-clingen-v1-1|                1           8 KB  ggd-genomics
      grch37-microsatellites-ucsc-v1-1|                1           7 KB  ggd-genomics
      ------------------------------------------------------------
                                             Total:          15 KB

  The following NEW packages will be INSTALLED:

    grch37-haploinsuf~ ggd-genomics/noarch::grch37-haploinsufficient-genes-clingen-v1-1-1
    grch37-microsatel~ ggd-genomics/noarch::grch37-microsatellites-ucsc-v1-1-1



  Downloading and Extracting Packages
  grch37-microsatellit | 7 KB      | ############################################################################ | 100%
  grch37-haploinsuffic | 8 KB      | ############################################################################ | 100%
  Preparing transaction: done
  Verifying transaction: done
  Executing transaction: done

  :ggd:install: Updating installed package list

  :ggd:install: Initiating data file content validation using checksum

  :ggd:install: Checksum for grch37-haploinsufficient-genes-clingen-v1
  :ggd:checksum: installed  file checksum: grch37-haploinsufficient-genes-clingen-v1.complement.bed.gz.tbi checksum: 5fc9e77bea58d2ef96d6f48a5e977a18
  :ggd:checksum: metadata checksum record: grch37-haploinsufficient-genes-clingen-v1.complement.bed.gz.tbi checksum: 5fc9e77bea58d2ef96d6f48a5e977a18

  :ggd:checksum: installed  file checksum: grch37-haploinsufficient-genes-clingen-v1.bed.gz checksum: 287eb021cf209ed4711bb69f66e38391
  :ggd:checksum: metadata checksum record: grch37-haploinsufficient-genes-clingen-v1.bed.gz checksum: 287eb021cf209ed4711bb69f66e38391

  :ggd:checksum: installed  file checksum: grch37-haploinsufficient-genes-clingen-v1.bed.gz.tbi checksum: 531f8c4dfd43e562cf0c81d2bceb96e0
  :ggd:checksum: metadata checksum record: grch37-haploinsufficient-genes-clingen-v1.bed.gz.tbi checksum: 531f8c4dfd43e562cf0c81d2bceb96e0

  :ggd:checksum: installed  file checksum: grch37-haploinsufficient-genes-clingen-v1.complement.bed.gz checksum: 0f347399371685e65df738b13e596f83
  :ggd:checksum: metadata checksum record: grch37-haploinsufficient-genes-clingen-v1.complement.bed.gz checksum: 0f347399371685e65df738b13e596f83

  :ggd:install: ** Successful Checksum **

  :ggd:install: Checksum for grch37-microsatellites-ucsc-v1
  :ggd:checksum: installed  file checksum: grch37-microsatellites-ucsc-v1.bed.gz checksum: f15e697a24cd2fa0ce42d4a7682ae2ed
  :ggd:checksum: metadata checksum record: grch37-microsatellites-ucsc-v1.bed.gz checksum: f15e697a24cd2fa0ce42d4a7682ae2ed

  :ggd:checksum: installed  file checksum: grch37-microsatellites-ucsc-v1.bed.gz.tbi checksum: 8c8dc0191b9f19c636ef13872ae15c80
  :ggd:checksum: metadata checksum record: grch37-microsatellites-ucsc-v1.bed.gz.tbi checksum: 8c8dc0191b9f19c636ef13872ae15c80

  :ggd:install: ** Successful Checksum **

  :ggd:install: Install Complete


  :ggd:install: Installed file locations
  ======================================================================================================================

           GGD Package                                     Environment Variable(s)
       ----------------------------------------------------------------------------------------------------
  -> grch37-haploinsufficient-genes-clingen-v1                  $ggd_grch37_haploinsufficient_genes_clingen_v1_dir


  Install Path: <conda root>/share/ggd/Homo_sapiens/GRCh37/grch37-haploinsufficient-genes-clingen-v1/1


       ----------------------------------------------------------------------------------------------------
  -> grch37-microsatellites-ucsc-v1                        $ggd_grch37_microsatellites_ucsc_v1_dir
                                                          $ggd_grch37_microsatellites_ucsc_v1_file


  Install Path: <conda root>/share/ggd/Homo_sapiens/GRCh37/grch37-microsatellites-ucsc-v1/1


       ----------------------------------------------------------------------------------------------------

  :ggd:install: To activate environment variables run `source activate base` in the environment the packages were installed in

  :ggd:install: NOTE: These environment variables are specific to the <env> conda environment and can only be accessed from within that environment
  ======================================================================================================================




  :ggd:install: Environment Variables
  *****************************

  Inactive or out-of-date environment variables:
  > $ggd_grch37_haploinsufficient_genes_clingen_v1_dir
  > $ggd_grch37_microsatellites_ucsc_v1_dir
  > $ggd_grch37_microsatellites_ucsc_v1_file

  To activate inactive or out-of-date vars, run:
  source activate base

  *****************************


  :ggd:install: DONE

Note

To activate environment variables run: source activate base

4. Successful install using the –file flag:

If we had a txt file named data_package_file.txt and the contents of the file is:

hg19-chromsizes-ggd-v1
hg19-gaps-ucsc-v1
hg19-cpg-islands-ucsc-v1

We could install each of those data packages at the same tile using the --file flag.

Note

If using a file to install data packages, the file needs to be formatted as a single column file with each data package on its own line.

$ ggd install --file data_package_file.txt



  :ggd:install: Looking for hg19-chromsizes-ggd-v1 in the 'ggd-genomics' channel

  :ggd:install: hg19-chromsizes-ggd-v1 exists in the ggd-genomics channel

  :ggd:install: hg19-chromsizes-ggd-v1 version 1 is not installed on your system

  :ggd:install: hg19-chromsizes-ggd-v1 has not been installed by conda


  :ggd:install: Looking for hg19-cpg-islands-ucsc-v1 in the 'ggd-genomics' channel

  :ggd:install: hg19-cpg-islands-ucsc-v1 exists in the ggd-genomics channel

  :ggd:install: hg19-cpg-islands-ucsc-v1 version 1 is not installed on your system

  :ggd:install: hg19-cpg-islands-ucsc-v1 has not been installed by conda


  :ggd:install: Looking for hg19-gaps-ucsc-v1 in the 'ggd-genomics' channel

  :ggd:install: hg19-gaps-ucsc-v1 exists in the ggd-genomics channel

  :ggd:install: hg19-gaps-ucsc-v1 version 1 is not installed on your system

  :ggd:install: hg19-gaps-ucsc-v1 has not been installed by conda

  :ggd:install: The hg19-chromsizes-ggd-v1 package is uploaded to an aws S3 bucket. To reduce processing time the package will be downloaded from an aws S3 bucket

  :ggd:install: The hg19-cpg-islands-ucsc-v1 package is uploaded to an aws S3 bucket. To reduce processing time the package will be downloaded from an aws S3 bucket

  :ggd:install: The hg19-gaps-ucsc-v1 package is uploaded to an aws S3 bucket. To reduce processing time the package will be downloaded from an aws S3 bucket


  :ggd:install:   Attempting to install the following cached package(s):
    hg19-chromsizes-ggd-v1
    hg19-cpg-islands-ucsc-v1
    hg19-gaps-ucsc-v1


  :ggd:utils:bypass: Installing hg19-chromsizes-ggd-v1, hg19-cpg-islands-ucsc-v1, hg19-gaps-ucsc-v1 from the ggd-genomics conda channel

  Collecting package metadata: done
  Processing data: done

  ## Package Plan ##

    environment location: <env>

    added / updated specs:
      - hg19-chromsizes-ggd-v1
      - hg19-cpg-islands-ucsc-v1
      - hg19-gaps-ucsc-v1


  The following packages will be downloaded:

      package                    |            build
      ---------------------------|-----------------
      hg19-chromsizes-ggd-v1-1   |                1           6 KB  ggd-genomics
      hg19-cpg-islands-ucsc-v1-1 |                1           6 KB  ggd-genomics
      hg19-gaps-ucsc-v1-1        |                1           6 KB  ggd-genomics
      ------------------------------------------------------------
                                             Total:          18 KB

  The following NEW packages will be INSTALLED:

    hg19-chromsizes-g~ ggd-genomics/noarch::hg19-chromsizes-ggd-v1-1-1
    hg19-cpg-islands-~ ggd-genomics/noarch::hg19-cpg-islands-ucsc-v1-1-1
    hg19-gaps-ucsc-v1  ggd-genomics/noarch::hg19-gaps-ucsc-v1-1-1



  Downloading and Extracting Packages
  hg19-chromsizes-ggd- | 6 KB      | ############################################################################ | 100%
  hg19-cpg-islands-ucs | 6 KB      | ############################################################################ | 100%
  hg19-gaps-ucsc-v1-1  | 6 KB      | ############################################################################ | 100%
  Preparing transaction: done
  Verifying transaction: done
  Executing transaction: done

  :ggd:install: Updating installed package list

  :ggd:install: Initiating data file content validation using checksum

  :ggd:install: Checksum for hg19-chromsizes-ggd-v1

  :ggd:install: ** Successful Checksum **

  :ggd:install: Checksum for hg19-cpg-islands-ucsc-v1

  :ggd:install: ** Successful Checksum **

  :ggd:install: Checksum for hg19-gaps-ucsc-v1

  :ggd:install: ** Successful Checksum **

  :ggd:install: Install Complete


  :ggd:install: Installed file locations
  ======================================================================================================================

           GGD Package                                     Environment Variable(s)
       ----------------------------------------------------------------------------------------------------
  -> hg19-chromsizes-ggd-v1                            $ggd_hg19_chromsizes_ggd_v1_dir
                                                      $ggd_hg19_chromsizes_ggd_v1_file


  Install Path: <conda root>/share/ggd/Homo_sapiens/hg19/hg19-chromsizes-ggd-v1/1


       ----------------------------------------------------------------------------------------------------
  ->  hg19-gaps-ucsc-v1                              $ggd_hg19_gaps_ucsc_v1_dir
                                                     $ggd_hg19_gaps_ucsc_v1_file


  Install Path: <conda root>/share/ggd/Homo_sapiens/hg19/hg19-gaps-ucsc-v1/1


       ----------------------------------------------------------------------------------------------------
  -> hg19-cpg-islands-ucsc-v1                           $ggd_hg19_cpg_islands_ucsc_v1_dir
                                                       $ggd_hg19_cpg_islands_ucsc_v1_file


  Install Path: <conda root>/share/ggd/Homo_sapiens/hg19/hg19-cpg-islands-ucsc-v1/1


       ----------------------------------------------------------------------------------------------------

  :ggd:install: To activate environment variables run `source activate base` in the environment the packages were installed in

  :ggd:install: NOTE: These environment variables are specific to the <env> conda environment and can only be accessed from within that environment
  ======================================================================================================================




  :ggd:install: Environment Variables
  *****************************

  Inactive or out-of-date environment variables:
  > $ggd_hg19_chromsizes_ggd_v1_dir
  > $ggd_hg19_chromsizes_ggd_v1_file
  > $ggd_hg19_cpg_islands_ucsc_v1_dir
  > $ggd_hg19_cpg_islands_ucsc_v1_file
  > $ggd_hg19_gaps_ucsc_v1_dir
  > $ggd_hg19_gaps_ucsc_v1_file

  To activate inactive or out-of-date vars, run:
  source activate base

  *****************************


  :ggd:install: DONE

Note

To activate environment variables run: source activate base

5. Successful install with –prefix flag:

You can install a data package into an existing conda environment using the --prefix flag. This is useful if you want to store all instances of data in one environment rather than having multiple instances of the data installed and spread throughout your system.

For this example, let’s say we have a conda environment called data where we store all of our data. We can install a data package into that conda environment without having to be in the conda environment using the --prefix flag.

$ ggd install grch37-microsatellites-ucsc-v1 --prefix data


  :ggd:install: Looking for grch37-microsatellites-ucsc-v1 in the 'ggd-genomics' channel

  :ggd:install: grch37-microsatellites-ucsc-v1 exists in the ggd-genomics channel

  :ggd:install: grch37-microsatellites-ucsc-v1 version 1 is not installed on your system

  :ggd:install: grch37-microsatellites-ucsc-v1 has not been installed by conda

  :ggd:install: The grch37-microsatellites-ucsc-v1 package is uploaded to an aws S3 bucket. To reduce processing time the package will be downloaded from an aws S3 bucket


  :ggd:install:   Attempting to install the following cached package(s):
    grch37-microsatellites-ucsc-v1


  :ggd:utils:bypass: Installing grch37-microsatellites-ucsc-v1 from the ggd-genomics conda channel

  Collecting package metadata: done
  Processing data: done

  ## Package Plan ##

    environment location: <data environment>

    added / updated specs:
      - grch37-microsatellites-ucsc-v1


  The following packages will be downloaded:

      package                    |            build
      ---------------------------|-----------------
      grch37-microsatellites-ucsc-v1-1|                1           7 KB  ggd-genomics
      ------------------------------------------------------------
                                             Total:           7 KB

  The following NEW packages will be INSTALLED:

    grch37-microsatel~ ggd-genomics/noarch::grch37-microsatellites-ucsc-v1-1-1



  Downloading and Extracting Packages
  grch37-microsatellit | 7 KB      | ############################################################################ | 100%
  Preparing transaction: done
  Verifying transaction: done
  Executing transaction: done

  :ggd:install: Updating package metadata in user defined prefix

  :ggd:install: Updating installed package list

  :ggd:install: Initiating data file content validation using checksum

  :ggd:install: Checksum for grch37-microsatellites-ucsc-v1
  :ggd:checksum: installed  file checksum: grch37-microsatellites-ucsc-v1.bed.gz checksum: f15e697a24cd2fa0ce42d4a7682ae2ed
  :ggd:checksum: metadata checksum record: grch37-microsatellites-ucsc-v1.bed.gz checksum: f15e697a24cd2fa0ce42d4a7682ae2ed

  :ggd:checksum: installed  file checksum: grch37-microsatellites-ucsc-v1.bed.gz.tbi checksum: 8c8dc0191b9f19c636ef13872ae15c80
  :ggd:checksum: metadata checksum record: grch37-microsatellites-ucsc-v1.bed.gz.tbi checksum: 8c8dc0191b9f19c636ef13872ae15c80

  :ggd:install: ** Successful Checksum **

  :ggd:install: Install Complete


  :ggd:install: Installed file locations
  ======================================================================================================================

           GGD Package                                     Environment Variable(s)
       ----------------------------------------------------------------------------------------------------
  -> grch37-microsatellites-ucsc-v1                        $ggd_grch37_microsatellites_ucsc_v1_dir
                                                          $ggd_grch37_microsatellites_ucsc_v1_file


  Install Path: <data environment>/share/ggd/Homo_sapiens/GRCh37/grch37-microsatellites-ucsc-v1/1


       ----------------------------------------------------------------------------------------------------

  :ggd:install: To activate environment variables run `source activate base` in the environment the packages were installed in

  :ggd:install: NOTE: These environment variables are specific to the <data environment> conda environment and can only be accessed from within that environment
  ======================================================================================================================




  :ggd:install: DONE

Note

The environment variables for any new data package installed into a different environment then the one you are currently in are NOT available for use. That is, the environment variables are local to the conda environment in which the the data package was installed. To access this data use the ggd get-files tool with the --prefix flag. See :ref:`ggd get-files`<ggd-get-files>,

6. Successful install of a meta-recipe:

A meta-recipe is installed with the --id parameter added. NOTE: you can use --prefix to install the meta-recipe into a different conda environment.

Note

Only a single meta-recipe can be installed at a time. If multiple meta-recipes or multiple recipes include at least one meta-recipe are added to the install command the install command will exit with a notification that while installing a meta-recipe only a single meta-recipe is allowed.

$ ggd install meta-recipe-geo-accession-geo-v1 --id GSE123

:ggd:install: Looking for meta-recipe-geo-accession-geo-v1 in the 'ggd-genomics' channel

:ggd:install: meta-recipe-geo-accession-geo-v1 exists in the ggd-genomics channel

:ggd:install: meta-recipe-geo-accession-geo-v1 is a meta-recipe. Checking meta-recipe for installation

:ggd:install: The ID specific recipe to be installed is 'gse123-geo-v1'.

:ggd:install: gse123-geo-v1 version 1 is not installed on your system

:ggd:repodata: Loading repodata from the Anaconda Cloud for the following channels: ggd-genomics

:ggd:meta-recipe: Downloading meta-recipe package from conda to: '<conda root>/pkgs'

:ggd:meta-recipe: Checking md5sum

:ggd:meta-recipe: Successfully downloaded meta-recipe-geo-accession-geo-v1-1-0.tar.bz2 to <conda root>/pkgs

:ggd:meta-recipe: Updating meta-recipe with ID info

:ggd:install: Building new ID specific pkg

:ggd:install: Successfully built new ID specific meta recipe

:ggd:install: gse123-geo-v1 version 1 is not installed on your system

:ggd:install: gse123-geo-v1 has not been installed by conda


:ggd:install:   Attempting to install the following non-cached package(s):
    gse123-geo-v1

## Package Plan ##

  environment location: <conda root>

  added / updated specs:
    - gse123-geo-v1


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    gse123-geo-v1-1            |                0           8 KB  local
    ------------------------------------------------------------
                                           Total:           8 KB

The following NEW packages will be INSTALLED:

  gse123-geo-v1      ::gse123-geo-v1-1-0


Downloading and Extracting Packages
gse123-geo-v1-1      | 8 KB      | ####################################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

:ggd:install: Loading Meta-Recipe ID specific environment variables

:ggd:meta-recipe: Updating meta-recipe package metadata

:ggd:install: Updating installed package list

:ggd:install: Initiating data file content validation using checksum

:ggd:install: Checksum for gse123-geo-v1

:ggd:install: NOTICE: Skipping checksum for meta-recipe meta-recipe-geo-accession-geo-v1 => gse123-geo-v1

:ggd:install: Install Complete


:ggd:install: Installed file locations
======================================================================================================================

         GGD Package                                     Environment Variable(s)
     ----------------------------------------------------------------------------------------------------
->      gse123-geo-v1                                $ggd_gse123_geo_v1_dir


Install Path: <conda root>/share/ggd/meta-recipe/meta-recipe/gse123-geo-v1/1


     ----------------------------------------------------------------------------------------------------

:ggd:install: To activate environment variables run `source activate base` in the environment the packages were installed in

:ggd:install: NOTE: These environment variables are specific to the <conda root> conda environment and can only be accessed from within that environment
======================================================================================================================


:ggd:install: Environment Variables
*****************************

Active environment variables:
> $ggd_gse123_geo_v1_dir

To activate inactive or out-of-date vars, run:
source activate base

*****************************

:ggd:install: DONE