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<div class="section" id="ggd-install">
<span id="id1"></span><h1>ggd install<a class="headerlink" href="#ggd-install" title="Permalink to this headline">¶</a></h1>
<p>[<a class="reference internal" href="index.html#home-page"><span class="std std-ref">Click here to return to the home page</span></a>]</p>
<p>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.</p>
<p>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 <code class="code docutils literal notranslate"><span class="pre">--file</span></code> flag.</p>
<p>ggd also provides functionality to install and use data packages into a different conda environment then the one you are currently
in using the <code class="code docutils literal notranslate"><span class="pre">--prefix</span></code> flag.</p>
<p>Examples are available at the bottom of this page that highlight the functionality of <code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">install</span></code></p>
<blockquote>
<div><div class="admonition note">
<p class="admonition-title">Note</p>
<p>Running <code class="code docutils literal notranslate"><span class="pre">conda</span> <span class="pre">install</span> <span class="pre"><package></span></code> will NOT work!! There are specific steps that GGD takes in order to install a
data package that conda does not. <strong>Please use</strong> <code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">install</span> <span class="pre"><package></span></code> <strong>when installing a ggd data package</strong>.</p>
</div>
</div></blockquote>
<div class="section" id="using-ggd-install">
<h2>Using ggd install<a class="headerlink" href="#using-ggd-install" title="Permalink to this headline">¶</a></h2>
<p>Use <code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">install</span></code> to install a data package hosted by ggd.
Running <code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">install</span> <span class="pre">-h</span></code> will give you the following message:</p>
<p>Install arguments:</p>
<table class="docutils align-default">
<colgroup>
<col style="width: 20%" />
<col style="width: 80%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>ggd install</p></th>
<th class="head"><p>Install a ggd data package into the current or specified conda environment</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">-h</span></code>, <code class="docutils literal notranslate"><span class="pre">--help</span></code></p></td>
<td><p>show this help message and exit</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">name</span></code></p></td>
<td><p><strong>Required</strong> 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)</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">-c</span></code>, <code class="docutils literal notranslate"><span class="pre">--channel</span></code></p></td>
<td><p>(Optional) The ggd channel the desired recipe is stored in.(Default = genomics)</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">-d</span></code>, <code class="docutils literal notranslate"><span class="pre">--debug</span></code></p></td>
<td><p>(Optional) When the -d flag is set debug output will be printed to stdout.</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--file</span></code></p></td>
<td><p>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> )</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--prefix</span></code></p></td>
<td><p>(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)</p></td>
</tr>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--id</span></code>,
<code class="docutils literal notranslate"><span class="pre">(meta-recipe</span> <span class="pre">ID)</span></code></p></td>
<td><p>The ID to use for the meta recipe being installed. For example, if installing the GEO meta-recipe
for GEO Accession ID GSE123, use <cite>–id GSE123</cite> NOTE: GGD will NOT try to correct the ID. The ID
must be accurately entered with case sensitive alphanumeric order</p></td>
</tr>
</tbody>
</table>
<div class="section" id="additional-argument-explanation">
<h3>Additional argument explanation:<a class="headerlink" href="#additional-argument-explanation" title="Permalink to this headline">¶</a></h3>
<p>Required arguments:</p>
<ul class="simple">
<li><p><em>name:</em> The <code class="code docutils literal notranslate"><span class="pre">name</span></code> 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</p></li>
</ul>
<p>Optional arguments:</p>
<ul>
<li><p><em>-c:</em> The <code class="code docutils literal notranslate"><span class="pre">-c</span></code> flag represents the ggd channel. The default channel is <em>genomics</em>. 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.</p>
<p>For example, if the data was located in the ‘proteomics’ channel, you would use:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">ggd</span> <span class="n">install</span> <span class="o"><</span><span class="n">package</span><span class="o">></span> <span class="o">-</span><span class="n">c</span> <span class="n">proteomics</span>
</pre></div>
</div>
</li>
<li><p><em>–file:</em> The <code class="code docutils literal notranslate"><span class="pre">--file</span></code> 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 <a class="reference internal" href="#ggd-install-example-4"><span class="std std-ref">example 4 below</span></a>.</p></li>
<li><p><em>–prefix:</em> The <code class="code docutils literal notranslate"><span class="pre">--prefix</span></code> 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 <code class="code docutils literal notranslate"><span class="pre">--prefix</span></code> flag available in other ggd tools</p></li>
</ul>
<p>Required if meta-recipe:</p>
<ul>
<li><dl>
<dt><em>id:</em> The <code class="code docutils literal notranslate"><span class="pre">--id</span></code> parameter is used to designate the ID to use when installing a meta-recipe. This ID is required in order</dt><dd><p>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 <cite>GSE123</cite>, you would add <code class="code docutils literal notranslate"><span class="pre">--id</span> <span class="pre">GSE123</span></code> 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.</p>
<blockquote>
<div><div class="admonition note">
<p class="admonition-title">Note</p>
<p>Installing a meta-recipe takes slightly longer then a normal recipe because the ID specific meta-recipe is build locally
prior to installation</p>
</div>
</div></blockquote>
</dd>
</dl>
</li>
</ul>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>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:
<strong>Executing Transaction |-</strong> 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.</p>
</div>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>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:
<code class="code docutils literal notranslate"><span class="pre">source</span> <span class="pre">activate</span> <span class="pre">base</span></code></p>
</div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
<div class="section" id="failed-install-example">
<h3>1. Failed install example:<a class="headerlink" href="#failed-install-example" title="Permalink to this headline">¶</a></h3>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ 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'
</pre></div>
</div>
</div>
<div class="section" id="successful-install-example">
<h3>2. Successful install example:<a class="headerlink" href="#successful-install-example" title="Permalink to this headline">¶</a></h3>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ggd install hg19-gaps-ucsc-v1
:ggd:install: Looking <span class="k">for</span> hg19-gaps-ucsc-v1 in the <span class="s1">'ggd-genomics'</span> channel
:ggd:install: hg19-gaps-ucsc-v1 exists in the ggd-genomics channel
:ggd:install: hg19-gaps-ucsc-v1 version <span class="m">1</span> 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 <span class="nb">time</span> the package will be downloaded from an aws S3 bucket
:ggd:install: Attempting to install the following cached package<span class="o">(</span>s<span class="o">)</span>:
hg19-gaps-ucsc-v1
:ggd:utils:bypass: Installing hg19-gaps-ucsc-v1 from the ggd-genomics conda channel
Collecting package metadata: <span class="k">done</span>
Processing data: <span class="k">done</span>
<span class="c1">## Package Plan ##</span>
environment location: <env>
added / updated specs:
- hg19-gaps-ucsc-v1
The following packages will be downloaded:
package <span class="p">|</span> build
---------------------------<span class="p">|</span>-----------------
hg19-gaps-ucsc-v1-1 <span class="p">|</span> <span class="m">1</span> <span class="m">6</span> KB ggd-genomics
------------------------------------------------------------
Total: <span class="m">6</span> 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 <span class="p">|</span> <span class="m">6</span> KB <span class="p">|</span> <span class="c1">############################################################################ | 100%</span>
Preparing transaction: <span class="k">done</span>
Verifying transaction: <span class="k">done</span>
Executing transaction: <span class="k">done</span>
:ggd:install: Updating installed package list
:ggd:install: Initiating data file content validation using checksum
:ggd:install: Checksum <span class="k">for</span> hg19-gaps-ucsc-v1
:ggd:install: ** Successful Checksum **
:ggd:install: Install Complete
:ggd:install: Installed file <span class="nv">locations</span>
<span class="o">======================================================================================================================</span>
GGD Package Environment Variable<span class="o">(</span>s<span class="o">)</span>
----------------------------------------------------------------------------------------------------
-> hg19-gaps-ucsc-v1 <span class="nv">$ggd_hg19_gaps_ucsc_v1_dir</span>
<span class="nv">$ggd_hg19_gaps_ucsc_v1_file</span>
Install Path: <conda root>/share/ggd/Homo_sapiens/hg19/hg19-gaps-ucsc-v1/1
----------------------------------------------------------------------------------------------------
:ggd:install: To activate environment variables run <span class="sb">`</span><span class="nb">source</span> activate base<span class="sb">`</span> 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 <span class="nv">environment</span>
<span class="o">======================================================================================================================</span>
:ggd:install: Environment Variables
*****************************
Inactive or out-of-date environment variables:
> <span class="nv">$ggd_hg19_gaps_ucsc_v1_dir</span>
> <span class="nv">$ggd_hg19_gaps_ucsc_v1_file</span>
To activate inactive or out-of-date vars, run:
<span class="nb">source</span> activate base
*****************************
:ggd:install: DONE
</pre></div>
</div>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>To activate environment variables run:
<code class="code docutils literal notranslate"><span class="pre">source</span> <span class="pre">activate</span> <span class="pre">base</span></code></p>
</div>
</div>
<div class="section" id="successful-install-with-multiple-packages">
<h3>3. Successful install with multiple packages:<a class="headerlink" href="#successful-install-with-multiple-packages" title="Permalink to this headline">¶</a></h3>
<p>You can install multiple data packages at the same time. You simply append the name of each data package after the <code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">install</span></code>
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.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>The more data packages you append to the install command the longer it will take to install them.</p>
</div>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>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</p>
</div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ggd install grch37-haploinsufficient-genes-clingen-v1 grch37-microsatellites-ucsc-v1
:ggd:install: Looking <span class="k">for</span> grch37-haploinsufficient-genes-clingen-v1 in the <span class="s1">'ggd-genomics'</span> channel
:ggd:install: grch37-haploinsufficient-genes-clingen-v1 exists in the ggd-genomics channel
:ggd:install: grch37-haploinsufficient-genes-clingen-v1 version <span class="m">1</span> is not installed on your system
:ggd:install: grch37-haploinsufficient-genes-clingen-v1 has not been installed by conda
:ggd:install: Looking <span class="k">for</span> grch37-microsatellites-ucsc-v1 in the <span class="s1">'ggd-genomics'</span> channel
:ggd:install: grch37-microsatellites-ucsc-v1 exists in the ggd-genomics channel
:ggd:install: grch37-microsatellites-ucsc-v1 version <span class="m">1</span> 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 <span class="nb">time</span> 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 <span class="nb">time</span> the package will be downloaded from an aws S3 bucket
:ggd:install: Attempting to install the following cached package<span class="o">(</span>s<span class="o">)</span>:
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: <span class="k">done</span>
Processing data: <span class="k">done</span>
<span class="c1">## Package Plan ##</span>
environment location: <envs>
added / updated specs:
- grch37-haploinsufficient-genes-clingen-v1
- grch37-microsatellites-ucsc-v1
The following packages will be downloaded:
package <span class="p">|</span> build
---------------------------<span class="p">|</span>-----------------
grch37-haploinsufficient-genes-clingen-v1-1<span class="p">|</span> <span class="m">1</span> <span class="m">8</span> KB ggd-genomics
grch37-microsatellites-ucsc-v1-1<span class="p">|</span> <span class="m">1</span> <span class="m">7</span> KB ggd-genomics
------------------------------------------------------------
Total: <span class="m">15</span> 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 <span class="p">|</span> <span class="m">7</span> KB <span class="p">|</span> <span class="c1">############################################################################ | 100%</span>
grch37-haploinsuffic <span class="p">|</span> <span class="m">8</span> KB <span class="p">|</span> <span class="c1">############################################################################ | 100%</span>
Preparing transaction: <span class="k">done</span>
Verifying transaction: <span class="k">done</span>
Executing transaction: <span class="k">done</span>
:ggd:install: Updating installed package list
:ggd:install: Initiating data file content validation using checksum
:ggd:install: Checksum <span class="k">for</span> 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 <span class="k">for</span> 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 <span class="nv">locations</span>
<span class="o">======================================================================================================================</span>
GGD Package Environment Variable<span class="o">(</span>s<span class="o">)</span>
----------------------------------------------------------------------------------------------------
-> grch37-haploinsufficient-genes-clingen-v1 <span class="nv">$ggd_grch37_haploinsufficient_genes_clingen_v1_dir</span>
Install Path: <conda root>/share/ggd/Homo_sapiens/GRCh37/grch37-haploinsufficient-genes-clingen-v1/1
----------------------------------------------------------------------------------------------------
-> grch37-microsatellites-ucsc-v1 <span class="nv">$ggd_grch37_microsatellites_ucsc_v1_dir</span>
<span class="nv">$ggd_grch37_microsatellites_ucsc_v1_file</span>
Install Path: <conda root>/share/ggd/Homo_sapiens/GRCh37/grch37-microsatellites-ucsc-v1/1
----------------------------------------------------------------------------------------------------
:ggd:install: To activate environment variables run <span class="sb">`</span><span class="nb">source</span> activate base<span class="sb">`</span> in the environment the packages were installed in
:ggd:install: NOTE: These environment variables are specific to the <env> conda environment and can only be accessed from within that <span class="nv">environment</span>
<span class="o">======================================================================================================================</span>
:ggd:install: Environment Variables
*****************************
Inactive or out-of-date environment variables:
> <span class="nv">$ggd_grch37_haploinsufficient_genes_clingen_v1_dir</span>
> <span class="nv">$ggd_grch37_microsatellites_ucsc_v1_dir</span>
> <span class="nv">$ggd_grch37_microsatellites_ucsc_v1_file</span>
To activate inactive or out-of-date vars, run:
<span class="nb">source</span> activate base
*****************************
:ggd:install: DONE
</pre></div>
</div>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>To activate environment variables run:
<code class="code docutils literal notranslate"><span class="pre">source</span> <span class="pre">activate</span> <span class="pre">base</span></code></p>
</div>
</div>
<div class="section" id="successful-install-using-the-file-flag">
<span id="ggd-install-example-4"></span><h3>4. Successful install using the –file flag:<a class="headerlink" href="#successful-install-using-the-file-flag" title="Permalink to this headline">¶</a></h3>
<p>If we had a txt file named <code class="code docutils literal notranslate"><span class="pre">data_package_file.txt</span></code> and the contents of the file is:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">hg19</span><span class="o">-</span><span class="n">chromsizes</span><span class="o">-</span><span class="n">ggd</span><span class="o">-</span><span class="n">v1</span>
<span class="n">hg19</span><span class="o">-</span><span class="n">gaps</span><span class="o">-</span><span class="n">ucsc</span><span class="o">-</span><span class="n">v1</span>
<span class="n">hg19</span><span class="o">-</span><span class="n">cpg</span><span class="o">-</span><span class="n">islands</span><span class="o">-</span><span class="n">ucsc</span><span class="o">-</span><span class="n">v1</span>
</pre></div>
</div>
<p>We could install each of those data packages at the same tile using the <code class="code docutils literal notranslate"><span class="pre">--file</span></code> flag.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>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.</p>
</div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ggd install --file data_package_file.txt
:ggd:install: Looking <span class="k">for</span> hg19-chromsizes-ggd-v1 in the <span class="s1">'ggd-genomics'</span> channel
:ggd:install: hg19-chromsizes-ggd-v1 exists in the ggd-genomics channel
:ggd:install: hg19-chromsizes-ggd-v1 version <span class="m">1</span> is not installed on your system
:ggd:install: hg19-chromsizes-ggd-v1 has not been installed by conda
:ggd:install: Looking <span class="k">for</span> hg19-cpg-islands-ucsc-v1 in the <span class="s1">'ggd-genomics'</span> channel
:ggd:install: hg19-cpg-islands-ucsc-v1 exists in the ggd-genomics channel
:ggd:install: hg19-cpg-islands-ucsc-v1 version <span class="m">1</span> is not installed on your system
:ggd:install: hg19-cpg-islands-ucsc-v1 has not been installed by conda
:ggd:install: Looking <span class="k">for</span> hg19-gaps-ucsc-v1 in the <span class="s1">'ggd-genomics'</span> channel
:ggd:install: hg19-gaps-ucsc-v1 exists in the ggd-genomics channel
:ggd:install: hg19-gaps-ucsc-v1 version <span class="m">1</span> 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 <span class="nb">time</span> 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 <span class="nb">time</span> 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 <span class="nb">time</span> the package will be downloaded from an aws S3 bucket
:ggd:install: Attempting to install the following cached package<span class="o">(</span>s<span class="o">)</span>:
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: <span class="k">done</span>
Processing data: <span class="k">done</span>
<span class="c1">## Package Plan ##</span>
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 <span class="p">|</span> build
---------------------------<span class="p">|</span>-----------------
hg19-chromsizes-ggd-v1-1 <span class="p">|</span> <span class="m">1</span> <span class="m">6</span> KB ggd-genomics
hg19-cpg-islands-ucsc-v1-1 <span class="p">|</span> <span class="m">1</span> <span class="m">6</span> KB ggd-genomics
hg19-gaps-ucsc-v1-1 <span class="p">|</span> <span class="m">1</span> <span class="m">6</span> KB ggd-genomics
------------------------------------------------------------
Total: <span class="m">18</span> 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- <span class="p">|</span> <span class="m">6</span> KB <span class="p">|</span> <span class="c1">############################################################################ | 100%</span>
hg19-cpg-islands-ucs <span class="p">|</span> <span class="m">6</span> KB <span class="p">|</span> <span class="c1">############################################################################ | 100%</span>
hg19-gaps-ucsc-v1-1 <span class="p">|</span> <span class="m">6</span> KB <span class="p">|</span> <span class="c1">############################################################################ | 100%</span>
Preparing transaction: <span class="k">done</span>
Verifying transaction: <span class="k">done</span>
Executing transaction: <span class="k">done</span>
:ggd:install: Updating installed package list
:ggd:install: Initiating data file content validation using checksum
:ggd:install: Checksum <span class="k">for</span> hg19-chromsizes-ggd-v1
:ggd:install: ** Successful Checksum **
:ggd:install: Checksum <span class="k">for</span> hg19-cpg-islands-ucsc-v1
:ggd:install: ** Successful Checksum **
:ggd:install: Checksum <span class="k">for</span> hg19-gaps-ucsc-v1
:ggd:install: ** Successful Checksum **
:ggd:install: Install Complete
:ggd:install: Installed file <span class="nv">locations</span>
<span class="o">======================================================================================================================</span>
GGD Package Environment Variable<span class="o">(</span>s<span class="o">)</span>
----------------------------------------------------------------------------------------------------
-> hg19-chromsizes-ggd-v1 <span class="nv">$ggd_hg19_chromsizes_ggd_v1_dir</span>
<span class="nv">$ggd_hg19_chromsizes_ggd_v1_file</span>
Install Path: <conda root>/share/ggd/Homo_sapiens/hg19/hg19-chromsizes-ggd-v1/1
----------------------------------------------------------------------------------------------------
-> hg19-gaps-ucsc-v1 <span class="nv">$ggd_hg19_gaps_ucsc_v1_dir</span>
<span class="nv">$ggd_hg19_gaps_ucsc_v1_file</span>
Install Path: <conda root>/share/ggd/Homo_sapiens/hg19/hg19-gaps-ucsc-v1/1
----------------------------------------------------------------------------------------------------
-> hg19-cpg-islands-ucsc-v1 <span class="nv">$ggd_hg19_cpg_islands_ucsc_v1_dir</span>
<span class="nv">$ggd_hg19_cpg_islands_ucsc_v1_file</span>
Install Path: <conda root>/share/ggd/Homo_sapiens/hg19/hg19-cpg-islands-ucsc-v1/1
----------------------------------------------------------------------------------------------------
:ggd:install: To activate environment variables run <span class="sb">`</span><span class="nb">source</span> activate base<span class="sb">`</span> 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 <span class="nv">environment</span>
<span class="o">======================================================================================================================</span>
:ggd:install: Environment Variables
*****************************
Inactive or out-of-date environment variables:
> <span class="nv">$ggd_hg19_chromsizes_ggd_v1_dir</span>
> <span class="nv">$ggd_hg19_chromsizes_ggd_v1_file</span>
> <span class="nv">$ggd_hg19_cpg_islands_ucsc_v1_dir</span>
> <span class="nv">$ggd_hg19_cpg_islands_ucsc_v1_file</span>
> <span class="nv">$ggd_hg19_gaps_ucsc_v1_dir</span>
> <span class="nv">$ggd_hg19_gaps_ucsc_v1_file</span>
To activate inactive or out-of-date vars, run:
<span class="nb">source</span> activate base
*****************************
:ggd:install: DONE
</pre></div>
</div>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>To activate environment variables run:
<code class="code docutils literal notranslate"><span class="pre">source</span> <span class="pre">activate</span> <span class="pre">base</span></code></p>
</div>
</div>
<div class="section" id="successful-install-with-prefix-flag">
<h3>5. Successful install with –prefix flag:<a class="headerlink" href="#successful-install-with-prefix-flag" title="Permalink to this headline">¶</a></h3>
<p>You can install a data package into an existing conda environment using the <code class="code docutils literal notranslate"><span class="pre">--prefix</span></code> 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.</p>
<p>For this example, let’s say we have a conda environment called <code class="code docutils literal notranslate"><span class="pre">data</span></code> 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 <code class="code docutils literal notranslate"><span class="pre">--prefix</span></code> flag.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ggd install grch37-microsatellites-ucsc-v1 --prefix data
:ggd:install: Looking <span class="k">for</span> grch37-microsatellites-ucsc-v1 in the <span class="s1">'ggd-genomics'</span> channel
:ggd:install: grch37-microsatellites-ucsc-v1 exists in the ggd-genomics channel
:ggd:install: grch37-microsatellites-ucsc-v1 version <span class="m">1</span> 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 <span class="nb">time</span> the package will be downloaded from an aws S3 bucket
:ggd:install: Attempting to install the following cached package<span class="o">(</span>s<span class="o">)</span>:
grch37-microsatellites-ucsc-v1
:ggd:utils:bypass: Installing grch37-microsatellites-ucsc-v1 from the ggd-genomics conda channel
Collecting package metadata: <span class="k">done</span>
Processing data: <span class="k">done</span>
<span class="c1">## Package Plan ##</span>
environment location: <data environment>
added / updated specs:
- grch37-microsatellites-ucsc-v1
The following packages will be downloaded:
package <span class="p">|</span> build
---------------------------<span class="p">|</span>-----------------
grch37-microsatellites-ucsc-v1-1<span class="p">|</span> <span class="m">1</span> <span class="m">7</span> KB ggd-genomics
------------------------------------------------------------
Total: <span class="m">7</span> 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 <span class="p">|</span> <span class="m">7</span> KB <span class="p">|</span> <span class="c1">############################################################################ | 100%</span>
Preparing transaction: <span class="k">done</span>
Verifying transaction: <span class="k">done</span>
Executing transaction: <span class="k">done</span>
: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 <span class="k">for</span> 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 <span class="nv">locations</span>
<span class="o">======================================================================================================================</span>
GGD Package Environment Variable<span class="o">(</span>s<span class="o">)</span>
----------------------------------------------------------------------------------------------------
-> grch37-microsatellites-ucsc-v1 <span class="nv">$ggd_grch37_microsatellites_ucsc_v1_dir</span>
<span class="nv">$ggd_grch37_microsatellites_ucsc_v1_file</span>
Install Path: <data environment>/share/ggd/Homo_sapiens/GRCh37/grch37-microsatellites-ucsc-v1/1
----------------------------------------------------------------------------------------------------
:ggd:install: To activate environment variables run <span class="sb">`</span><span class="nb">source</span> activate base<span class="sb">`</span> 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 <span class="nv">environment</span>
<span class="o">======================================================================================================================</span>
:ggd:install: DONE
</pre></div>
</div>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>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
<code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">get-files</span></code> tool with the <code class="code docutils literal notranslate"><span class="pre">--prefix</span></code> flag. See :ref:<a href="#id2"><span class="problematic" id="id3">`</span></a>ggd get-files`<ggd-get-files>,</p>
</div>
</div>
<div class="section" id="successful-install-of-a-meta-recipe">
<h3>6. Successful install of a meta-recipe:<a class="headerlink" href="#successful-install-of-a-meta-recipe" title="Permalink to this headline">¶</a></h3>
<p>A meta-recipe is installed with the <code class="code docutils literal notranslate"><span class="pre">--id</span></code> parameter added. NOTE: you can use <code class="code docutils literal notranslate"><span class="pre">--prefix</span></code> to install the meta-recipe
into a different conda environment.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>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.</p>
</div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ggd install meta-recipe-geo-accession-geo-v1 --id GSE123
:ggd:install: Looking <span class="k">for</span> meta-recipe-geo-accession-geo-v1 in the <span class="s1">'ggd-genomics'</span> 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 <span class="k">for</span> installation
:ggd:install: The ID specific recipe to be installed is <span class="s1">'gse123-geo-v1'</span>.
:ggd:install: gse123-geo-v1 version <span class="m">1</span> is not installed on your system
:ggd:repodata: Loading repodata from the Anaconda Cloud <span class="k">for</span> the following channels: ggd-genomics
:ggd:meta-recipe: Downloading meta-recipe package from conda to: <span class="s1">'<conda root>/pkgs'</span>
: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 <span class="m">1</span> 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<span class="o">(</span>s<span class="o">)</span>:
gse123-geo-v1
<span class="c1">## Package Plan ##</span>
environment location: <conda root>
added / updated specs:
- gse123-geo-v1
The following packages will be downloaded:
package <span class="p">|</span> build
---------------------------<span class="p">|</span>-----------------
gse123-geo-v1-1 <span class="p">|</span> <span class="m">0</span> <span class="m">8</span> KB <span class="nb">local</span>
------------------------------------------------------------
Total: <span class="m">8</span> KB
The following NEW packages will be INSTALLED:
gse123-geo-v1 ::gse123-geo-v1-1-0
Downloading and Extracting Packages
gse123-geo-v1-1 <span class="p">|</span> <span class="m">8</span> KB <span class="p">|</span> <span class="c1">####################################################################################################################################### | 100%</span>
Preparing transaction: <span class="k">done</span>
Verifying transaction: <span class="k">done</span>
Executing transaction: <span class="k">done</span>
: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 <span class="k">for</span> gse123-geo-v1
:ggd:install: NOTICE: Skipping checksum <span class="k">for</span> meta-recipe meta-recipe-geo-accession-geo-v1 <span class="o">=</span>> gse123-geo-v1
:ggd:install: Install Complete
:ggd:install: Installed file <span class="nv">locations</span>
<span class="o">======================================================================================================================</span>
GGD Package Environment Variable<span class="o">(</span>s<span class="o">)</span>
----------------------------------------------------------------------------------------------------
-> gse123-geo-v1 <span class="nv">$ggd_gse123_geo_v1_dir</span>
Install Path: <conda root>/share/ggd/meta-recipe/meta-recipe/gse123-geo-v1/1
----------------------------------------------------------------------------------------------------
:ggd:install: To activate environment variables run <span class="sb">`</span><span class="nb">source</span> activate base<span class="sb">`</span> in the environment the packages were installed in
:ggd:install: NOTE: These environment variables are specific to the <conda root> conda environment and can only be accessed from within that <span class="nv">environment</span>
<span class="o">======================================================================================================================</span>
:ggd:install: Environment Variables
*****************************
Active environment variables:
> <span class="nv">$ggd_gse123_geo_v1_dir</span>
To activate inactive or out-of-date vars, run:
<span class="nb">source</span> activate base
*****************************
:ggd:install: DONE
</pre></div>
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