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<li class="toctree-l1 current"><a class="current reference internal" href="#">GGD meta-recipes</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#ggd-commands-with-meta-recipes">GGD commands with meta-recipes</a></li>
<li class="toctree-l2"><a class="reference internal" href="#conda-environments-and-prefix">Conda Environments and Prefix</a></li>
<li class="toctree-l2"><a class="reference internal" href="#installation-time">Installation Time</a></li>
<li class="toctree-l2"><a class="reference internal" href="#installing-a-meta-recipe">Installing a meta-recipe</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#creating-and-testing-meta-recipes">Creating and Testing meta-recipes</a></li>
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<div class="section" id="ggd-meta-recipes">
<span id="meta-recipes"></span><h1>GGD meta-recipes<a class="headerlink" href="#ggd-meta-recipes" 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><strong>To see and/or search for data packages available through GGD, see:</strong> <a class="reference internal" href="recipes.html#recipes"><span class="std std-ref">Available data packages</span></a></p>
<div class="admonition important">
<p class="admonition-title">Important</p>
<p>If you use GGD, please cite the <a class="reference external" href="https://www.nature.com/articles/s41467-021-22381-z">Nature Communications GGD paper</a></p>
</div>
<p>GGD supports the creation and use of non-specific recipes called <cite>meta-recipe</cite>. Meta-recipes are general recipes that can be used to access more specific recipes
based on an Identifier. For example, the Gene Expression Omnibus (GEO) database is a large database of data from gene expression experiments: <a class="reference external" href="http://www.ncbi.nlm.nih.gov/geo">http://www.ncbi.nlm.nih.gov/geo</a>.
The GEO database contains millions of entries based on a GEO accession IDs. Storing each GEO accession ID as a single GGD recipe would be quite cumbersome and
unrealistic to maintain. Therefore, rather then creating a single GGD recipe for every single GEO accession ID, a single GGD meta-recipe can be created which can be used
to access any GEO accession ID.</p>
<p>GGD meta-recipes provide a powerful source of data access, reproducibility, and provenance. These meta-recipes contain the information on how to access, process,
and install data based on the supplied ID. The installed pkg name will be specific to the ID supplied, making each ID specific meta-recipe unique. The specific
commands used to install the data can be stored within the installed ID specific meta-recipe pkg metadata. Additionally, metadata for the installed ID specific
meta-recipe pkg can be updated using information from the ID specific data. Therefore, in addition to being able to access data from a database like GEO with
a single GGD meta-recipe, each ID specific meta-recipe installed will have updated metadata that is accessible specific to the ID and accessible through the
<code class="code docutils literal notranslate"><span class="pre">pkg-info</span></code> command.</p>
<div class="section" id="ggd-commands-with-meta-recipes">
<h2>GGD commands with meta-recipes<a class="headerlink" href="#ggd-commands-with-meta-recipes" title="Permalink to this headline">¶</a></h2>
<p>Most GGD commands work with meta-recipes. These include:</p>
<blockquote>
<div><ul class="simple">
<li><p><code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">install</span></code> to install an ID specific meta-recipe</p></li>
<li><p><code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">list</span></code> to list installed ID specific meta-recipes</p></li>
<li><p><code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">show-env</span></code> to show the environment variables for ID specific meta-recipe(s)</p></li>
<li><p><code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">pkg-info</span></code> to get the metadata/information of a ID specific meta-recipe</p></li>
<li><p><code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">get-files</span></code> to get the installed data files for an ID specific meta-recipe</p></li>
<li><p><code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">predict-path</span></code> to predict the directory path of an ID specific meta-recipe</p></li>
<li><p><code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">uninstall</span></code> to uninstall an ID specific meta-recipe(s)</p></li>
<li><p><code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">make-meta-recipe</span></code> to make a meta-recipe from a single or group of scripts</p></li>
<li><p><code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">check-recipe</span></code> to test and check a new meta-recipe</p></li>
<li><p><code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">search</span></code> to search for a meta-recipe (NOT an ID specific recipe)</p></li>
</ul>
</div></blockquote>
<p>Commands the don’t work with meta-recipes include:</p>
<blockquote>
<div><ul class="simple">
<li><p><code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">make-recipe</span></code>: This command will only created a GGD recipe not a GGD meta-recipe.</p></li>
</ul>
</div></blockquote>
</div>
<div class="section" id="conda-environments-and-prefix">
<h2>Conda Environments and Prefix<a class="headerlink" href="#conda-environments-and-prefix" title="Permalink to this headline">¶</a></h2>
<p>One main advantage of GGD is the ability to install and access data files from GGD packages that are in different conda environments then the current
active one. This is supported throughout GGD with the <code class="code docutils literal notranslate"><span class="pre">--prefix</span></code> parameter.</p>
<p>The <code class="code docutils literal notranslate"><span class="pre">--prefix</span></code> parameter works for meta-recipes as well. This means you can install and access data files and metadata for ID specific meta-recipes
in a different environment then the currently active conda environment.</p>
</div>
<div class="section" id="installation-time">
<h2>Installation Time<a class="headerlink" href="#installation-time" title="Permalink to this headline">¶</a></h2>
<p>The process of installing a meta-recipe requires that the ID specific pkg be built locally. Therefore, installation time of a meta-recipe will be
slightly longer then a GGD recipe that will install a similar number and size of data files.</p>
</div>
<div class="section" id="installing-a-meta-recipe">
<h2>Installing a meta-recipe<a class="headerlink" href="#installing-a-meta-recipe" title="Permalink to this headline">¶</a></h2>
<p>Installing a meta-recipe is just like installing a normal GGD recipe, except for the addition of the <code class="code docutils literal notranslate"><span class="pre">--id</span></code> parameter. The <code class="code docutils literal notranslate"><span class="pre">--id</span></code> parameter
is required in order to install a meta-recipe. If <code class="code docutils literal notranslate"><span class="pre">--id</span></code> is not provided then the recipe will not be installed. If the <code class="code docutils literal notranslate"><span class="pre">--id</span></code> parameter is
provided but there is no meta-recipe being installed the id won’t be used but a warning will be issued.</p>
<div class="section" id="example">
<h3>Example:<a class="headerlink" href="#example" title="Permalink to this headline">¶</a></h3>
<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>
</div>
</div>
</div>
<div class="section" id="accessing-installed-id-specific-meta-recipe">
<h2>Accessing installed ID specific meta-recipe<a class="headerlink" href="#accessing-installed-id-specific-meta-recipe" title="Permalink to this headline">¶</a></h2>
<p>ID specific meta-recipe data files can be accessed just like any other GGD recipe.</p>
<ol class="arabic simple">
<li><p>Get a list of installed data files:</p></li>
</ol>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ggd list
# Packages in environment: <conda env>
#
------------------------------------------------------------------------------------------------------------------------
Name Pkg-Version Pkg-Build Channel Environment-Variables
------------------------------------------------------------------------------------------------------------------------
-> gse123-geo-v1 1 [WARNING: Present in GGD but missing from Conda] $ggd_gse123_geo_v1_dir
# To use the environment variables run `source activate base`
# You can see the available ggd data package environment variables by running `ggd show-env`
#
# NOTE: Packages with the '[WARNING: Present in GGD but missing from Conda]' messages represent packages where the ggd package(s) are installed, but the package metadata has been removed from conda storage. This happens when one of the following happen:
1) The package represents an ID specific meta-recipe installed by GGD.
2) When the recipe is built locally using 'ggd check-recipe' and has not been uninstalled. (Commonly for private data packages).
Or
3) The package is uninstalled using conda rather then ggd. The package is still available for use and is in the same state as before the 'conda uninstall'. To fix the problem on conda's side, uninstall the package with 'ggd uninstall' and re-install with 'ggd install'.
</pre></div>
</div>
<ol class="arabic simple" start="2">
<li><p>Show the env variable for installed pkgs:</p></li>
</ol>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ggd show-env
*****************************
Active environment variables:
> <span class="nv">$ggd_gse123_geo_v1_dir</span>
Inactive or out-of-date environment variables:
To activate inactive or out-of-date vars, run:
<span class="nb">source</span> activate base
*****************************
</pre></div>
</div>
<ol class="arabic simple" start="3">
<li><p>Get the files from an ID specific meta-recipe</p></li>
</ol>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ggd get-files gse123-geo-v1
<conda root>/share/ggd/meta-recipe/meta-recipe/gse123-geo-v1/1/GSM3225_jzo016-rp1-v5-u74av2.CEL.gz
<conda root>/share/ggd/meta-recipe/meta-recipe/gse123-geo-v1/1/GSE123_series_matrix.txt.gz
<conda root>/share/ggd/meta-recipe/meta-recipe/gse123-geo-v1/1/GSE123_family.soft.gz
<conda root>/share/ggd/meta-recipe/meta-recipe/gse123-geo-v1/1/GSM3226_jzo022-rp1-v5-u74av2.CEL.gz
<conda root>/share/ggd/meta-recipe/meta-recipe/gse123-geo-v1/1/GSM3227_jzo026-rp1-v5-u74av2.CEL.gz
$ ggd get-files gse123-geo-v1 --pattern <span class="s2">"*.soft*"</span>
<conda root>/share/ggd/meta-recipe/meta-recipe/gse123-geo-v1/1/GSE123_family.soft.gz
</pre></div>
</div>
<ol class="arabic simple" start="4">
<li><p>Get ID specific meta-recipe metadata info</p></li>
</ol>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ggd pkg-info gse123-geo-v1 -sr
----------------------------------------------------------------------------------------------------
GGD-Package: gse123-geo-v1
GGD Parent Meta-Recipe: meta-recipe-geo-accession-geo-v1
GGD-Channel: ggd-genomics
GGD Pkg Version: <span class="m">1</span>
Summary: GEO Accession ID: GSE123. Title: P7 knockout. GEO Accession site url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ<span class="o">=</span>self<span class="p">&</span><span class="nv">acc</span><span class="o">=</span>GSE123 <span class="o">(</span>See the url <span class="k">for</span> additional information about GSE123<span class="o">)</span>. Summary: Mice used were in a mixed background between <span class="m">129</span>/SvEv and C57BL/6. They were Rp1 knockout mice <span class="o">(</span>Rp1-/-<span class="o">)</span>. Triplicates of RNA samples from Rp1-/- neural retinas <span class="k">for</span> hybridization were collected at P7. Each RNA sample included a pool of neural retinas from <span class="m">3</span>-4 mice. Retinas were all collected at <span class="m">1</span>-2 pm of the day., Keywords: repeat sample Type: Expression profiling by array
Species: <span class="o">(</span>Updated<span class="o">)</span> Mus musculus
Genome Build: meta-recipe
Keywords: Gene-Expression-Omnibus, GEO, GEO-Accession-ID, GEO-meta-recipe, GSE123, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ<span class="o">=</span>self<span class="p">&</span><span class="nv">acc</span><span class="o">=</span>GSE123, Expression profiling by array, ,
Data Provider: GEO
Data Version: Submission date: Dec <span class="m">17</span> <span class="m">2002</span>. Status: Public on Apr <span class="m">15</span> <span class="m">2004</span>. Last Update Date: Feb <span class="m">18</span> <span class="m">2018</span>. Download Date: <span class="m">12</span>-30-2020
File type<span class="o">(</span>s<span class="o">)</span>:
Data file coordinate base: NA
Included Data Files:
GSM3225_jzo016-rp1-v5-u74av2.CEL.gz
GSE123_series_matrix.txt.gz
GSE123_family.soft.gz
GSM3226_jzo022-rp1-v5-u74av2.CEL.gz
GSM3227_jzo026-rp1-v5-u74av2.CEL.gz
Approximate Data File Sizes:
GSE123_family.soft.gz: <span class="m">3</span>.62M
GSE123_series_matrix.txt.gz: <span class="m">130</span>.06K
GSM3225_jzo016-rp1-v5-u74av2.CEL.gz: <span class="m">2</span>.51M
GSM3226_jzo022-rp1-v5-u74av2.CEL.gz: <span class="m">2</span>.58M
GSM3227_jzo026-rp1-v5-u74av2.CEL.gz: <span class="m">2</span>.64M
Pkg File Path: <conda root>/share/ggd/meta-recipe/meta-recipe/gse123-geo-v1/1
Installed Pkg Files:
<conda root>/share/ggd/meta-recipe/meta-recipe/gse123-geo-v1/1/GSM3225_jzo016-rp1-v5-u74av2.CEL.gz
<conda root>/share/ggd/meta-recipe/meta-recipe/gse123-geo-v1/1/GSE123_series_matrix.txt.gz
<conda root>/share/ggd/meta-recipe/meta-recipe/gse123-geo-v1/1/GSE123_family.soft.gz
<conda root>/share/ggd/meta-recipe/meta-recipe/gse123-geo-v1/1/GSM3226_jzo022-rp1-v5-u74av2.CEL.gz
<conda root>/share/ggd/meta-recipe/meta-recipe/gse123-geo-v1/1/GSM3227_jzo026-rp1-v5-u74av2.CEL.gz
----------------------------------------------------------------------------------------------------
gse123-geo-v1 recipe file:
*****************************************************************************
*
* curl <span class="s2">"https://ftp.ncbi.nlm.nih.gov/geo/series/GSEnnn/GSE123/soft/GSE123_family.soft.gz"</span> -O -J --silent
*
* curl <span class="s2">"https://ftp.ncbi.nlm.nih.gov/geo/series/GSEnnn/GSE123/matrix/GSE123_series_matrix.txt.gz"</span> -O -J --silent
*
* curl <span class="s2">"https://ftp.ncbi.nlm.nih.gov/geo/series/GSEnnn/GSE123/suppl/GSE123_RAW.tar"</span> -O -J --silent
*
* tar -xf GSE123_RAW.tar
*****************************************************************************
:ggd:pkg-info: NOTE: The recipe provided above outlines where the data was accessed and how it was processed
</pre></div>
</div>
<ol class="arabic simple" start="5">
<li><p>PREFIX</p></li>
</ol>
<p>As mentioned above, any GGD command that can use the <code class="code docutils literal notranslate"><span class="pre">--prefix</span></code> parameter can be used with meta-recipes.</p>
<p>Therefore, one can install and access the data files of a ID specific meta-recipe in an environment that is different then the active one. Additionally,
a meta-recipes metadata can be accessed in a different environment using <code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">pkg-info</span></code> with the <code class="code docutils literal notranslate"><span class="pre">--prefix</span></code> parameter.</p>
</div>
<div class="section" id="creating-and-testing-meta-recipes">
<h2>Creating and Testing meta-recipes<a class="headerlink" href="#creating-and-testing-meta-recipes" title="Permalink to this headline">¶</a></h2>
<p>Creating and testing a meta-recipe is similar to a normal recipe. However, meta-recipes required more detail within the data curation script(s).</p>
<p>For more information about creating and testing a meta-recipe see <a class="reference internal" href="making-meta-recipes.html#contribute-meta-recipe"><span class="std std-ref">Creating a ggd meta-recipe</span></a>.</p>
</div>
<div class="section" id="meta-recipe-caveats">
<h2>Meta-Recipe Caveats<a class="headerlink" href="#meta-recipe-caveats" title="Permalink to this headline">¶</a></h2>
<ol class="arabic simple">
<li><p>GGD currently only allows a single meta-recipe to be installed at a time. Therefore, if more than one meta-recipe needs to be installed each one would need
to be installed separately.</p></li>
<li><p>GGD does not cache meta-recipes. Therefore, if the database maintainer were to change/update ID specific data files, GGD would not be able to reproduce
data prior to the change. Additionally, meta-recipes do not get the installation speed up other general GGD recipes get.</p></li>
<li><p>GGD does not check the contents of installed data files for ID specific meta-recipes using md5 checksums as it does with normal GGD recipes. This is because
database like GEO do not provide md5sum hash values for data hosted on their site. Therefore, GGD would have to precompute md5sum values for every single possible
file that could be downloaded. These md5sum hash values could potentially become stale very quickly with the possibility of database maintainers add/updating/changing
the hosted data. If a database provider does provide md5sums for data hosted on their site, the meta-recipe itself could implement a checksum, however, currently
GGD does not plan to implement md5sum checking of data files for ID specific meta-recipes.</p></li>
</ol>
</div>
</div>
</div>
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