-
Notifications
You must be signed in to change notification settings - Fork 1
/
pkg-info.html
379 lines (286 loc) · 18.3 KB
/
pkg-info.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>ggd pkg-info — GGD documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="_static/style.css" />
<link rel="stylesheet" type="text/css" href="_static/font-awesome-4.7.0/css/font-awesome.min.css" />
<script id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="ggd show-env" href="show-env.html" />
<link rel="prev" title="ggd get-files" href="list-file.html" />
<link href="https://fonts.googleapis.com/css?family=Lato|Raleway" rel="stylesheet">
<link href="https://fonts.googleapis.com/css?family=Inconsolata" rel="stylesheet">
<meta name="msapplication-TileColor" content="#ffffff">
<meta name="msapplication-TileImage" content="_static/ms-icon-144x144.png">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.6/css/selectize.bootstrap3.min.css">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.3.1/css/bootstrap.min.css">
<script src="https://cdnjs.cloudflare.com/ajax/libs/datatables/1.10.21/js/jquery.dataTables.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.6/js/standalone/selectize.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.3.1/js/bootstrap.bundle.min.js"></script>
</head><body>
<div class="document">
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
<p class="logo">
<a href="index.html">
<img class="logo" src="_static/logo/GoGetData_name_logo.png" alt="Logo"/>
</a>
</p>
<h3>Navigation</h3>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="quick-start.html">GGD Quick Start</a></li>
<li class="toctree-l1"><a class="reference internal" href="using-ggd.html">Using GGD</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="GGD-CLI.html">GGD Commands</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="ggd-search.html">ggd search</a></li>
<li class="toctree-l2"><a class="reference internal" href="install.html">ggd install</a></li>
<li class="toctree-l2"><a class="reference internal" href="predict-path.html">ggd predict-path</a></li>
<li class="toctree-l2"><a class="reference internal" href="uninstall.html">ggd uninstall</a></li>
<li class="toctree-l2"><a class="reference internal" href="list.html">ggd list</a></li>
<li class="toctree-l2"><a class="reference internal" href="list-file.html">ggd get-files</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">ggd pkg-info</a></li>
<li class="toctree-l2"><a class="reference internal" href="show-env.html">ggd show-env</a></li>
<li class="toctree-l2"><a class="reference internal" href="make-recipe.html">ggd make-recipe</a></li>
<li class="toctree-l2"><a class="reference internal" href="make-metarecipe.html">ggd make-meta-recipe</a></li>
<li class="toctree-l2"><a class="reference internal" href="check-recipe.html">ggd check-recipe</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="meta-recipes.html">GGD meta-recipes</a></li>
<li class="toctree-l1"><a class="reference internal" href="contribute.html">Contribute</a></li>
<li class="toctree-l1"><a class="reference internal" href="private_recipes.html">Private Recipes</a></li>
<li class="toctree-l1"><a class="reference internal" href="workflows.html">Using GGD in Workflows</a></li>
<li class="toctree-l1"><a class="reference internal" href="recipes.html">Available Data Packages</a></li>
</ul>
<ul>
<li class="toctree-l1"><a href="https://github.com/gogetdata/ggd-recipes">ggd-recipes @ Github</a></li>
<li class="toctree-l1"><a href="https://github.com/gogetdata/ggd-cli">ggd-cli @ Github</a></li>
</ul>
<div id="searchbox" style="display: none" role="search">
<h3 id="searchlabel">Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
<input type="text" name="q" aria-labelledby="searchlabel" />
<input type="submit" value="Go" />
</form>
</div>
</div>
<script>$('#searchbox').show(0);</script>
</div>
</div>
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body" role="main">
<div class="section" id="ggd-pkg-info">
<span id="id1"></span><h1>ggd pkg-info<a class="headerlink" href="#ggd-pkg-info" 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><code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">pkg-info</span></code> is used to get package information for a specific ggd data package installed on your system.</p>
<p>This is a great resource for identifying the information for a specific ggd data package installed on your system.
It will provide information about the data type, the provider of the data, the actual version of the data, the
version of the ggd data package, and more.</p>
<p>The examples below help to illustrate what is available from <code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">pkg-info</span></code>.</p>
<p>This tool provides a resource to help enforce reproducibility. The information provide from running
<code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">pkg-info</span></code> will help to distinguish the data package and allow you to provide such information to
others or in a citation</p>
<div class="section" id="using-ggd-pkg-info">
<h2>Using ggd pkg-info<a class="headerlink" href="#using-ggd-pkg-info" title="Permalink to this headline">¶</a></h2>
<p>pkg-info is useful when you want to know a bit more about the data package you have installed. This tool
provides general information about the data package and can access the original recipe used to download
and process the data.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>The ggd data package must be installed on your system in order to get the package information</p>
</div>
<p>Running <code class="code docutils literal notranslate"><span class="pre">ggd</span> <span class="pre">pkg-info</span> <span class="pre">-h</span></code> will give you the following help message:</p>
<p>pkg-info arguments:</p>
<table class="docutils align-default">
<colgroup>
<col style="width: 26%" />
<col style="width: 74%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>pkg-info</p></th>
<th class="head"><p>Get the information for a specific ggd data package installed in the current
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 name of the recipe to get info about.</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 of the recipe to list info about (default: genomics)</p></td>
</tr>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">-sr</span></code>, <code class="docutils literal notranslate"><span class="pre">--show_recipe</span></code></p></td>
<td><p>(Optional) When the flag is set, the recipe will be printed to the
stdout. This will provide info on where the data is hosted and how
it was processed. (NOTE: -sr flag does not accept arguments)</p></td>
</tr>
<tr class="row-even"><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 a conda environment where a ggd
recipe is stored. (Only needed if listing pkg data info for a pkg not installed
in the current environment)</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> argument represents the name of the ggd data package for which to retrieve info.
No flag is required for this argument, just supply the name.</p></li>
</ul>
<p>Optional arguments:</p>
<ul class="simple">
<li><p><em>-c:</em> The <code class="code docutils literal notranslate"><span class="pre">-c</span></code> flag represents the ggd channel the package came from. The default is genomics.</p></li>
<li><p><em>-sr:</em> The <code class="code docutils literal notranslate"><span class="pre">-sr</span></code> flag is used to <em>show the recipe</em> for the data package. Showing the recipe will allow
the user to identify where the data was originally downloaded, how it was processed, and other information
about the data being used.</p></li>
<li><p><em>–prefix:</em> The <code class="code docutils literal notranslate"><span class="pre">--prefix</span></code> flag is used to designate which conda environment/prefix to get the file from.
<strong>This allows one to store ggd data packages in one environment and access it from another.</strong></p></li>
</ul>
<p>If the package has not been installed on your system then the package info will not be displayed and the recipe will not be accessible.</p>
</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="example-listing-pkg-info">
<h3>1. Example listing pkg info:<a class="headerlink" href="#example-listing-pkg-info" title="Permalink to this headline">¶</a></h3>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ggd pkg-info hg19-gaps-ucsc-v1
----------------------------------------------------------------------------------------------------
GGD-Package: hg19-gaps-ucsc-v1
GGD-Channel: ggd-genomics
GGD Pkg Version: <span class="m">1</span>
Summary: Assembly gaps from UCSC in bed format
Species: Homo_sapiens
Genome Build: hg19
Keywords: gaps, region, bed-file
Cached: uploaded_to_aws
Data Version: <span class="m">27</span>-Apr-2009
File type<span class="o">(</span>s<span class="o">)</span>: bed
Data file coordinate base: <span class="m">0</span>-based-inclusive
Included Data Files:
hg19-gaps-ucsc-v1.bed.gz
hg19-gaps-ucsc-v1.bed.gz.tbi
Approximate Data File Sizes:
hg19-gaps-ucsc-v1.bed.gz: <span class="m">5</span>.16K
hg19-gaps-ucsc-v1.bed.gz.tbi: <span class="m">8</span>.22K
Pkg File Path: <conda root>/share/ggd/Homo_sapiens/hg19/hg19-gaps-ucsc-v1/1
Installed Pkg Files:
<conda root>/share/ggd/Homo_sapiens/hg19/hg19-gaps-ucsc-v1/1/hg19-gaps-ucsc-v1.bed.gz.tbi
<conda root>/share/ggd/Homo_sapiens/hg19/hg19-gaps-ucsc-v1/1/hg19-gaps-ucsc-v1.bed.gz
----------------------------------------------------------------------------------------------------
</pre></div>
</div>
</div>
<div class="section" id="example-listing-pkg-info-and-recipe">
<h3>2. Example listing pkg info and recipe:<a class="headerlink" href="#example-listing-pkg-info-and-recipe" title="Permalink to this headline">¶</a></h3>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ggd pkg-info hg19-gaps-ucsc-v1 -sr
----------------------------------------------------------------------------------------------------
GGD-Package: hg19-gaps-ucsc-v1
GGD-Channel: ggd-genomics
GGD Pkg Version: <span class="m">1</span>
Summary: Assembly gaps from UCSC in bed format
Species: Homo_sapiens
Genome Build: hg19
Keywords: gaps, region, bed-file
Cached: uploaded_to_aws
Data Version: <span class="m">27</span>-Apr-2009
File type<span class="o">(</span>s<span class="o">)</span>: bed
Data file coordinate base: <span class="m">0</span>-based-inclusive
Included Data Files:
hg19-gaps-ucsc-v1.bed.gz
hg19-gaps-ucsc-v1.bed.gz.tbi
Approximate Data File Sizes:
hg19-gaps-ucsc-v1.bed.gz: <span class="m">5</span>.16K
hg19-gaps-ucsc-v1.bed.gz.tbi: <span class="m">8</span>.22K
Pkg File Path: <conda root>/share/ggd/Homo_sapiens/hg19/hg19-gaps-ucsc-v1/1
Installed Pkg Files:
<conda root>/share/ggd/Homo_sapiens/hg19/hg19-gaps-ucsc-v1/1/hg19-gaps-ucsc-v1.bed.gz.tbi
<conda root>/share/ggd/Homo_sapiens/hg19/hg19-gaps-ucsc-v1/1/hg19-gaps-ucsc-v1.bed.gz
----------------------------------------------------------------------------------------------------
hg19-gaps-ucsc-v1 recipe file:
*****************************************************************************
* <span class="c1">#!/bin/sh</span>
* <span class="nb">set</span> -eo pipefail -o nounset
* <span class="nv">genome</span><span class="o">=</span>https://raw.githubusercontent.com/gogetdata/ggd-recipes/master/genomes/Homo_sapiens/hg19/hg19.genome
* wget --quiet -O - http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/gap.txt.gz <span class="se">\</span>
* <span class="p">|</span> gzip -dc <span class="se">\</span>
* <span class="p">|</span> awk -v <span class="nv">OFS</span><span class="o">=</span><span class="s2">"\t"</span> <span class="s1">'BEGIN {print "#chrom\tstart\tend\tsize\ttype\tstrand"} {print $2,$3,$4,$7,$8,"+"}'</span> <span class="se">\</span>
* <span class="p">|</span> gsort /dev/stdin <span class="nv">$genome</span> <span class="se">\</span>
* <span class="p">|</span> bgzip -c > hg19-gaps-ucsc-v1.bed.gz
*
* tabix hg19-gaps-ucsc-v1.bed.gz
*****************************************************************************
:ggd:pkg-info: NOTE: The recipe provided above outlines where the data was accessed and how it was processed
</pre></div>
</div>
</div>
<div class="section" id="example-listing-pkg-info-and-recipe-in-a-different-prefix">
<h3>3. Example listing pkg info and recipe in a different prefix:<a class="headerlink" href="#example-listing-pkg-info-and-recipe-in-a-different-prefix" title="Permalink to this headline">¶</a></h3>
<p>Using the code:<cite>ggd pkg-info</cite> to get the package metadata info in a different conda environment such as a conda environment called <cite>ggd_data</cite></p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ggd pkg-info hg19-gaps-ucsc-v1 -sr --prefix ggd_data
----------------------------------------------------------------------------------------------------
GGD-Package: hg19-gaps-ucsc-v1
GGD-Channel: ggd-genomics
GGD Pkg Version: <span class="m">1</span>
Summary: Assembly gaps from UCSC in bed format
Species: Homo_sapiens
Genome Build: hg19
Keywords: gaps, region, bed-file
Cached: uploaded_to_aws
Data Version: <span class="m">27</span>-Apr-2009
File type<span class="o">(</span>s<span class="o">)</span>: bed
Data file coordinate base: <span class="m">0</span>-based-inclusive
Included Data Files:
hg19-gaps-ucsc-v1.bed.gz
hg19-gaps-ucsc-v1.bed.gz.tbi
Approximate Data File Sizes:
hg19-gaps-ucsc-v1.bed.gz: <span class="m">5</span>.16K
hg19-gaps-ucsc-v1.bed.gz.tbi: <span class="m">8</span>.22K
Pkg File Path: <ggd_data env>/share/ggd/Homo_sapiens/hg19/hg19-gaps-ucsc-v1/1
Installed Pkg Files:
<ggd_data env>/share/ggd/Homo_sapiens/hg19/hg19-gaps-ucsc-v1/1/hg19-gaps-ucsc-v1.bed.gz.tbi
<ggd_data env>/share/ggd/Homo_sapiens/hg19/hg19-gaps-ucsc-v1/1/hg19-gaps-ucsc-v1.bed.gz
----------------------------------------------------------------------------------------------------
hg19-gaps-ucsc-v1 recipe file:
*****************************************************************************
* <span class="c1">#!/bin/sh</span>
* <span class="nb">set</span> -eo pipefail -o nounset
* <span class="nv">genome</span><span class="o">=</span>https://raw.githubusercontent.com/gogetdata/ggd-recipes/master/genomes/Homo_sapiens/hg19/hg19.genome
* wget --quiet -O - http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/gap.txt.gz <span class="se">\</span>
* <span class="p">|</span> gzip -dc <span class="se">\</span>
* <span class="p">|</span> awk -v <span class="nv">OFS</span><span class="o">=</span><span class="s2">"\t"</span> <span class="s1">'BEGIN {print "#chrom\tstart\tend\tsize\ttype\tstrand"} {print $2,$3,$4,$7,$8,"+"}'</span> <span class="se">\</span>
* <span class="p">|</span> gsort /dev/stdin <span class="nv">$genome</span> <span class="se">\</span>
* <span class="p">|</span> bgzip -c > hg19-gaps-ucsc-v1.bed.gz
*
* tabix hg19-gaps-ucsc-v1.bed.gz
*****************************************************************************
:ggd:pkg-info: NOTE: The recipe provided above outlines where the data was accessed and how it was processed
</pre></div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
©2016-2021, The GoGetData team.
|
<a href="_sources/pkg-info.rst.txt"
rel="nofollow">Page source</a>
</div>
</body>
</html>