Skip to content

Commit 515dc92

Browse files
mikecormiermikecormier
committed
Fix spelling, cookie, and other errors. Add data package link to more pages
1 parent a0466c4 commit 515dc92

596 files changed

Lines changed: 6330 additions & 6865 deletions

File tree

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

‎GGD-CLI.html‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -72,7 +72,7 @@ <h3>Navigation</h3>
7272
</ul>
7373
</li>
7474
<li class="toctree-l1"><a class="reference internal" href="contribute.html">Contribute</a></li>
75-
<li class="toctree-l1"><a class="reference internal" href="recipes.html">Available data packages</a></li>
75+
<li class="toctree-l1"><a class="reference internal" href="recipes.html">Available Data Packages</a></li>
7676
</ul>
7777

7878
<ul>
@@ -103,6 +103,7 @@ <h3 id="searchlabel">Quick search</h3>
103103
<div class="section" id="ggd-commands">
104104
<span id="ggd-cli-page"></span><h1>GGD Commands<a class="headerlink" href="#ggd-commands" title="Permalink to this headline"></a></h1>
105105
<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>
106+
<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>
106107
<p>The ggd command line interface (cli) has multiple tools for data access and local management. Below you can find a short
107108
description of each tool, as well as links to specific pages about each.</p>
108109
<p>Tabs for each tool are also available on the left tab bar.</p>

‎_sources/GGD-CLI.rst.txt‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -6,6 +6,8 @@ GGD Commands
66

77
[:ref:`Click here to return to the home page <home-page>`]
88

9+
**To see and/or search for data packages available through GGD, see:** :ref:`Available data packages <recipes>`
10+
911
The ggd command line interface (cli) has multiple tools for data access and local management. Below you can find a short
1012
description of each tool, as well as links to specific pages about each.
1113

‎_sources/contribute.rst.txt‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,8 @@ Contribute
55

66
[:ref:`Click here to return to the home page <home-page>`]
77

8+
**To see and/or search for data packages available through GGD, see:** :ref:`Available data packages <recipes>`
9+
810
Similar to **Conda** and **Bioconda**, ggd encourages and relies on community contributions. Our vision is that
911
ggd will become a widely used data management system in genomics and other research fields. ggd will help reduce
1012
the time it takes to find, extract, and process the necessary data for any analysis and support research

‎_sources/index.rst.txt‎

Lines changed: 7 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -7,6 +7,8 @@
77

88
.. image:: GoGetData_name_logo.png
99

10+
**To see and/or search for data packages available through GGD, see:** :ref:`Available data packages <recipes>`
11+
1012
**For a quick-start guide to using ggd see:** :ref:`GGD Quick Start <quick-start>`
1113

1214
**To request a new data recipe please fill out the** `GGD Recipe Request <https://forms.gle/3WEWgGGeh7ohAjcJA>`_ **Form.**
@@ -33,7 +35,7 @@ and provides a platform upon which to cite data access and use by way of the ggd
3335

3436
Go Get Data acts as a multi use tool for genomic data access and management. It provide a system for simple data access all the way to a
3537
complete data management including version tracking, dependency handling, data format standards, and more. Whether using ggd for data
36-
access in genomic workflows, for an analysis, or for any other reason, ggd has bee developed to work in many situations.
38+
access in genomic workflows, for an analysis, or for any other reason, ggd has been developed to work in many situations.
3739

3840
We want to briefly highlight ggd's ability to work with multiple conda environments at the same time. Multiple tools in ggd use a
3941
:code:`--prefix` flag. This prefix flag allows a user to install, manage, and access data in a specific conda environment. Therefore,
@@ -83,11 +85,11 @@ desired data set into a bash script. Once the bash script has been created they
8385
a ggd data recipe.
8486

8587
A data recipe consists of a meta data file, a data curation script, a local file and environment handling script, and
86-
a checksum file. Together, these file represent the necessary instructions ggd will use to install and manage a data
88+
a checksum file. Together, these files represent the necessary instructions ggd will use to install and manage a data
8789
recipe on your local system.
8890

89-
Validation of the new recipe is a required part of the contribution process. ggd provides an additional tool for recipe
90-
validation. After creating a recipe, simply run :code:`ggd check-recipe` to validate the recipe is working correctly.
91+
Validation of the new recipe is a required part of the contribution process. After creating a recipe, simply run
92+
:code:`ggd check-recipe` to validate the recipe is working correctly.
9193

9294
For further details about contributing data recipes to ggd see :ref:`Contribute <make-data-packages>`.
9395

@@ -99,7 +101,7 @@ Data package infrastructure
99101
Another vital part of ggd is the infrastructure used to provide access to available data recipes. ggd has integrated multiple
100102
ecosystems together in order to control such access.
101103

102-
First, recipes are complied together as "cookbooks" on github. This github repo acts as the first stage of recipe access.
104+
First, recipes are compiled together as "cookbooks" on github. This github repo acts as the first stage of recipe access.
103105

104106
Second, a continuous integration (CI) system provides automatic data recipe validation. This CI system acts as a the second stage
105107
to ensure that each data recipe works correctly.

‎_sources/quick-start.rst.txt‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -11,6 +11,8 @@ GGD Quick Start
1111
be focused on python 3. This decision is based on the End-Of-Life of python 2 starting on January 1, 2020. GGD will maintain
1212
python 2 compatibility for 1 year from the End-Of-Life of python 2.
1313

14+
**To see and/or search for data packages available through GGD, see:** :ref:`Available data packages <recipes>`
15+
1416
Go Get Data (ggd) is a genomics data management system that provides access to processed and curated genomic data files.
1517
ggd alleviates the difficulties and complexities of finding, obtaining, and processing the data sets and annotations
1618
germane to your experiments and analyses.

‎_sources/recipes.rst.txt‎

Lines changed: 35 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
.. _recipes:
22

3-
Available data packages
3+
Available Data Packages
44
=======================
55

66
.. toctree::
@@ -40,7 +40,7 @@ Available data packages
4040
</div>
4141
<div class="row">
4242
<div class="col-sm-12">
43-
<p><center><small> NOTE: A <b>GGD Channel selection</b> is required before a <b>Species</b> selection and a <b>Species</b> selection is required before a <b>Genome Build</b> selection </small></center></p>
43+
<p><center><small> NOTE: A <b>GGD Channel</b> selection is required before a <b>Species</b> selection and a <b>Species</b> selection is required before a <b>Genome Build</b> selection </small></center></p>
4444
</div>
4545
</div>
4646
<hr>
@@ -56,22 +56,22 @@ Available data packages
5656

5757

5858
<script>
59-
59+
6060
/*
6161
------------------------------------------------------------------------------------------------------------------
6262
Initiate
6363
------------------------------------------------------------------------------------------------------------------
6464
*/
6565
66+
var channel_default = "genomics"
6667
var cur_channel = "None"
6768
var cur_species = "None"
6869
var cur_build = "None"
6970
70-
//Add channles to the GGD channel selector
71-
add_channel_selection()
72-
73-
//Update view based on avaiable cookie info
74-
getCookie()
71+
//update view based on avaiable cookie info
72+
$( document ).ready(function(){
73+
getCookie()
74+
})
7575
7676
/*
7777
------------------------------------------------------------------------------------------------------------------
@@ -85,6 +85,10 @@ Available data packages
8585
$("#ggd_channel").children().remove().end()
8686
$("#ggd_channel").append("<option>choose one</option>")
8787
88+
//Remove species and build info until a species is select
89+
$("#species_select").children().remove().end()
90+
$("#build_select").children().remove().end()
91+
8892
for (channel of Object.keys(recipe_data)) {
8993
//Add region to select options
9094
$("#ggd_channel").append("<option>" + channel + "</option>")
@@ -218,34 +222,40 @@ Available data packages
218222
219223
var cookieElements = document.cookie.split(";")
220224
221-
let unset = false
222-
cookieElements.forEach(item => {
225+
//check cookie
226+
for (item of cookieElements) {
223227
224228
if (item.split("=")[0].trim() == "channel") {
225-
cur_channel = item.split("=")[1]
229+
230+
//check for set channel cookie. if none, set to default
231+
if (item.split("=")[1] == "None") {
232+
cur_channel = channel_default
233+
} else {
234+
cur_channel = item.split("=")[1]
235+
}
236+
237+
//check species cookie
226238
} else if (item.split("=")[0].trim() == "species") {
227239
cur_species = item.split("=")[1]
240+
241+
//check build cookie
228242
} else if (item.split("=")[0].trim() == "build") {
229243
cur_build = item.split("=")[1]
244+
245+
//check cookie expires
230246
} else if (item.split("=")[0].trim() == "expires") {
231-
//Check if the cookie has expired
247+
248+
//check if the cookie has expired
232249
if (d.toUTCString() > item.split("=")[1]) {
233-
unset = true
250+
cur_channel = channel_default
251+
cur_species = "None"
252+
cur_build = "None"
253+
unsetCookie()
254+
break;
234255
}
235-
236256
}
237-
});
238-
239-
//If cookie is expired, unset cookie info
240-
if (unset == true) {
241-
242-
cur_channel = "None"
243-
cur_species = "None"
244-
cur_build = "None"
245-
246-
unsetCookie()
257+
};
247258
248-
}
249259
250260
//Add Channel Selection options
251261
add_channel_selection()
@@ -336,6 +346,5 @@ Available data packages
336346
}
337347
338348
});
339-
340349
341350
</script>

‎_sources/recipes/genomics/Danio_rerio/GRCz10/grcz10-reference-genome-ensembl-v1/README.rst.txt‎

Lines changed: 17 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -7,25 +7,23 @@ grcz10-reference-genome-ensembl-v1
77

88
The GRCz10 release 91 reference genome from Ensembl
99

10-
=========================== ====================================
11-
GGD Pacakge grcz10-reference-genome-ensembl-v1
12-
Species Danio_rerio
13-
Genome Build GRCz10
14-
GGD Channel ggd-genomics
15-
Package Version 1
16-
Recipe Author mjc
17-
Data Provider NA
18-
Data Version Release-91
19-
Genomic File Type NA
20-
Data file coordinate basing NA
21-
Package's Data Files NA
22-
Size of Each Data File NA
23-
Package Keywords ref, reference, zebrafish, genome, Ensembl, fasta-file
24-
Package Dependencies: samtools, zlib
25-
Recipe https://github.com/gogetdata/ggd-recipes/tree/master/recipes/genomics/Danio_rerio/GRCz10/grcz10-reference-genome-ensembl-v1
26-
=========================== ====================================
27-
28-
10+
================================== ====================================
11+
GGD Pacakge grcz10-reference-genome-ensembl-v1
12+
Species Danio_rerio
13+
Genome Build GRCz10
14+
GGD Channel ggd-genomics
15+
Package Version 1
16+
Recipe Author mjc
17+
Data Provider NA
18+
Data Version Release-91
19+
Genomic File Type NA
20+
Data file coordinate basing NA
21+
Package's Data Files NA
22+
Approximate Size of Each Data File NA
23+
Package Keywords ref, reference, zebrafish, genome, Ensembl, fasta-file
24+
Package Dependencies: samtools, zlib
25+
Recipe https://github.com/gogetdata/ggd-recipes/tree/master/recipes/genomics/Danio_rerio/GRCz10/grcz10-reference-genome-ensembl-v1
26+
================================== ====================================
2927

3028

3129

‎_sources/recipes/genomics/Danio_rerio/GRCz11/grcz11-reference-genome-ensembl-v1/README.rst.txt‎

Lines changed: 17 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -7,25 +7,23 @@ grcz11-reference-genome-ensembl-v1
77

88
The GRCz11 release 96 reference genome from Ensembl
99

10-
=========================== ====================================
11-
GGD Pacakge grcz11-reference-genome-ensembl-v1
12-
Species Danio_rerio
13-
Genome Build GRCz11
14-
GGD Channel ggd-genomics
15-
Package Version 1
16-
Recipe Author mjc
17-
Data Provider NA
18-
Data Version Release-96
19-
Genomic File Type NA
20-
Data file coordinate basing NA
21-
Package's Data Files NA
22-
Size of Each Data File NA
23-
Package Keywords ref, reference, zebrafish, genome, Ensembl, fasta-file
24-
Package Dependencies: samtools, zlib
25-
Recipe https://github.com/gogetdata/ggd-recipes/tree/master/recipes/genomics/Danio_rerio/GRCz11/grcz11-reference-genome-ensembl-v1
26-
=========================== ====================================
27-
28-
10+
================================== ====================================
11+
GGD Pacakge grcz11-reference-genome-ensembl-v1
12+
Species Danio_rerio
13+
Genome Build GRCz11
14+
GGD Channel ggd-genomics
15+
Package Version 1
16+
Recipe Author mjc
17+
Data Provider NA
18+
Data Version Release-96
19+
Genomic File Type NA
20+
Data file coordinate basing NA
21+
Package's Data Files NA
22+
Approximate Size of Each Data File NA
23+
Package Keywords ref, reference, zebrafish, genome, Ensembl, fasta-file
24+
Package Dependencies: samtools, zlib
25+
Recipe https://github.com/gogetdata/ggd-recipes/tree/master/recipes/genomics/Danio_rerio/GRCz11/grcz11-reference-genome-ensembl-v1
26+
================================== ====================================
2927

3028

3129

‎_sources/recipes/genomics/Danio_rerio/danRer10/danrer10-gtf-ensembl-v1/README.rst.txt‎

Lines changed: 17 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -7,25 +7,23 @@ danrer10-gtf-ensembl-v1
77

88
The GRCz10 gtf file from ensembl remapped to danRer10 (Any unmapped entries are removed from the file)
99

10-
=========================== ====================================
11-
GGD Pacakge danrer10-gtf-ensembl-v1
12-
Species Danio_rerio
13-
Genome Build danRer10
14-
GGD Channel ggd-genomics
15-
Package Version 1
16-
Recipe Author yliu
17-
Data Provider NA
18-
Data Version 91
19-
Genomic File Type NA
20-
Data file coordinate basing NA
21-
Package's Data Files NA
22-
Size of Each Data File NA
23-
Package Keywords gtf, gtf-file, ensembl
24-
Package Dependencies: gsort, htslib, zlib
25-
Recipe https://github.com/gogetdata/ggd-recipes/tree/master/recipes/genomics/Danio_rerio/danRer10/danrer10-gtf-ensembl-v1
26-
=========================== ====================================
27-
28-
10+
================================== ====================================
11+
GGD Pacakge danrer10-gtf-ensembl-v1
12+
Species Danio_rerio
13+
Genome Build danRer10
14+
GGD Channel ggd-genomics
15+
Package Version 1
16+
Recipe Author yliu
17+
Data Provider NA
18+
Data Version 91
19+
Genomic File Type NA
20+
Data file coordinate basing NA
21+
Package's Data Files NA
22+
Approximate Size of Each Data File NA
23+
Package Keywords gtf, gtf-file, ensembl
24+
Package Dependencies: gsort, htslib, zlib
25+
Recipe https://github.com/gogetdata/ggd-recipes/tree/master/recipes/genomics/Danio_rerio/danRer10/danrer10-gtf-ensembl-v1
26+
================================== ====================================
2927

3028

3129

‎_sources/recipes/genomics/Danio_rerio/danRer10/danrer10-gtf-refseq-ucsc-v1/README.rst.txt‎

Lines changed: 17 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -7,25 +7,23 @@ danrer10-gtf-refseq-ucsc-v1
77

88
The UCSC RefSeq gene track converted into GTF format containing known zebrafish protein-coding and non-protein-coding genes from RefSeq. (RefSeq: NCBI RNA reference sequence collection) (UCSC GTF format info: https://genome.ucsc.edu/FAQ/FAQformat.html#format3)
99

10-
=========================== ====================================
11-
GGD Pacakge danrer10-gtf-refseq-ucsc-v1
12-
Species Danio_rerio
13-
Genome Build danRer10
14-
GGD Channel ggd-genomics
15-
Package Version 1
16-
Recipe Author yliu
17-
Data Provider NA
18-
Data Version 21-May-2019
19-
Genomic File Type NA
20-
Data file coordinate basing NA
21-
Package's Data Files NA
22-
Size of Each Data File NA
23-
Package Keywords GTF, RefSeq, protein-coding, non-protein-coding, refGene, UCSC
24-
Package Dependencies: gsort, htslib, zlib
25-
Recipe https://github.com/gogetdata/ggd-recipes/tree/master/recipes/genomics/Danio_rerio/danRer10/danrer10-gtf-refseq-ucsc-v1
26-
=========================== ====================================
27-
28-
10+
================================== ====================================
11+
GGD Pacakge danrer10-gtf-refseq-ucsc-v1
12+
Species Danio_rerio
13+
Genome Build danRer10
14+
GGD Channel ggd-genomics
15+
Package Version 1
16+
Recipe Author yliu
17+
Data Provider NA
18+
Data Version 21-May-2019
19+
Genomic File Type NA
20+
Data file coordinate basing NA
21+
Package's Data Files NA
22+
Approximate Size of Each Data File NA
23+
Package Keywords GTF, RefSeq, protein-coding, non-protein-coding, refGene, UCSC
24+
Package Dependencies: gsort, htslib, zlib
25+
Recipe https://github.com/gogetdata/ggd-recipes/tree/master/recipes/genomics/Danio_rerio/danRer10/danrer10-gtf-refseq-ucsc-v1
26+
================================== ====================================
2927

3028

3129

0 commit comments

Comments
 (0)