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[TCDR-2137] Enclone deprecated #558

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[TCDR-2137] Enclone deprecated #558

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0196178
deprecation messasing
abhijna Nov 21, 2024
5794280
Update pages/index.html.src
abhijna Nov 21, 2024
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Update pages/index.html.src
abhijna Nov 21, 2024
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abhijna Nov 21, 2024
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abhijna Nov 25, 2024
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removed mailto
abhijna Nov 25, 2024
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Delete yarn.lock
abhijna Nov 25, 2024
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Delete pages/index.html.src
abhijna Nov 25, 2024
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44 changes: 3 additions & 41 deletions index.html
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Expand Up @@ -31,7 +31,7 @@
</a>

<header>
<h1><b><span style="color:rgb(120,123,175);font-weight:900">enclone</span></b> (beta)</h1>
<h1><b><span style="color:rgb(120,123,175);font-weight:900">enclone</span></b></h1>
<h3>Accurate and user-friendly computational tool for clonal grouping to study the adaptive immune system
<h3>
<h4>(Antigen analysis is not supported)</h4>
Expand All @@ -49,11 +49,8 @@ <h4>(Antigen analysis is not supported)</h4>
</p>
<p style="border: 2px; border-style: solid; border-color: black; background-color: #EBF4FC;
padding: 8px; font-size: 110%">
<span style="color:rgb(120,123,175);font-weight:900">enclone</span> (beta) is provided as a tool for use
<span style="color:rgb(120,123,175);font-weight:900">enclone</span> is provided as a tool for use
by the community to accelerate immunology research.
<span style="color:rgb(120,123,175);font-weight:900">enclone</span> is only supported via
<a href="mailto:[email protected]"><span
style="color:rgb(120,123,175);font-weight:900">enclone</span>@10xgenomics.com</a>.
The clonotype assignment algorithm that is part of <span
style="color:rgb(120,123,175);font-weight:900">enclone</span> is integrated into Cell Ranger.
</p>
Expand Down Expand Up @@ -239,7 +236,7 @@ <h2>Inputs to <span style="color:rgb(120,123,175);font-weight:900">enclone</span
<p><a name="software" style="display:block; position:relative; top:-20px;"></a></p>
<h2>The <span style="color:rgb(120,123,175);font-weight:900">enclone</span> software</h2>

<p><span style="color:rgb(120,123,175);font-weight:900">enclone</span> is beta software<sup>††</sup> released
<p><span style="color:rgb(120,123,175);font-weight:900">enclone</span> was a beta software<sup>††</sup> released
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Suggested change
<p><span style="color:rgb(120,123,175);font-weight:900">enclone</span> was a beta software<sup>††</sup> released
<p><span style="color:rgb(120,123,175);font-weight:900">enclone</span> was beta software<sup>††</sup> released

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This file appears to have been auto-generated from index.html.src but the two appear different. Was this file edited by hand?

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@macklin-10x I did a find in folder for the word "beta". Should I just delete this file?

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Definitely not this one. If anything, we should delete the .src versions since we're never going to regenerate the help site.

under <a href="LICENSE.txt">this license</a>.
Binary executables for Linux and Mac and Windows can be directly downloaded from this page, as can
sample 10x Genomics datasets.
Expand Down Expand Up @@ -270,13 +267,6 @@ <h2>The <span style="color:rgb(120,123,175);font-weight:900">enclone</span> soft
solution</a>.
</p>

<p>
<sup>††</sup><i>beta software implies that it is still being actively developed, with
features being added/modified,
and on rare occasions may involve breaking syntax that previously worked. See
<a href="pages/auto/history.html">this page</a> for the history of changes.</i>
</p>

<hr>

<p><a name="download" style="display:block; position:relative; top:-20px;"></a></p>
Expand Down Expand Up @@ -935,34 +925,6 @@ <h2>The power of <span style="color:rgb(120,123,175);font-weight:900">enclone</s

<hr>

<p><a name="questions" style="display:block; position:relative; top:-20px;"></a></p>
<h2>Questions</h2>

<p>
Please contact us with your questions and comments! We look forward to hearing your feedback and ideas to
further evolve <span style="color:rgb(120,123,175);font-weight:900">enclone</span>.
</p>

<p>
Our address is <a href="mailto:[email protected]"><span
style="color:rgb(120,123,175);font-weight:900">enclone</span>@10xgenomics.com</a>.
</p>

<p>
To send us <span style="color:rgb(120,123,175);font-weight:900">enclone</span> output, please simply
<b>cut and paste text</b>, rather than send a
screenshot, except when necessary. Please send <b>both the command you used and the output</b>.
</p>

<p style="border: 2px; border-style: solid; border-color: black; background-color: #EBF4FC;
padding: 8px; font-size: 110%">
<span style="color:rgb(120,123,175);font-weight:900">enclone</span> is provided as a tool for use by the
community.
<span style="color:rgb(120,123,175);font-weight:900">enclone</span> is beta software and thus a work in
progress. We are actively making many changes and may
be unable to respond promptly to your particular request.
</p>

<hr>

<p><a name="whereami" style="display:block; position:relative; top:-20px;"></a></p>
Expand Down
10 changes: 10 additions & 0 deletions node_modules/.yarn-integrity
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8 changes: 3 additions & 5 deletions pages/auto/help.all.html
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Expand Up @@ -109,9 +109,7 @@

(for the main help page, please type instead: enclone)

Here we go through several setup tests. If you have any problem that you can't
resolve, please email us at [email protected].

Here we go through several setup tests.

1. Are you using a fixed width font?
Look at this:
Expand Down Expand Up @@ -1879,8 +1877,8 @@

<span style="color:#c23621;font-weight:bold;">Frequently Asked Questions</span>

We're sorry you're having difficulty! Please see the answers below, check out the other help
guides, and if you're still stuck, write to us at [email protected].
We're sorry you're having difficulty! Please see the answers below or check out the other help
guides.

<span style="color:#5833ff;font-weight:bold;">1. Why is my enclone output garbled?</span>

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4 changes: 2 additions & 2 deletions pages/auto/help.faq.html
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Expand Up @@ -48,8 +48,8 @@
<pre style='font-family: "DejaVuSansMono"; line-height: 110%'><span style="font-size: 14px">
<span style="color:#c23621;font-weight:bold;">Frequently Asked Questions</span>

We're sorry you're having difficulty! Please see the answers below, check out the other help
guides, and if you're still stuck, write to us at [email protected].
We're sorry you're having difficulty! Please see the answers below or check out the other help
guides.

<span style="color:#5833ff;font-weight:bold;">1. Why is my enclone output garbled?</span>

Expand Down
3 changes: 1 addition & 2 deletions pages/auto/help.setup.html
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Expand Up @@ -54,8 +54,7 @@

(for the main help page, please type instead: enclone)

Here we go through several setup tests. If you have any problem that you can't
resolve, please email us at [email protected].
Here we go through several setup tests.


1. Are you using a fixed width font?
Expand Down
36 changes: 0 additions & 36 deletions pages/auto/install_issues.html
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Expand Up @@ -68,37 +68,6 @@ <h2>Case 2: download is so slow that it doesn't finish</h2>

<hr>

<h2>Case 3: installation seems to succeed but you get <code>command not found</code></h2>

<p>In this case, the install script appears to succeed, but when you
<b>open a new terminal window</b> and
type <span style="color:rgb(120,123,175);font-weight:900">enclone</span>, you get a message about the command not being found.</p>

<p>This should not happen, and we do not know <i>why</i> it happened to you, but we provide
instructions here on how you can report the problem to us. Please do this and we will try to
find a solution.</p>

<p>Please <b>open a new terminal window</b>, type the following commands, and then cut and paste
the entirety (commands plus responses) as <b>text</b> into an email to
<a href="mailto:[email protected]"><span style="color:rgb(120,123,175);font-weight:900">enclone</span>@10xgenomics.com</a>.

<br>

<p><b>1.</b> <code>enclone --check</code></p>

<p>This should say something about <span style="color:rgb(120,123,175);font-weight:900">enclone</span> not being found. Otherwise you have a different
problem.</p>

<p><b>2.</b> <code>echo $PATH</code></p>

<p>This reveals what directories are searched when you type a command.</p>

<p><b>3.</b> <code>curl -sSf -L bit.ly/enclone_install_debug | bash</code>

<p>This generates some further debugging information</p>

<hr>

<h2>Case 4: installation seems to succeed but <code>enclone</code> is killed</h2>

<p>In this case, when you type <code>enclone</code> from the command line, you'll get a message
Expand All @@ -125,10 +94,5 @@ <h2>Case 5: installation seems to succeed but you get a message about

<hr>

<h2>Case 6: something else goes wrong</h2>

Then please write to us at
<a href="mailto:[email protected]"><span style="color:rgb(120,123,175);font-weight:900">enclone</span>@10xgenomics.com</a>.</p>

</body>
</html>
3 changes: 0 additions & 3 deletions pages/auto/installation_details.html
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Expand Up @@ -84,8 +84,5 @@ <h1><span style="color:rgb(120,123,175);font-weight:900">enclone</span> installa
your path. (Which file is used depends on the version of Linux that you're using.) If you
want, when the script is done, you can manually tidy up the file to make it more readable.</p>

<p><b>Questions?</b> You can email us at
<a href="mailto:[email protected]"><span style="color:rgb(120,123,175);font-weight:900">enclone</span>@10xgenomics.com</a>.</p>

</body>
</html>
9 changes: 0 additions & 9 deletions pages/auto/visual.html
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Expand Up @@ -276,15 +276,6 @@ <h2>Debugging under Linux</h2>
with details as above.</p>

<! --- ▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ --->

<h2>Feedback</h2>

<p>You can send your thoughts to us here:
<a href="mailto:[email protected]"><span style="color:rgb(120,123,175);font-weight:900">enclone</span>@10xgenomics.com</a>. It is also possible for you
to contribute directly to the code and thereby extend capabilities yourself. Regardless, please
let us know if and how you are using <span style="color:rgb(120,123,175);font-weight:900">enclone visual</span>. We are very interested in your experiences!
</p>

<! --- ▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓ --->

</body>
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