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[TCDR-2137] Enclone deprecated #558

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merged 13 commits into from
Dec 17, 2024
Merged

[TCDR-2137] Enclone deprecated #558

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0746da1
deprecation messasing
abhijna Nov 21, 2024
f0a72e6
Update pages/index.html.src
abhijna Nov 21, 2024
bc3901c
Update pages/index.html.src
abhijna Nov 21, 2024
ee904a6
Update pages/index.html.src
abhijna Nov 21, 2024
149a25c
Update pages/index.html.src
abhijna Nov 25, 2024
97f9952
removed mailto
abhijna Nov 25, 2024
e318598
Delete yarn.lock
abhijna Nov 25, 2024
8256e7a
Delete pages/index.html.src
abhijna Nov 25, 2024
f487683
Delete pages/install_issues.html.src
abhijna Nov 25, 2024
53a21f8
Delete pages/installation_details.html.src
abhijna Nov 25, 2024
5cfe3f7
Renumber
evolvedmicrobe Dec 16, 2024
fe1b990
More updates
evolvedmicrobe Dec 17, 2024
de79829
Remove off target
evolvedmicrobe Dec 17, 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:enclone@10xgenomics.com"><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
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:enclone@10xgenomics.com"><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 enclone@10xgenomics.com.

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 enclone@10xgenomics.com.
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 enclone@10xgenomics.com.
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 enclone@10xgenomics.com.
Here we go through several setup tests.


1. Are you using a fixed width font?
Expand Down
40 changes: 2 additions & 38 deletions pages/auto/install_issues.html
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Expand Up @@ -68,38 +68,7 @@ <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>
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@abhijna Sorry I missed this before, but minor nitpick, if you delete case 3 then the subsequent cases should be re numbered (unless there is some permalink structure I am not thinking about.

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Actually never mind, just went ahead and made the changes myself to avoid churn, going to merge.


<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:enclone@10xgenomics.com"><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>
<h2>Case 3: 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
about it being killed. This has happened to some Mac users. In one case we observed that the
Expand All @@ -111,7 +80,7 @@ <h2>Case 4: installation seems to succeed but <code>enclone</code> is killed</h2

<hr>

<h2>Case 5: installation seems to succeed but you get a message about
<h2>Case 4: installation seems to succeed but you get a message about
<code>GLIBC</code> not found</h2>

<p>This probably means that you are using a Linux machine which has a very old version of the
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:enclone@10xgenomics.com"><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:enclone@10xgenomics.com"><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:enclone@10xgenomics.com"><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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