From 0196178adb282cee3b544dc0adacb4e1ef2ec819 Mon Sep 17 00:00:00 2001 From: Abhijna Parigi Date: Thu, 21 Nov 2024 13:41:20 -0800 Subject: [PATCH 01/10] deprecation messasing --- index.html | 16 +++------------- node_modules/.yarn-integrity | 10 ++++++++++ pages/index.html.src | 23 +++++++++++------------ yarn.lock | 4 ++++ 4 files changed, 28 insertions(+), 25 deletions(-) create mode 100644 node_modules/.yarn-integrity create mode 100644 yarn.lock diff --git a/index.html b/index.html index f9cb94376..b0609ecb2 100644 --- a/index.html +++ b/index.html @@ -31,7 +31,7 @@
-

enclone (beta)

+

enclone

Accurate and user-friendly computational tool for clonal grouping to study the adaptive immune system

(Antigen analysis is not supported)

@@ -49,7 +49,7 @@

(Antigen analysis is not supported)

- enclone (beta) is provided as a tool for use + enclone is provided as a tool for use by the community to accelerate immunology research. enclone is only supported via Inputs to enclone

The enclone software

-

enclone is beta software†† released +

enclone was a beta software†† released under this license. Binary executables for Linux and Mac and Windows can be directly downloaded from this page, as can sample 10x Genomics datasets. @@ -270,13 +270,6 @@

The enclone soft solution.

-

- ††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 - this page for the history of changes. -

-

@@ -958,9 +951,6 @@

Questions

padding: 8px; font-size: 110%"> enclone is provided as a tool for use by the community. - enclone 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.

diff --git a/node_modules/.yarn-integrity b/node_modules/.yarn-integrity new file mode 100644 index 000000000..20d6d4881 --- /dev/null +++ b/node_modules/.yarn-integrity @@ -0,0 +1,10 @@ +{ + "systemParams": "darwin-arm64-108", + "modulesFolders": [], + "flags": [], + "linkedModules": [], + "topLevelPatterns": [], + "lockfileEntries": {}, + "files": [], + "artifacts": {} +} \ No newline at end of file diff --git a/pages/index.html.src b/pages/index.html.src index a23c7897d..1664581df 100644 --- a/pages/index.html.src +++ b/pages/index.html.src @@ -7,8 +7,15 @@ enclone banner +

+#The enclone tool is deprecated and will no longer receive updates or feature enhancements. +#It will remain available for a limited time but will be fully disabled the future. We recommend transitioning to the enhanced functionality now integrated directly within Cell Ranger. +

+ +
-

#enclone (beta)

+

#enclone

Accurate and user-friendly computational tool for clonal grouping to study the adaptive immune system

(Antigen analysis is not supported)

@@ -23,7 +30,7 @@ acids.

-#enclone (beta) is provided as a tool for use by the community to accelerate immunology research. +#enclone is provided as a tool for use by the community to accelerate immunology research. #enclone is only supported via #enclone@10xgenomics.com. The clonotype assignment algorithm that is part of #enclone is integrated into Cell Ranger. @@ -183,7 +190,7 @@ sgRNA, and other cellular features. You can see a list of publications that use

The #enclone software

-

#enclone is beta software†† released under this license. +

#enclone software†† is released under this license. Binary executables for Linux and Mac and Windows can be directly downloaded from this page, as can sample 10x Genomics datasets. #enclone can be run on a laptop, desktop, or server. @@ -207,13 +214,6 @@ analysis of V(D)J and other data from the solution.

-

- ††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 -this page for the history of changes. -

-

@@ -777,8 +777,7 @@ screenshot, except when necessary. Please send both the command you used and

#enclone is provided as a tool for use by the community. -#enclone 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. +#enclone is now deprecated and will no longer receive updates or feature enhancements.

diff --git a/yarn.lock b/yarn.lock new file mode 100644 index 000000000..fb57ccd13 --- /dev/null +++ b/yarn.lock @@ -0,0 +1,4 @@ +# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY. +# yarn lockfile v1 + + From 5794280b4d2ed7f0d9ce40b1437369e5f6ca6b45 Mon Sep 17 00:00:00 2001 From: Abhijna Parigi Date: Thu, 21 Nov 2024 13:45:45 -0800 Subject: [PATCH 02/10] Update pages/index.html.src --- pages/index.html.src | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/index.html.src b/pages/index.html.src index 1664581df..93edd6da6 100644 --- a/pages/index.html.src +++ b/pages/index.html.src @@ -9,7 +9,7 @@

-#The enclone tool is deprecated and will no longer receive updates or feature enhancements. +#enclone is deprecated and will no longer receive updates or feature enhancements. #It will remain available for a limited time but will be fully disabled the future. We recommend transitioning to the enhanced functionality now integrated directly within Cell Ranger.

From 2b6eca9511c11e4df3400c087f0a1ba3509e522e Mon Sep 17 00:00:00 2001 From: Abhijna Parigi Date: Thu, 21 Nov 2024 13:46:09 -0800 Subject: [PATCH 03/10] Update pages/index.html.src --- pages/index.html.src | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/index.html.src b/pages/index.html.src index 93edd6da6..573ab225e 100644 --- a/pages/index.html.src +++ b/pages/index.html.src @@ -10,7 +10,7 @@

#enclone is deprecated and will no longer receive updates or feature enhancements. -#It will remain available for a limited time but will be fully disabled the future. We recommend transitioning to the enhanced functionality now integrated directly within Cell Ranger. +#It will remain available for a limited time but will be disabled the future. We recommend transitioning to the enhanced functionality now integrated directly within Cell Ranger.

From 0134c4473d109a4b49c153e7739d6f4aa1fce6a0 Mon Sep 17 00:00:00 2001 From: Abhijna Parigi Date: Thu, 21 Nov 2024 13:46:57 -0800 Subject: [PATCH 04/10] Update pages/index.html.src --- pages/index.html.src | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/index.html.src b/pages/index.html.src index 573ab225e..5fcec687c 100644 --- a/pages/index.html.src +++ b/pages/index.html.src @@ -10,7 +10,7 @@

#enclone is deprecated and will no longer receive updates or feature enhancements. -#It will remain available for a limited time but will be disabled the future. We recommend transitioning to the enhanced functionality now integrated directly within Cell Ranger. +#It will remain available for a limited time but will be disabled the future. We recommend transitioning to the improved functionality now integrated directly within Cell Ranger.

From 10867a10471d2fdbe612a75dd9a33cd166407b84 Mon Sep 17 00:00:00 2001 From: Abhijna Parigi Date: Mon, 25 Nov 2024 10:04:33 -0800 Subject: [PATCH 05/10] Update pages/index.html.src Co-authored-by: Chris Macklin --- pages/index.html.src | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pages/index.html.src b/pages/index.html.src index 5fcec687c..4af921c63 100644 --- a/pages/index.html.src +++ b/pages/index.html.src @@ -10,7 +10,7 @@

#enclone is deprecated and will no longer receive updates or feature enhancements. -#It will remain available for a limited time but will be disabled the future. We recommend transitioning to the improved functionality now integrated directly within Cell Ranger. +#It will remain available for a limited time but will be removed in the future. We recommend transitioning to the improved functionality now integrated directly within Cell Ranger version 9.0 and later.

From 26072e621d4add4534a9ed6a0de36fc8ea7d8891 Mon Sep 17 00:00:00 2001 From: Abhijna Parigi Date: Mon, 25 Nov 2024 10:26:37 -0800 Subject: [PATCH 06/10] removed mailto --- index.html | 28 ---------------------- pages/auto/help.all.html | 8 +++---- pages/auto/help.faq.html | 4 ++-- pages/auto/help.setup.html | 3 +-- pages/auto/install_issues.html | 36 ---------------------------- pages/auto/installation_details.html | 3 --- pages/auto/visual.html | 9 ------- pages/index.html.src | 11 --------- pages/install_issues.html.src | 20 ---------------- pages/installation_details.html.src | 3 --- 10 files changed, 6 insertions(+), 119 deletions(-) diff --git a/index.html b/index.html index b0609ecb2..e6ac94218 100644 --- a/index.html +++ b/index.html @@ -51,9 +51,6 @@

(Antigen analysis is not supported)

padding: 8px; font-size: 110%"> enclone is provided as a tool for use by the community to accelerate immunology research. - enclone is only supported via - enclone@10xgenomics.com. The clonotype assignment algorithm that is part of enclone is integrated into Cell Ranger.

@@ -928,31 +925,6 @@

The power of enclone -

-

Questions

- -

- Please contact us with your questions and comments! We look forward to hearing your feedback and ideas to - further evolve enclone. -

- -

- Our address is enclone@10xgenomics.com. -

- -

- To send us enclone output, please simply - cut and paste text, rather than send a - screenshot, except when necessary. Please send both the command you used and the output. -

- -

- enclone is provided as a tool for use by the - community. -

-

diff --git a/pages/auto/help.all.html b/pages/auto/help.all.html index 1c142033d..1ee8f0210 100644 --- a/pages/auto/help.all.html +++ b/pages/auto/help.all.html @@ -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: @@ -1879,8 +1877,8 @@ Frequently Asked Questions -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. 1. Why is my enclone output garbled? diff --git a/pages/auto/help.faq.html b/pages/auto/help.faq.html index 4916c1c58..6cb6c0e37 100644 --- a/pages/auto/help.faq.html +++ b/pages/auto/help.faq.html @@ -48,8 +48,8 @@ 

 Frequently Asked Questions
 
-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.
 
 1. Why is my enclone output garbled?
 
diff --git a/pages/auto/help.setup.html b/pages/auto/help.setup.html
index 329ea83f3..59961662f 100644
--- a/pages/auto/help.setup.html
+++ b/pages/auto/help.setup.html
@@ -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?
diff --git a/pages/auto/install_issues.html b/pages/auto/install_issues.html
index e2a41ea3f..08fab4e1b 100644
--- a/pages/auto/install_issues.html
+++ b/pages/auto/install_issues.html
@@ -68,37 +68,6 @@ 
Case 2: download is so slow that it doesn't finish

 
 

 
-
Case 3: installation seems to succeed but you get command not found

-
-
In this case, the install script appears to succeed, but when you 
-open a new terminal window and
-type enclone, you get a message about the command not being found.

-
-
This should not happen, and we do not know why 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.

-
-
Please open a new terminal window, type the following commands, and then cut and paste 
-the entirety (commands plus responses) as text into an email to
-enclone@10xgenomics.com.
-
-

-
-
1. enclone --check

-
-
This should say something about enclone not being found.  Otherwise you have a different 
-problem.

-
-
2. echo $PATH

-
-
This reveals what directories are searched when you type a command.

-
-
3. curl -sSf -L bit.ly/enclone_install_debug | bash
-
-
This generates some further debugging information

-
-

-
 
Case 4: installation seems to succeed but enclone is killed

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

 
-
Case 6: something else goes wrong

-
-Then please write to us at
-enclone@10xgenomics.com.

-
 
 
diff --git a/pages/auto/installation_details.html b/pages/auto/installation_details.html
index 950f8ad86..638bd3afb 100644
--- a/pages/auto/installation_details.html
+++ b/pages/auto/installation_details.html
@@ -84,8 +84,5 @@ 
enclone 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.

 
-
Questions?  You can email us at
-enclone@10xgenomics.com.

-
 
 
diff --git a/pages/auto/visual.html b/pages/auto/visual.html
index 87d24fb88..03623f06b 100644
--- a/pages/auto/visual.html
+++ b/pages/auto/visual.html
@@ -276,15 +276,6 @@ 
Debugging under Linux

 with details as above.

 
 
-
-
Feedback

-
-
You can send your thoughts to us here:
-enclone@10xgenomics.com.  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 enclone visual.  We are very interested in your experiences!
-

-
 
 
 
diff --git a/pages/index.html.src b/pages/index.html.src
index 4af921c63..a7b6f6671 100644
--- a/pages/index.html.src
+++ b/pages/index.html.src
@@ -28,13 +28,6 @@ padding: 8px; font-size: 110%">
         (clonotypes) and
 	compactly displays each clonotype along with its salient features, including mutated amino 
         acids.

-

-#enclone is provided as a tool for use by the community to accelerate immunology research.  
-#enclone is only supported via
-#enclone@10xgenomics.com.
-The clonotype assignment algorithm that is part of #enclone is integrated into Cell Ranger.
-

 
 
#enclone has been designed for immunologists but anyone can download and experiment with it.

 
@@ -765,10 +758,6 @@ Please contact us with your questions and comments! We look forward to hearing y
 further evolve #enclone.
 

 
-

-Our address is #enclone@10xgenomics.com.
-

-
 

 To send us #enclone output, please simply cut and paste text, rather than send a 
 screenshot, except when necessary.  Please send both the command you used and the output.
diff --git a/pages/install_issues.html.src b/pages/install_issues.html.src
index d0fcbfaeb..50c3b0b4c 100644
--- a/pages/install_issues.html.src
+++ b/pages/install_issues.html.src
@@ -34,21 +34,6 @@ characteristics of your connection.

 
 

 
-
Case 3: installation seems to succeed but you get command not found

-
-
In this case, the install script appears to succeed, but when you 
-open a new terminal window and
-type #enclone, you get a message about the command not being found.

-
-
This should not happen, and we do not know why 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.

-
-
Please open a new terminal window, type the following commands, and then cut and paste 
-the entirety (commands plus responses) as text into an email to
-#enclone@10xgenomics.com.
-
-

 
 
1. enclone --check

 
@@ -91,10 +76,5 @@ operating system on it.  Your options are:
 
 

 
-
Case 6: something else goes wrong

-
-Then please write to us at
-#enclone@10xgenomics.com.

-
 
 
diff --git a/pages/installation_details.html.src b/pages/installation_details.html.src
index be0b58d5a..8f2365225 100644
--- a/pages/installation_details.html.src
+++ b/pages/installation_details.html.src
@@ -50,8 +50,5 @@ if ~/bin is not in your path, the script adds a line to
 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.

 
-
Questions?  You can email us at
-#enclone@10xgenomics.com.

-
 
 

From 012f0c6970f42a7647edbfe17968d880c44570ea Mon Sep 17 00:00:00 2001
From: Abhijna Parigi 
Date: Mon, 25 Nov 2024 10:27:11 -0800
Subject: [PATCH 07/10] Delete yarn.lock

---
 yarn.lock | 4 ----
 1 file changed, 4 deletions(-)
 delete mode 100644 yarn.lock

diff --git a/yarn.lock b/yarn.lock
deleted file mode 100644
index fb57ccd13..000000000
--- a/yarn.lock
+++ /dev/null
@@ -1,4 +0,0 @@
-# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY.
-# yarn lockfile v1
-
-

From 0b62a22685e23a31256039e9e380b0cd31793ac1 Mon Sep 17 00:00:00 2001
From: Abhijna Parigi 
Date: Mon, 25 Nov 2024 13:25:36 -0800
Subject: [PATCH 08/10] Delete pages/index.html.src

---
 pages/index.html.src | 781 -------------------------------------------
 1 file changed, 781 deletions(-)
 delete mode 100644 pages/index.html.src

diff --git a/pages/index.html.src b/pages/index.html.src
deleted file mode 100644
index a7b6f6671..000000000
--- a/pages/index.html.src
+++ /dev/null
@@ -1,781 +0,0 @@
-enclone (bit.ly/enclone)
-
-
-
-

-
-enclone banner
-
-
-

-#enclone is deprecated and will no longer receive updates or feature enhancements. 
-#It will remain available for a limited time but will be removed in the future. We recommend transitioning to the improved functionality now integrated directly within Cell Ranger version 9.0 and later.
-

-
-
-

-
#enclone

-
Accurate and user-friendly computational tool for clonal grouping to study the adaptive immune system

-
(Antigen analysis is not supported)

-

-
-
10x Genomics Chromium Single Cell V(D)J data 
-        containing B cell 
-	receptor (BCR) and T cell receptor (TCR) RNA sequences are entered as input data to 
-        #enclone. Based on the
-	input, #enclone finds and organizes cells arising from the same progenitors into groups 
-        (clonotypes) and
-	compactly displays each clonotype along with its salient features, including mutated amino 
-        acids.

-
-
#enclone has been designed for immunologists but anyone can download and experiment with it.

-
-
Background: when you get sick, your body mounts an immune response by selectively 
-amplifying immune cells and mutations within these selected cells.  #enclone allows you to see the 
-history of
-single immune cells within a biological sample (such as a blood draw or biopsy).  This history
-reflects how the cognate receptors of these cells evolved in response to antigens, including
-viruses, bacteria, and tumors.

-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
 1. Introduction  8. Help 
 2. Objective  9. Understanding #enclone output 
 3. Why #enclone?  10. Combining multiomic data 
 4. Data input  11. Visualizing multiple clonotypes at once 
 5. Software  12. The power of #enclone 
 6. Installing #enclone  13. Questions 
 7. Running #enclone  14. Where am I? 

-
-

-
-

-
-

-
Introduction

-
The body defends itself from antigens, like viruses, bacteria, and tumors, by recognizing the
-antigens and mounting an immune response through selective amplification of immune cells and
-mutations within selected cells. #enclone enables profiling of the history of single immune
-cells within a biological sample (such as a blood draw or a biopsy) by mapping the evolution of the
-cognate BCRs and TCRs of those cells responding to antigen exposure. This history reflects how the
-cognate receptors of these cells evolved in response to various antigens.

-
-

-
Objective

-
-
-
Using #enclone to profile B and T cell receptors for any sample using Chromium Single Cell
-V(D)J as input enables you to make the best use of your data. You can explore the biology of these
-cells without help from a computational expert!
	
-
-
The objective of #enclone is to:

-
-
-  
-  
-  
-  
-

-       

-       Find and display clonotypes:
-       groups of T and B cells sharing the same fully rearranged common ancestor.
-       

-  		
-	  
Find: 
-          It is easy to mistakenly put unrelated cells in 
-          the same clonotype, or "pollute" a clonotype with extraneous chains. 
-          #enclone's algorithms make finding accurate.
 
-	  
Display: 
-          It is challenging to compactly represent a 
-          large repertoire of data. #enclone enables compact, easy-to-grasp data 
-  display.

-  

-
-
The diversity of BCR and TCR chains, containing various combinations of V, D, and/or J segments,
-broadens the immune repertoire to protect against a wide variety of pathogens. The figure below
-illustrates the concept of a BCR clonotype. A similar concept applies to TCRs but without 
-somatic hypermutations.

-
-
-what is a clonotype
-
-
Each cell in a clonotype is typically represented by two or three chains, and this information is
-present and directly observable in single cell V(D)J data. #enclone computationally approximates 
-the clonotypes
-from the data with high accuracy (see below). The methods of #enclone are described
-briefly in the online documentation for #enclone, and see
-below.

-
-

-
-

-
Why use #enclone?

-

-#enclone has unique features!
-

-

-Unique insights into 10x Genomics data: #enclone has been designed and tested 
-extensively to
-gain in-depth insight and perspective regarding 10x Genomics single cell V(D)J datasets. Other 
-similar tools
-may be used, but frequently, #enclone will provide a different answer, which in turn may affect
-the biological interpretation of the data.	
-

-

-Speed: #enclone is very fast, allowing analysis of datasets in seconds.
-

-

-Easy installation: The software is easy to install and to use.
-

-
-

-
-

-
Inputs to #enclone

-
-
10x Genomics single cell 5' data†

-
-
†
-BCR or TCR RNA sequences generated using the 10x Genomics
-Chromium Single Cell Immune Profiling Solution and Cell Ranger 3.1 or higher are the inputs to
-#enclone. #enclone can also process and display gene expression and Feature Barcode data
-from the same cells. The latter can be used to quantify cell surface proteins, antigen binding, CRISPR
-sgRNA, and other cellular features. You can see a list of publications that use 10x VDJ data
-here.
-
-

-
-

-
-

-
The #enclone software

-
-
#enclone software†† is released under this license.  
-Binary executables for Linux and Mac and Windows can be directly downloaded from this page, as can 
-sample 10x Genomics datasets.
-#enclone can be run on a laptop, desktop, or server.
-

-

-To use #enclone, basic knowledge of the command line is necessary. The command line is easy to 
-learn, and a
-colleague may be able to help you if you are unfamiliar. Additional skills, like programming, 
-are not required. The command line can be dynamically changed to select specific clonotypes and 
-fields you wish to
-see.  #enclone is fast, typically responding in seconds (if run on a single dataset).
-

-
-

-#enclone, in addition to Cell Ranger and 
-Loupe
-(and in which the core algorithm of #enclone will be integrated at a later point in time), 
-supports the
-analysis of V(D)J and other data from the 
-Chromium Single Cell Immune Profiling
-solution.
-

-
-

-
-

-
Installing #enclone

-
-

-You can run #enclone directly from a Linux or Mac terminal window; see 
-here for Windows instructions.
-

-
-
-
-
-
-
-
-
Type this 
-
curl -sSf -L bit.ly/enclone_install | bash -s SIZE

-		
- where SIZE is 
-small, medium, large, or colossus, according to:
-

-
-

-
-
-  
-  
-
-  
-  
-  
-  
-  
-  
-  
-  
-  
-  
-  
-  
-  
-  
-  
-  
-  
-  
-  
-  
-  
-  
-

-       

-       small
-       

-  		
-       

-       load small dataset collection (one dataset, 123085)
-       

-  		
-       

-       30 MB
-       

-  		
-       

-       do this if your internet connection is very slow
-       

-  

-       

-       medium
-       

-  		
-       

-       load medium dataset collection
-       

-  		
-       

-       3400 MB
-       

-  		
-       

-       do this for a moderate number of datasets (~120)
-       

-  

-       

-       large
-       

-  		
-       

-       load large dataset collection
-       

-  		
-       

-       4700 MB
-       

-  		
-       

-	do this for a large number of datasets (~240)
-       

-  

-       

-       colossus
-       

-  		
-       

-       load colossus dataset collection
-       

-  		
-       

-       26400 MB
-       

-  		
-       

-        same as large but includes gene expression data for many datasets
-       

-  

-
-
The command does three things:

-
    
-
  1. Puts the #enclone executable (for Linux or Mac as appropriate) in ~/bin.
    2. 
-
  2. If needed, adds a line to your bash initialization file so that ~/bin is included.
-
    3. 
-
  3. Puts #enclone datasets in ~/enclone.
    4. 
-

-Additional details can be found here.
-
-Restart your terminal session; you can now run #enclone.

-
-
-
-
-
-

-Please see 
-here if you have an installation problem.
-

-
-
To update, type the same command!
-
-You can also type enclone UPDATE, which does the same thing (except for older versions
-of #enclone).  Only required files will be downloaded.  
-See history for the history of changes to 
-#enclone.
-

-
-
Information about previous releases of #enclone, matching particular Cell Ranger releases is
-here, along with an inventory of #enclone changes that
-affect Cell Ranger output.

-
-
-
-
-
-

-On a Mac, the Terminal application can enter weird states.  One behavior is an intermittently 
-spinning disk.  Another is that some executables (perhaps #enclone) may respond with
-Command not found or Permission denied.  In such cases, it may work
-to close the Terminal application (Quit Terminal on the top bar), then reopen it.
-This should only be needed rarely, if at all.
-

-
-

-
-

-
Running #enclone

-
-
Running #enclone can be as simple as typing e.g.

-
enclone BCR=/home/my_name/experiment_123
-

-
where the path is where your Cell Ranger outputs live, but there are many options to learn
-about.  For example, if you want to combine many datasets, you can do that, but you probably
-need to provide a metadata file that describes the datasets.  You can find most of the #enclone
-documentation within its online menus.  To get started you should:

-
    
-
  1. 
-
    Type enclone help, to make sure your terminal window works for 
-#enclone.
    
-
    
-A few things you need to know:
-
    1. To view the online help, your terminal window needs to be 100 characters wide 
-              (or wider).
-
    2. When you view #enclone output, you will in general need to make your window even 
-              wider.
-
    3. How wide depends on the data and the fields you choose to show.
-
    4. If it's not wide enough, the output will "wrap" and be very confusing!
-
    5. Having clonotype tables in a Terminal on a Mac can make the Terminal less
-              responsive.  This may depend on the operating system version.
-
    
-
    2. 
-
  2. 
-
    Type enclone to get to the main #enclone help menu.
    
-
    3. 
-

-

-
-

-
Help

-
-

-From any page, clicking on the banner at the top will take you back 
-here.

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pages on site and accessible from command line
commandwhat it provides
enclone helphelp to test for correct setup
enclonewhat you see here; guide to all the docs
enclone help quickquick guide to getting started
enclone help howoutline of how #enclone works, see also heuristics
enclone help commandinfo about #enclone command line processing
enclone help glossaryglossary of terms used by #enclone, conventions
enclone help example1explanation of an example
enclone help example2example of gene expression, feature barcodes
enclone help inputhow to provide input to #enclone
enclone help input_techhow to provide input to #enclone (technical notes)
enclone help parseableparseable output
enclone help filterclonotype filtering, feature enrichment scanning
enclone help specialspecial filtering options
enclone help lvarslead column options
enclone help cvarsper chain column options
enclone help aminoper chain column options for amino acids
enclone help displayother clonotype display options
enclone help indelsinsertion and deletion handling
enclone help colorhow #enclone uses color, and related things
enclone help faqfrequently asked questions
enclone help allconcatenation of all the help pages 
 (USE THIS TO SEARCH ALL HELP PAGES)

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other pages on site
pageaudience
history of changeseveryone
detecting illusory clonotypeseveryone
enclone developers guidepeople who want to contribute code
licenseeveryone
Windowspeople using Windows computers
notes on heuristicsthose curious about the algorithm
#enclone default filteringthose curious about the algorithm
plotseveryone
making phylogenetic treeseveryone
installation troubleshooting
-     if you have trouble installing
installation details
-     those curious what install command does
iNKT and MAIT cells
-     those curious about iNKT and MAIT cells
V(D)J features
-     those curious about CDR*, etc. calculations
enclone variable inventory
-     everyone
D genes, junction regions
-     everyone
#enclone in cellranger
-     everyone

-
-

-
-
-
-
-

-Additional information may be found in our bioRxiv preprint
-

-
-enclone: precision clonotyping and analysis of immune receptors.
-

-

-
-
And we're here to help!  See the bottom of this page for how to contact us.

-
-

-
-

-
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-
-

-
Understanding #enclone output

-
-
The example below shows how #enclone displays clonotypes. Understanding this display is
-important for using #enclone.  Consult the available #enclone documentation and use
-the sample datasets to understand #enclone features and output.
	
-
-enclone annotated example
-
-Notice the compression in two directions:
-
    
-	
  1. Vertically to group cells into a single line if they have identical V(D)J 
-                transcripts
-		(instead of showing one line for every cell).
    2. 
-	
  2. Horizontally, a flexible concept, to show by default all positions exhibiting a
-		difference from the reference and all positions in the CDR3 (instead of showing
-		all transcript positions, only "interesting" positions are shown).
    3. 
-

-
-
Approximately the same output would be obtained by typing:

-
enclone BCR=123085 CDR3=CTRDRDLRGATDAFDIW
-

-(As we change the algorithm, results are perturbed, and we have not updated the
-diagram each time.  All other outputs shown on this site are kept current.)
-
-
The directory 123085 is in the directory ~/enclone/datasets and 
-contains some files from a Cell Ranger run, obtained from a human ovarian cancer sample.

-
-

-How does #enclone find my data?
-It uses a search path called PRE that is preset to 
-~/enclone/datasets,~/enclone/datasets2, and which can be set to any value, either
-by setting PRE=... on the command line, or by setting the environment variable
-ENCLONE_PRE.  To find your data, #enclone prepends PRE to the value of 
-BCR or TCR given on the command line.
-For example, all of the following argument combinations do the same thing:
-
1. BCR=123085 (using the default value of PRE)
-
2. PRE=~/enclone/datasets BCR=123085
-
3. PRE=~/enclone BCR=datasets/123085
-
4. BCR=~/enclone/datasets/123085.
-
There is also an argument META that is convenient for specifying multiple
-datasets.  See here for how.
-

-

-Please note that while paths can have non-Latin characters, best practice is to not have 
-blanks, tabs, etc. in path names.  #enclone can be made to work with such characters by double
-quoting the paths, but it makes things harder, and other programs you might use may break.
-

-
-
The argument CDR3=CTRDRDLRGATDAFDIW causes #enclone to display only clonotypes in 
-which 
-the given CDR3 sequence occurs.  Many other filters are provided.  In the absence of filters, all 
-clonotypes are shown.  Clonotypes are shown from largest to smallest, and the output is 
-automatically paged, so you can scroll through it.

-
By default, #enclone prints clonotypes in this human-readable form.  You can also instruct 
-#enclone
-to print clonotypes in machine-readable forms that are suitable for input to other programs.

-

-
-

-
Combining multiomic data

-
-
Gene expression and Feature Barcode data can be displayed simultaneously alongside VDJ data.  For
-example, here we add columns for the same clonotype, showing the median number of UMIs detected
-for all genes, and a particular gene:

-
-#include pages/auto/clonotype_with_gex.html
-
-
To obtain this, we added the extra arguments
-GEX=123217 LVARSP=gex,IGHV3-49_g
-to the previous command.  The GEX part points to the directory containing gene 
-expression data.  The LVARSP part defines the additional columns 
-to be displayed.

-
Other types of data can be brought in via Feature Barcoding / Feature Barcode Technology.
-For example, the response to multiple antigens can be measured using approaches such as those
-mentioned in the LIBRA-seq
-and Wilson/Stamper/Dugan et al.
-papers. These data can be displayed as additional columns.

-

-
-

-
Visualizing multiple clonotypes

-
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-  
-

-       honeycomb plot
-  
-	  
After selecting multiple clonotypes in #enclone, you can display them using
-		  a "honeycomb" plot.

-      
In this instance, pre- and post-vaccination samples were collected from four individuals,
-      many datasets were generated for each sample, and these were combined in a single call
-      to #enclone.  Clonotypes containing at least ten cells are shown.  
-      The plot was generated by adding

-
MIN_CELLS=10 PLOT="clono.svg,pre->blue,post->red
-LEGEND=blue,"pre-vaccination cell",
-       red,"post-vaccination cell"

-      
to the #enclone command line, yielding the image shown here as the file 
-      clono.svg.

-      
For more information about honeycomb plots, 
-         see here.

-  

-
-

-

-
-

-
The power of #enclone

-
-
There are many ways to use 10x Genomics data to study immunobiology.

-
Response to an antigen or vaccine: #enclone is a great tool for studying responses to a
-vaccine. For example, in the previous section, the red clonotypes may represent responses to 
-antigens in the vaccine.

-
Vaccine and therapeutic antibody development: For certain infectious agents e.g. COVID-19,
-a vaccine does not currently exist; different approaches may be employed in pursuit of this goal. One such
-approach is to identify patient and survivor B cell clonotypes that expand in response to the infectious
-disease. These define antibodies that can be used to design passive or active vaccines.

-
Additional power is added by mapping antigen specificity to multiple antigens directly via Feature 
-Barcode Technology (one example of this is the LIBRA-seq
-publication). These data are easy to display in #enclone.  Candidates can be selected directly for vaccine or therapeutic 
-development by picking large clonotypes with high antigen counts and single or multiple antigen specificities.

-
We are actively working on further functionality that will make this process even more effective.
 
-
See this vignette to learn how to generate phylogenetic trees using
-#enclone.
-
Another example use of #enclone is the detection of
-illusory clonotypes.

-
-

-
-

-
Questions

-
-

-Please contact us with your questions and comments! We look forward to hearing your feedback and ideas to
-further evolve #enclone.
-

-
-

-To send us #enclone output, please simply cut and paste text, rather than send a 
-screenshot, except when necessary.  Please send both the command you used and the output.
-

-
-

-#enclone is provided as a tool for use by the community.  
-#enclone is now deprecated and will no longer receive updates or feature enhancements.
-

-
-

-
-

-
Where am I?

-
-
-
bit.ly/#enclone

-
-
-

From 6a318cdeb9cd8617f416ddd25dd064e559c6c90c Mon Sep 17 00:00:00 2001
From: Abhijna Parigi 
Date: Mon, 25 Nov 2024 13:25:52 -0800
Subject: [PATCH 09/10] Delete pages/install_issues.html.src

---
 pages/install_issues.html.src | 80 -----------------------------------
 1 file changed, 80 deletions(-)
 delete mode 100644 pages/install_issues.html.src

diff --git a/pages/install_issues.html.src b/pages/install_issues.html.src
deleted file mode 100644
index 50c3b0b4c..000000000
--- a/pages/install_issues.html.src
+++ /dev/null
@@ -1,80 +0,0 @@
-enclone installation problems
-
-
-
-

-
-enclone banner
-
-
-
#enclone installation troubleshooting

-
-
The purpose of this page is to provide guidance in case the #enclone installation fails.

-
-

-
-
Case 1: the curl command is not found

-
-
The command curl is not installed on your computer.  In that case,
-you should have the command wget, and can use that instead.  To do so, run the
-following command:
-
wget -nv bit.ly/enclone_install -O - | sh -s SIZE

-where SIZE
-is as described on the main #enclone page.
-

-
-

-
-
Case 2: download is so slow that it doesn't finish

-
-
In this case, please use the SMALL option, and if you
-still have difficulty, please contact us.  We might be able to reduce the download size.  Please
-let us know your typical download rate (MB/sec) and any other relevant information about the
-characteristics of your connection.

-
-

-
-
-
1. enclone --check

-
-
This should say something about #enclone not being found.  Otherwise you have a different 
-problem.

-
-
2. echo $PATH

-
-
This reveals what directories are searched when you type a command.

-
-
3. curl -sSf -L bit.ly/enclone_install_debug | bash
-
-
This generates some further debugging information

-
-

-
-
Case 4: installation seems to succeed but enclone is killed

-
-
In this case, when you type enclone 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
-problem went away if the executable was deleted
-
rm ~/bin/enclone
-
and then the installation line was repeated.  We are actively looking for a robust solution.
-Please let us know if you are stuck.
-

-
-

-
-
Case 5: installation seems to succeed but you get a message about 
-GLIBC not found

-
-
This probably means that you are using a Linux machine which has a very old version of the
-operating system on it.  Your options are:
-
    
-
  1. Get the operating system on the machine upgraded.
    2. 
-
  2. Use a different machine.
    3. 
-
  3. Install #enclone from source code.  This is not necessarily difficult.
    4. 
-

-

-
-

-
-
-

From fd85bf7057e01ca94f9be339a57c8fd03cb6c748 Mon Sep 17 00:00:00 2001
From: Abhijna Parigi 
Date: Mon, 25 Nov 2024 13:26:03 -0800
Subject: [PATCH 10/10] Delete pages/installation_details.html.src

---
 pages/installation_details.html.src | 54 -----------------------------
 1 file changed, 54 deletions(-)
 delete mode 100644 pages/installation_details.html.src

diff --git a/pages/installation_details.html.src b/pages/installation_details.html.src
deleted file mode 100644
index 8f2365225..000000000
--- a/pages/installation_details.html.src
+++ /dev/null
@@ -1,54 +0,0 @@
-enclone installation details
-
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-
-

-
-enclone banner
-
-
-
#enclone installation details

-
-
The purpose of this page is to provide some information about what the #enclone installation
-command does, in case you're curious.

-
-
The command is:

-
-

-curl -sSf -L bit.ly/enclone_install | bash -s SIZE
- where SIZE is -small, medium or large -

- -

1. First, bit.ly/enclone_install is a redirect to -https://10xgenomics.github.io/enclone/install.sh, as you can see if you type -bit.ly/enclone_install+ (the + is the way that bit.ly -provides for seeing what a redirect does).

- -

2. The -sSf option to curl causes it to run quietly if it -is successful, print an error message if it fails, and importantly, not pass logging or error -messages to sh.

- -

3. The overall command just causes the script install.sh to be executed.

- -

4. On a first invocation, the script downloads the #enclone executable and datasets.

- -

5. On subsequent invocations, the script checks to see if the local copies are current, -and if not, redownloads them. In principle, the executable could be downloaded as a compressed -file, which would be more efficient. For the case where -SIZE is medium, the action is -also inefficient, as it downloads everything if anything has changed.

- -

6. The script puts the executable in ~/bin and the datasets in -~/enclone. These directories are created if they don't already exist.

- -

7. The following step makes it so you don't have to type -~/bin/enclone every time you want to run it, and can instead type just -enclone. To enable this, -if ~/bin is not in your path, the script adds a line to -.bash_profile or .profile that makes ~/bin first in -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.

- - -