diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractGatk4Wrapper.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractGatk4Wrapper.java
index 91959921b..29ac8b8ee 100644
--- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractGatk4Wrapper.java
+++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractGatk4Wrapper.java
@@ -91,6 +91,7 @@ public List<String> getBaseArgs(@Nullable String toolName)
         args.add(SequencePipelineService.get().getJavaFilepath());
         args.addAll(SequencePipelineService.get().getJavaOpts(_maxRamOverride));
         args.add("-DGATK_STACKTRACE_ON_USER_EXCEPTION=true");
+        args.add("-Dsamjdk.optimistic_vcf_4_4=true");
         args.add("-jar");
         args.add(getJAR().getPath());
 
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java
index 17c0fb2d4..58f6be91a 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java
@@ -17,16 +17,16 @@
 
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
 import org.junit.Assert;
 import org.junit.Test;
 import org.labkey.api.module.Module;
 import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.pipeline.PipelineJobService;
-import org.labkey.api.resource.FileResource;
 import org.labkey.api.resource.DirectoryResource;
+import org.labkey.api.resource.FileResource;
 import org.labkey.api.resource.Resource;
 import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
 import org.labkey.api.settings.AppProps;
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java
index 9a21691b5..66e61f3a9 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java
@@ -115,6 +115,10 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
         plinkArgs.add("--max-alleles");
         plinkArgs.add("2");
 
+        // NOTE: tools like sawfish can report half-called genotypes, like 0/.. For now, be most conservative in PCA:
+        plinkArgs.add("--vcf-half-call");
+        plinkArgs.add("missing");
+
         Integer threads = SequencePipelineService.get().getMaxThreads(getPipelineCtx().getLogger());
         if (threads != null)
         {
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java
index 63d1d3315..a6aa4c6dd 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java
@@ -227,6 +227,10 @@ private void runBatch(File inputVCF, File outputDirectory, VariantProcessingStep
             args.add(String.valueOf(maxRam));
         }
 
+        // NOTE: tools like sawfish can report half-called genotypes, like 0/.. For now, be most conservative in PCA:
+        args.add("--vcf-half-call");
+        args.add("missing");
+
         args.addAll(getClientCommandArgs());
 
         getWrapper().execute(args);
diff --git a/Studies/resources/queries/studies/studies/.qview.xml b/Studies/resources/queries/studies/studies/.qview.xml
new file mode 100644
index 000000000..a694c9520
--- /dev/null
+++ b/Studies/resources/queries/studies/studies/.qview.xml
@@ -0,0 +1,13 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView" hidden="false" canOverride="false">
+    <columns>
+        <column name="rowId"/>
+        <column name="studyName"/>
+        <column name="label"/>
+        <column name="category"/>
+        <column name="description"/>
+        <column name="cohorts"/>
+    </columns>
+    <sorts>
+        <sort column="studyName" descending="false"/>
+    </sorts>
+</customView>
\ No newline at end of file
diff --git a/Studies/resources/schemas/studies.xml b/Studies/resources/schemas/studies.xml
index fd0d0a189..5dbd8d185 100644
--- a/Studies/resources/schemas/studies.xml
+++ b/Studies/resources/schemas/studies.xml
@@ -132,6 +132,7 @@
         <auditLogging>DETAILED</auditLogging>
         <columns>
             <column columnName="rowid">
+                <columnTitle>Study Id</columnTitle>
                 <isAutoInc>true</isAutoInc>
                 <shownInUpdateView>false</shownInUpdateView>
                 <shownInInsertView>false</shownInInsertView>
diff --git a/Studies/resources/views/studiesOverview.html b/Studies/resources/views/studiesOverview.html
index f257fc184..2d1d6a280 100644
--- a/Studies/resources/views/studiesOverview.html
+++ b/Studies/resources/views/studiesOverview.html
@@ -12,7 +12,7 @@
                 name: 'query',
                 schemaName: 'studies',
                 queryName: 'studies',
-                maxRows: 20
+                maxRows: 10
             }).render(webpart.wrapperDivId + '-studies');
 
             // LABKEY.Query.selectRows({
@@ -62,4 +62,5 @@
 }(jQuery, LABKEY));
 
 </script>
+<div style="padding-bottom: 20px;">Below is a list of the studies tracked in this folder. Please use the <a href="<%=contextPath%>/project/<%=containerPath%>/begin.view?pageId=dataBrowser">Data Browser</a> tab to browse the dataset tracked in this project.</div>
 
diff --git a/Studies/src/org/labkey/studies/query/LookupSetTable.java b/Studies/src/org/labkey/studies/query/LookupSetTable.java
index b333008f3..022fc5802 100644
--- a/Studies/src/org/labkey/studies/query/LookupSetTable.java
+++ b/Studies/src/org/labkey/studies/query/LookupSetTable.java
@@ -22,7 +22,6 @@
 import org.labkey.api.ldk.LDKService;
 import org.labkey.api.ldk.table.AbstractDataDefinedTable;
 import org.labkey.api.query.QueryUpdateService;
-import org.labkey.api.query.SimpleUserSchema;
 
 import java.util.Map;
 
@@ -101,15 +100,7 @@ public LookupSetTable init()
     @Override
     public QueryUpdateService getUpdateService()
     {
-        return new EHRLookupsUpdateService(this);
-    }
-
-    protected class EHRLookupsUpdateService extends UpdateService
-    {
-        public EHRLookupsUpdateService(SimpleUserSchema.SimpleTable<StudiesUserSchema> ti)
-        {
-            super(ti);
-        }
+        return new UpdateService(this);
     }
 }
 
diff --git a/Studies/src/org/labkey/studies/query/StudiesUserSchema.java b/Studies/src/org/labkey/studies/query/StudiesUserSchema.java
index 715d4aa0c..928d882c6 100644
--- a/Studies/src/org/labkey/studies/query/StudiesUserSchema.java
+++ b/Studies/src/org/labkey/studies/query/StudiesUserSchema.java
@@ -1,5 +1,6 @@
 package org.labkey.studies.query;
 
+import com.google.gwt.user.client.ui.TabBar;
 import org.apache.logging.log4j.Logger;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
 import org.labkey.api.collections.CaseInsensitiveTreeSet;
@@ -7,12 +8,15 @@
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.data.DbSchema;
+import org.labkey.api.data.JdbcType;
+import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SchemaTableInfo;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
 import org.labkey.api.ldk.table.ContainerScopedTable;
 import org.labkey.api.ldk.table.CustomPermissionsTable;
+import org.labkey.api.query.ExprColumn;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.query.QueryDefinition;
 import org.labkey.api.query.QueryException;
@@ -134,7 +138,7 @@ else if (TABLE_LOOKUPS.equalsIgnoreCase(name))
         }
         else if (TABLE_STUDIES.equalsIgnoreCase(name))
         {
-            return createStudyDesignTable(name, cf, false);
+            return createStudiesTable(name, cf, false);
         }
         else if (TABLE_COHORTS.equalsIgnoreCase(name))
         {
@@ -165,7 +169,22 @@ else if (TABLE_EVENT_TYPES.equalsIgnoreCase(name))
         return super.createTable(name, cf);
     }
 
-    private TableInfo createStudyDesignTable(String name, ContainerFilter cf, boolean addTriggers)
+    private TableInfo createStudiesTable(String name, ContainerFilter cf, boolean addTriggers)
+    {
+        CustomPermissionsTable<?> ret = createStudyDesignTable(name, cf, addTriggers);
+
+        final String chr = ret.getSqlDialect().isPostgreSQL() ? "chr" : "char";
+        SQLFragment sql1 = new SQLFragment("(SELECT ").append(ret.getSqlDialect().getGroupConcat(new SQLFragment("c.label"), true, true, new SQLFragment(chr + "(10)"))).append(" as expr FROM " + StudiesSchema.NAME + "." + TABLE_COHORTS + " c WHERE c.studyId = " + ExprColumn.STR_TABLE_ALIAS + ".rowId)");
+        ExprColumn col1 = new ExprColumn(ret, "cohorts", sql1, JdbcType.VARCHAR, ret.getColumn("rowid"));
+        col1.setLabel("Cohort(s)");
+        col1.setDescription("This column lists the cohort labels for this study");
+
+        ret.addColumn(col1);
+
+        return ret;
+    }
+
+    private CustomPermissionsTable<?> createStudyDesignTable(String name, ContainerFilter cf, boolean addTriggers)
     {
         CustomPermissionsTable<SimpleUserSchema> ret = new CustomPermissionsTable<>(this, createSourceTable(name), cf);
         ret.addPermissionMapping(InsertPermission.class, StudiesDataAdminPermission.class);
diff --git a/jbrowse/build.gradle b/jbrowse/build.gradle
index 4de29862b..0e597ab4e 100644
--- a/jbrowse/build.gradle
+++ b/jbrowse/build.gradle
@@ -30,7 +30,7 @@ dependencies {
 	external "org.apache.lucene:lucene-backward-codecs:${luceneVersion}"
 }
 
-def jbPkgTask = project.tasks.named("npm_run_jb-pkg")
+def jbPkgTask = project.tasks.named("npm_run_jb-sea")
 
 jbPkgTask.configure {
     outputs.cacheIf {false}
diff --git a/jbrowse/package-lock.json b/jbrowse/package-lock.json
index b2b8218e0..5a1abd52f 100644
--- a/jbrowse/package-lock.json
+++ b/jbrowse/package-lock.json
@@ -18,7 +18,6 @@
         "@labkey/api": "^1.39.0",
         "@labkey/components": "^6.32.2",
         "@mui/x-data-grid": "^7.28.1",
-        "@yao-pkg/pkg": "^6.3.2",
         "assert": "^2.1.0",
         "browserify-zlib": "^0.2.0",
         "buffer": "^6.0.3",
@@ -48,7 +47,9 @@
         "@types/react": "^18.3.0",
         "@types/react-dom": "^18.3.0",
         "rimraf": "^6.0.1",
-        "typescript": "^5.1.6"
+        "tar": "^7.4.3",
+        "typescript": "^5.1.6",
+        "unzipper": "^0.12.3"
       }
     },
     "node_modules/@adobe/css-tools": {
@@ -2218,6 +2219,7 @@
       "version": "8.0.2",
       "resolved": "https://registry.npmjs.org/@isaacs/cliui/-/cliui-8.0.2.tgz",
       "integrity": "sha512-O8jcjabXaleOG9DQ0+ARXWZBTfnP4WNAqzuiJK7ll44AmxGKv/J2M4TPjxjY3znBCfvBXFzucm1twdyFybFqEA==",
+      "dev": true,
       "dependencies": {
         "string-width": "^5.1.2",
         "string-width-cjs": "npm:string-width@^4.2.0",
@@ -2234,6 +2236,7 @@
       "version": "6.0.1",
       "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-6.0.1.tgz",
       "integrity": "sha512-n5M855fKb2SsfMIiFFoVrABHJC8QtHwVx+mHWP3QcEqBHYienj5dHSgjbxtC0WEZXYt4wcD6zrQElDPhFuZgfA==",
+      "dev": true,
       "engines": {
         "node": ">=12"
       },
@@ -2245,6 +2248,7 @@
       "version": "6.2.1",
       "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-6.2.1.tgz",
       "integrity": "sha512-bN798gFfQX+viw3R7yrGWRqnrN2oRkEkUjjl4JNn4E8GxxbjtG3FbrEIIY3l8/hrwUwIeCZvi4QuOTP4MErVug==",
+      "dev": true,
       "engines": {
         "node": ">=12"
       },
@@ -2255,12 +2259,14 @@
     "node_modules/@isaacs/cliui/node_modules/emoji-regex": {
       "version": "9.2.2",
       "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-9.2.2.tgz",
-      "integrity": "sha512-L18DaJsXSUk2+42pv8mLs5jJT2hqFkFE4j21wOmgbUqsZ2hL72NsUU785g9RXgo3s0ZNgVl42TiHp3ZtOv/Vyg=="
+      "integrity": "sha512-L18DaJsXSUk2+42pv8mLs5jJT2hqFkFE4j21wOmgbUqsZ2hL72NsUU785g9RXgo3s0ZNgVl42TiHp3ZtOv/Vyg==",
+      "dev": true
     },
     "node_modules/@isaacs/cliui/node_modules/string-width": {
       "version": "5.1.2",
       "resolved": "https://registry.npmjs.org/string-width/-/string-width-5.1.2.tgz",
       "integrity": "sha512-HnLOCR3vjcY8beoNLtcjZ5/nxn2afmME6lhrDrebokqMap+XbeW8n9TXpPDOqdGK5qcI3oT0GKTW6wC7EMiVqA==",
+      "dev": true,
       "dependencies": {
         "eastasianwidth": "^0.2.0",
         "emoji-regex": "^9.2.2",
@@ -2277,6 +2283,7 @@
       "version": "7.1.0",
       "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-7.1.0.tgz",
       "integrity": "sha512-iq6eVVI64nQQTRYq2KtEg2d2uU7LElhTJwsH4YzIHZshxlgZms/wIc4VoDQTlG/IvVIrBKG06CrZnp0qv7hkcQ==",
+      "dev": true,
       "dependencies": {
         "ansi-regex": "^6.0.1"
       },
@@ -2291,6 +2298,7 @@
       "version": "8.1.0",
       "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-8.1.0.tgz",
       "integrity": "sha512-si7QWI6zUMq56bESFvagtmzMdGOtoxfR+Sez11Mobfc7tm+VkUckk9bW2UeffTGVUbOksxmSw0AA2gs8g71NCQ==",
+      "dev": true,
       "dependencies": {
         "ansi-styles": "^6.1.0",
         "string-width": "^5.0.1",
@@ -2307,6 +2315,7 @@
       "version": "4.0.1",
       "resolved": "https://registry.npmjs.org/@isaacs/fs-minipass/-/fs-minipass-4.0.1.tgz",
       "integrity": "sha512-wgm9Ehl2jpeqP3zw/7mo3kRHFp5MEDhqAdwy1fTGkHAwnkGOVsgpvQhL8B5n1qlb01jV3n/bI0ZfZp5lWA1k4w==",
+      "dev": true,
       "dependencies": {
         "minipass": "^7.0.4"
       },
@@ -3827,6 +3836,7 @@
       "version": "0.11.0",
       "resolved": "https://registry.npmjs.org/@pkgjs/parseargs/-/parseargs-0.11.0.tgz",
       "integrity": "sha512-+1VkjdD0QBLPodGrJUeqarH8VAIvQODIbwh9XpP5Syisf7YoQgsJKPNFoqqLQlu+VQ/tVSshMR6loPMn8U+dPg==",
+      "dev": true,
       "optional": true,
       "engines": {
         "node": ">=14"
@@ -4517,73 +4527,6 @@
       "resolved": "https://registry.npmjs.org/@xtuc/long/-/long-4.2.2.tgz",
       "integrity": "sha512-NuHqBY1PB/D8xU6s/thBgOAiAP7HOYDQ32+BFZILJ8ivkUkAHQnWfn6WhL79Owj1qmUnoN/YPhktdIoucipkAQ=="
     },
-    "node_modules/@yao-pkg/pkg": {
-      "version": "6.3.2",
-      "resolved": "https://registry.npmjs.org/@yao-pkg/pkg/-/pkg-6.3.2.tgz",
-      "integrity": "sha512-gd4fh8dVC5qnKQD8HTwQrVLvT8TyQqwE59ky3LHtnke+6fBcTTrWavtbsVOwdL09IWqY+eSB+2AGCrSUnZ4wwg==",
-      "dependencies": {
-        "@babel/generator": "^7.23.0",
-        "@babel/parser": "^7.23.0",
-        "@babel/types": "^7.23.0",
-        "@yao-pkg/pkg-fetch": "3.5.19",
-        "into-stream": "^6.0.0",
-        "minimist": "^1.2.6",
-        "multistream": "^4.1.0",
-        "picocolors": "^1.1.0",
-        "picomatch": "^4.0.2",
-        "prebuild-install": "^7.1.1",
-        "resolve": "^1.22.10",
-        "stream-meter": "^1.0.4",
-        "tar": "^7.4.3",
-        "tinyglobby": "^0.2.11",
-        "unzipper": "^0.12.3"
-      },
-      "bin": {
-        "pkg": "lib-es5/bin.js"
-      },
-      "engines": {
-        "node": ">=18.0.0"
-      }
-    },
-    "node_modules/@yao-pkg/pkg-fetch": {
-      "version": "3.5.19",
-      "resolved": "https://registry.npmjs.org/@yao-pkg/pkg-fetch/-/pkg-fetch-3.5.19.tgz",
-      "integrity": "sha512-EEURrS1Q5sSSAwaQ4zD0wZsquDiG8CroY3SCi7jYBoM0NG3eRA239mW6YMUYPNWUK4zCMhuK3bzFT5aIZP/rDg==",
-      "dependencies": {
-        "https-proxy-agent": "^5.0.0",
-        "node-fetch": "^2.6.6",
-        "picocolors": "^1.1.0",
-        "progress": "^2.0.3",
-        "semver": "^7.3.5",
-        "tar-fs": "^2.1.1",
-        "yargs": "^16.2.0"
-      },
-      "bin": {
-        "pkg-fetch": "lib-es5/bin.js"
-      }
-    },
-    "node_modules/@yao-pkg/pkg-fetch/node_modules/semver": {
-      "version": "7.7.1",
-      "resolved": "https://registry.npmjs.org/semver/-/semver-7.7.1.tgz",
-      "integrity": "sha512-hlq8tAfn0m/61p4BVRcPzIGr6LKiMwo4VM6dGi6pt4qcRkmNzTcWq6eCEjEh+qXjkMDvPlOFFSGwQjoEa6gyMA==",
-      "bin": {
-        "semver": "bin/semver.js"
-      },
-      "engines": {
-        "node": ">=10"
-      }
-    },
-    "node_modules/@yao-pkg/pkg/node_modules/picomatch": {
-      "version": "4.0.2",
-      "resolved": "https://registry.npmjs.org/picomatch/-/picomatch-4.0.2.tgz",
-      "integrity": "sha512-M7BAV6Rlcy5u+m6oPhAPFgJTzAioX/6B0DxyvDlo9l8+T3nLKbrczg2WLUyzd45L8RqfUMyGPzekbMvX2Ldkwg==",
-      "engines": {
-        "node": ">=12"
-      },
-      "funding": {
-        "url": "https://github.com/sponsors/jonschlinkert"
-      }
-    },
     "node_modules/accepts": {
       "version": "1.3.8",
       "resolved": "https://registry.npmjs.org/accepts/-/accepts-1.3.8.tgz",
@@ -4640,17 +4583,6 @@
         "node": ">=8.9"
       }
     },
-    "node_modules/agent-base": {
-      "version": "6.0.2",
-      "resolved": "https://registry.npmjs.org/agent-base/-/agent-base-6.0.2.tgz",
-      "integrity": "sha512-RZNwNclF7+MS/8bDg70amg32dyeZGZxiDuQmZxKLAlQjr3jGyLx+4Kkk58UO7D2QdgFIQCovuSuZESne6RG6XQ==",
-      "dependencies": {
-        "debug": "4"
-      },
-      "engines": {
-        "node": ">= 6.0.0"
-      }
-    },
     "node_modules/ajv": {
       "version": "8.17.1",
       "license": "MIT",
@@ -4978,6 +4910,7 @@
     },
     "node_modules/balanced-match": {
       "version": "1.0.2",
+      "dev": true,
       "license": "MIT"
     },
     "node_modules/base64-arraybuffer": {
@@ -5032,53 +4965,12 @@
         "url": "https://github.com/sponsors/sindresorhus"
       }
     },
-    "node_modules/bl": {
-      "version": "4.1.0",
-      "license": "MIT",
-      "dependencies": {
-        "buffer": "^5.5.0",
-        "inherits": "^2.0.4",
-        "readable-stream": "^3.4.0"
-      }
-    },
-    "node_modules/bl/node_modules/buffer": {
-      "version": "5.7.1",
-      "funding": [
-        {
-          "type": "github",
-          "url": "https://github.com/sponsors/feross"
-        },
-        {
-          "type": "patreon",
-          "url": "https://www.patreon.com/feross"
-        },
-        {
-          "type": "consulting",
-          "url": "https://feross.org/support"
-        }
-      ],
-      "license": "MIT",
-      "dependencies": {
-        "base64-js": "^1.3.1",
-        "ieee754": "^1.1.13"
-      }
-    },
-    "node_modules/bl/node_modules/readable-stream": {
-      "version": "3.6.2",
-      "license": "MIT",
-      "dependencies": {
-        "inherits": "^2.0.3",
-        "string_decoder": "^1.1.1",
-        "util-deprecate": "^1.0.1"
-      },
-      "engines": {
-        "node": ">= 6"
-      }
-    },
     "node_modules/bluebird": {
       "version": "3.7.2",
       "resolved": "https://registry.npmjs.org/bluebird/-/bluebird-3.7.2.tgz",
-      "integrity": "sha512-XpNj6GDQzdfW+r2Wnn7xiSAd7TM3jzkxGXBGTtWKuSXv1xUV+azxAm8jdWZN06QTQk+2N2XB9jRDkvbmQmcRtg=="
+      "integrity": "sha512-XpNj6GDQzdfW+r2Wnn7xiSAd7TM3jzkxGXBGTtWKuSXv1xUV+azxAm8jdWZN06QTQk+2N2XB9jRDkvbmQmcRtg==",
+      "dev": true,
+      "license": "MIT"
     },
     "node_modules/bn.js": {
       "version": "5.2.1",
@@ -5156,6 +5048,7 @@
       "version": "2.0.2",
       "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-2.0.2.tgz",
       "integrity": "sha512-Jt0vHyM+jmUBqojB7E1NIYadt0vI0Qxjxd2TErW94wDz+E2LAm5vKMXXwg6ZZBTHPuUlDgQHKXvjGBdfcF1ZDQ==",
+      "dev": true,
       "dependencies": {
         "balanced-match": "^1.0.0"
       }
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@@ -9723,30 +9420,6 @@
       "dev": true,
       "license": "MIT"
     },
-    "node_modules/prebuild-install": {
-      "version": "7.1.1",
-      "license": "MIT",
-      "dependencies": {
-        "detect-libc": "^2.0.0",
-        "expand-template": "^2.0.3",
-        "github-from-package": "0.0.0",
-        "minimist": "^1.2.3",
-        "mkdirp-classic": "^0.5.3",
-        "napi-build-utils": "^1.0.1",
-        "node-abi": "^3.3.0",
-        "pump": "^3.0.0",
-        "rc": "^1.2.7",
-        "simple-get": "^4.0.0",
-        "tar-fs": "^2.0.0",
-        "tunnel-agent": "^0.6.0"
-      },
-      "bin": {
-        "prebuild-install": "bin.js"
-      },
-      "engines": {
-        "node": ">=10"
-      }
-    },
     "node_modules/pretty-error": {
       "version": "4.0.0",
       "resolved": "https://registry.npmjs.org/pretty-error/-/pretty-error-4.0.0.tgz",
@@ -9798,14 +9471,6 @@
       "version": "2.0.1",
       "license": "MIT"
     },
-    "node_modules/progress": {
-      "version": "2.0.3",
-      "resolved": "https://registry.npmjs.org/progress/-/progress-2.0.3.tgz",
-      "integrity": "sha512-7PiHtLll5LdnKIMw100I+8xJXR5gW2QwWYkT6iJva0bXitZKa/XMrSbdmg3r2Xnaidz9Qumd0VPaMrZlF9V9sA==",
-      "engines": {
-        "node": ">=0.4.0"
-      }
-    },
     "node_modules/prop-types": {
       "version": "15.8.1",
       "license": "MIT",
@@ -9859,14 +9524,6 @@
       "resolved": "https://registry.npmjs.org/bn.js/-/bn.js-4.12.1.tgz",
       "integrity": "sha512-k8TVBiPkPJT9uHLdOKfFpqcfprwBFOAAXXozRubr7R7PfIuKvQlzcI4M0pALeqXN09vdaMbUdUj+pass+uULAg=="
     },
-    "node_modules/pump": {
-      "version": "3.0.0",
-      "license": "MIT",
-      "dependencies": {
-        "end-of-stream": "^1.1.0",
-        "once": "^1.3.1"
-      }
-    },
     "node_modules/punycode": {
       "version": "2.3.1",
       "resolved": "https://registry.npmjs.org/punycode/-/punycode-2.3.1.tgz",
@@ -9972,26 +9629,6 @@
         "quickselect": "^2.0.0"
       }
     },
-    "node_modules/rc": {
-      "version": "1.2.8",
-      "license": "(BSD-2-Clause OR MIT OR Apache-2.0)",
-      "dependencies": {
-        "deep-extend": "^0.6.0",
-        "ini": "~1.3.0",
-        "minimist": "^1.2.0",
-        "strip-json-comments": "~2.0.1"
-      },
-      "bin": {
-        "rc": "cli.js"
-      }
-    },
-    "node_modules/rc/node_modules/strip-json-comments": {
-      "version": "2.0.1",
-      "license": "MIT",
-      "engines": {
-        "node": ">=0.10.0"
-      }
-    },
     "node_modules/react": {
       "version": "18.3.1",
       "resolved": "https://registry.npmjs.org/react/-/react-18.3.1.tgz",
@@ -10467,14 +10104,6 @@
         "strip-ansi": "^6.0.1"
       }
     },
-    "node_modules/require-directory": {
-      "version": "2.1.1",
-      "resolved": "https://registry.npmjs.org/require-directory/-/require-directory-2.1.1.tgz",
-      "integrity": "sha512-fGxEI7+wsG9xrvdjsrlmL22OMTTiHRwAMroiEeMgq8gzoLC/PQr7RsRDSTLUg/bZAZtF+TVIkHc6/4RIKrui+Q==",
-      "engines": {
-        "node": ">=0.10.0"
-      }
-    },
     "node_modules/require-from-string": {
       "version": "2.0.2",
       "license": "MIT",
@@ -11033,6 +10662,7 @@
     },
     "node_modules/shebang-command": {
       "version": "2.0.0",
+      "dev": true,
       "license": "MIT",
       "dependencies": {
         "shebang-regex": "^3.0.0"
@@ -11043,6 +10673,7 @@
     },
     "node_modules/shebang-regex": {
       "version": "3.0.0",
+      "dev": true,
       "license": "MIT",
       "engines": {
         "node": ">=8"
@@ -11076,47 +10707,6 @@
         "url": "https://github.com/sponsors/ljharb"
       }
     },
-    "node_modules/simple-concat": {
-      "version": "1.0.1",
-      "funding": [
-        {
-          "type": "github",
-          "url": "https://github.com/sponsors/feross"
-        },
-        {
-          "type": "patreon",
-          "url": "https://www.patreon.com/feross"
-        },
-        {
-          "type": "consulting",
-          "url": "https://feross.org/support"
-        }
-      ],
-      "license": "MIT"
-    },
-    "node_modules/simple-get": {
-      "version": "4.0.1",
-      "funding": [
-        {
-          "type": "github",
-          "url": "https://github.com/sponsors/feross"
-        },
-        {
-          "type": "patreon",
-          "url": "https://www.patreon.com/feross"
-        },
-        {
-          "type": "consulting",
-          "url": "https://feross.org/support"
-        }
-      ],
-      "license": "MIT",
-      "dependencies": {
-        "decompress-response": "^6.0.0",
-        "once": "^1.3.1",
-        "simple-concat": "^1.0.0"
-      }
-    },
     "node_modules/sirv": {
       "version": "2.0.4",
       "dev": true,
@@ -11307,13 +10897,6 @@
         "node": ">= 6"
       }
     },
-    "node_modules/stream-meter": {
-      "version": "1.0.4",
-      "license": "MIT",
-      "dependencies": {
-        "readable-stream": "^2.1.4"
-      }
-    },
     "node_modules/string_decoder": {
       "version": "1.3.0",
       "license": "MIT",
@@ -11323,6 +10906,7 @@
     },
     "node_modules/string-width": {
       "version": "4.2.3",
+      "dev": true,
       "license": "MIT",
       "dependencies": {
         "emoji-regex": "^8.0.0",
@@ -11336,6 +10920,7 @@
     "node_modules/string-width-cjs": {
       "name": "string-width",
       "version": "4.2.3",
+      "dev": true,
       "license": "MIT",
       "dependencies": {
         "emoji-regex": "^8.0.0",
@@ -11348,6 +10933,7 @@
     },
     "node_modules/strip-ansi": {
       "version": "6.0.1",
+      "dev": true,
       "license": "MIT",
       "dependencies": {
         "ansi-regex": "^5.0.1"
@@ -11359,6 +10945,7 @@
     "node_modules/strip-ansi-cjs": {
       "name": "strip-ansi",
       "version": "6.0.1",
+      "dev": true,
       "license": "MIT",
       "dependencies": {
         "ansi-regex": "^5.0.1"
@@ -11442,6 +11029,7 @@
       "version": "7.4.3",
       "resolved": "https://registry.npmjs.org/tar/-/tar-7.4.3.tgz",
       "integrity": "sha512-5S7Va8hKfV7W5U6g3aYxXmlPoZVAwUMy9AOKyF2fVuZa2UD3qZjg578OrLRt8PcNN1PleVaL/5/yYATNL0ICUw==",
+      "dev": true,
       "dependencies": {
         "@isaacs/fs-minipass": "^4.0.0",
         "chownr": "^3.0.0",
@@ -11454,47 +11042,11 @@
         "node": ">=18"
       }
     },
-    "node_modules/tar-fs": {
-      "version": "2.1.3",
-      "resolved": "https://registry.npmjs.org/tar-fs/-/tar-fs-2.1.3.tgz",
-      "integrity": "sha512-090nwYJDmlhwFwEW3QQl+vaNnxsO2yVsd45eTKRBzSzu+hlb1w2K9inVq5b0ngXuLVqQ4ApvsUHHnu/zQNkWAg==",
-      "dependencies": {
-        "chownr": "^1.1.1",
-        "mkdirp-classic": "^0.5.2",
-        "pump": "^3.0.0",
-        "tar-stream": "^2.1.4"
-      }
-    },
-    "node_modules/tar-stream": {
-      "version": "2.2.0",
-      "license": "MIT",
-      "dependencies": {
-        "bl": "^4.0.3",
-        "end-of-stream": "^1.4.1",
-        "fs-constants": "^1.0.0",
-        "inherits": "^2.0.3",
-        "readable-stream": "^3.1.1"
-      },
-      "engines": {
-        "node": ">=6"
-      }
-    },
-    "node_modules/tar-stream/node_modules/readable-stream": {
-      "version": "3.6.2",
-      "license": "MIT",
-      "dependencies": {
-        "inherits": "^2.0.3",
-        "string_decoder": "^1.1.1",
-        "util-deprecate": "^1.0.1"
-      },
-      "engines": {
-        "node": ">= 6"
-      }
-    },
     "node_modules/tar/node_modules/chownr": {
       "version": "3.0.0",
       "resolved": "https://registry.npmjs.org/chownr/-/chownr-3.0.0.tgz",
       "integrity": "sha512-+IxzY9BZOQd/XuYPRmrvEVjF/nqj5kgT4kEq7VofrDoM1MxoRjEWkrCC3EtLi59TVawxTAn+orJwFQcrqEN1+g==",
+      "dev": true,
       "engines": {
         "node": ">=18"
       }
@@ -11503,6 +11055,7 @@
       "version": "5.0.0",
       "resolved": "https://registry.npmjs.org/yallist/-/yallist-5.0.0.tgz",
       "integrity": "sha512-YgvUTfwqyc7UXVMrB+SImsVYSmTS8X/tSrtdNZMImM+n7+QTriRXyXim0mBrTXNeqzVF0KWGgHPeiyViFFrNDw==",
+      "dev": true,
       "engines": {
         "node": ">=18"
       }
@@ -11625,6 +11178,7 @@
       "version": "0.2.12",
       "resolved": "https://registry.npmjs.org/tinyglobby/-/tinyglobby-0.2.12.tgz",
       "integrity": "sha512-qkf4trmKSIiMTs/E63cxH+ojC2unam7rJ0WrauAzpT3ECNTxGRMlaXxVbfxMUC/w0LaYk6jQ4y/nGR9uBO3tww==",
+      "dev": true,
       "dependencies": {
         "fdir": "^6.4.3",
         "picomatch": "^4.0.2"
@@ -11640,6 +11194,7 @@
       "version": "6.4.3",
       "resolved": "https://registry.npmjs.org/fdir/-/fdir-6.4.3.tgz",
       "integrity": "sha512-PMXmW2y1hDDfTSRc9gaXIuCCRpuoz3Kaz8cUelp3smouvfT632ozg2vrT6lJsHKKOF59YLbOGfAWGUcKEfRMQw==",
+      "dev": true,
       "peerDependencies": {
         "picomatch": "^3 || ^4"
       },
@@ -11653,6 +11208,7 @@
       "version": "4.0.2",
       "resolved": "https://registry.npmjs.org/picomatch/-/picomatch-4.0.2.tgz",
       "integrity": "sha512-M7BAV6Rlcy5u+m6oPhAPFgJTzAioX/6B0DxyvDlo9l8+T3nLKbrczg2WLUyzd45L8RqfUMyGPzekbMvX2Ldkwg==",
+      "dev": true,
       "engines": {
         "node": ">=12"
       },
@@ -11711,11 +11267,6 @@
         "node": ">=6"
       }
     },
-    "node_modules/tr46": {
-      "version": "0.0.3",
-      "resolved": "https://registry.npmjs.org/tr46/-/tr46-0.0.3.tgz",
-      "integrity": "sha512-N3WMsuqV66lT30CrXNbEjx4GEwlow3v6rr4mCcv6prnfwhS01rkgyFdjPNBYd9br7LpXV1+Emh01fHnq2Gdgrw=="
-    },
     "node_modules/tree-dump": {
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/tree-dump/-/tree-dump-1.0.2.tgz",
@@ -11765,16 +11316,6 @@
       "resolved": "https://registry.npmjs.org/tty-browserify/-/tty-browserify-0.0.1.tgz",
       "integrity": "sha512-C3TaO7K81YvjCgQH9Q1S3R3P3BtN3RIM8n+OvX4il1K1zgE8ZhI0op7kClgkxtutIE8hQrcrHBXvIheqKUUCxw=="
     },
-    "node_modules/tunnel-agent": {
-      "version": "0.6.0",
-      "license": "Apache-2.0",
-      "dependencies": {
-        "safe-buffer": "^5.0.1"
-      },
-      "engines": {
-        "node": "*"
-      }
-    },
     "node_modules/type-fest": {
       "version": "4.38.0",
       "resolved": "https://registry.npmjs.org/type-fest/-/type-fest-4.38.0.tgz",
@@ -11873,6 +11414,7 @@
     },
     "node_modules/universalify": {
       "version": "2.0.1",
+      "dev": true,
       "license": "MIT",
       "engines": {
         "node": ">= 10.0.0"
@@ -11891,6 +11433,8 @@
       "version": "0.12.3",
       "resolved": "https://registry.npmjs.org/unzipper/-/unzipper-0.12.3.tgz",
       "integrity": "sha512-PZ8hTS+AqcGxsaQntl3IRBw65QrBI6lxzqDEL7IAo/XCEqRTKGfOX56Vea5TH9SZczRVxuzk1re04z/YjuYCJA==",
+      "dev": true,
+      "license": "MIT",
       "dependencies": {
         "bluebird": "~3.7.2",
         "duplexer2": "~0.1.4",
@@ -12080,11 +11624,6 @@
         "minimalistic-assert": "^1.0.0"
       }
     },
-    "node_modules/webidl-conversions": {
-      "version": "3.0.1",
-      "resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-3.0.1.tgz",
-      "integrity": "sha512-2JAn3z8AR6rjK8Sm8orRC0h/bcl/DqL7tRPdGZ4I1CjdF+EaMLmYxBHyXuKL849eucPFhvBoxMsflfOb8kxaeQ=="
-    },
     "node_modules/webpack": {
       "version": "5.99.7",
       "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.99.7.tgz",
@@ -12441,17 +11980,9 @@
         "node": ">=0.8.0"
       }
     },
-    "node_modules/whatwg-url": {
-      "version": "5.0.0",
-      "resolved": "https://registry.npmjs.org/whatwg-url/-/whatwg-url-5.0.0.tgz",
-      "integrity": "sha512-saE57nupxk6v3HY35+jzBwYa0rKSy0XR8JSxZPwgLr7ys0IBzhGviA1/TUGJLmSVqs8pb9AnvICXEuOHLprYTw==",
-      "dependencies": {
-        "tr46": "~0.0.3",
-        "webidl-conversions": "^3.0.0"
-      }
-    },
     "node_modules/which": {
       "version": "2.0.2",
+      "dev": true,
       "license": "ISC",
       "dependencies": {
         "isexe": "^2.0.0"
@@ -12489,25 +12020,10 @@
       "integrity": "sha512-CC1bOL87PIWSBhDcTrdeLo6eGT7mCFtrg0uIJtqJUFyK+eJnzl8A1niH56uu7KMa5XFrtiV+AQuHO3n7DsHnLQ==",
       "dev": true
     },
-    "node_modules/wrap-ansi": {
-      "version": "7.0.0",
-      "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-7.0.0.tgz",
-      "integrity": "sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q==",
-      "dependencies": {
-        "ansi-styles": "^4.0.0",
-        "string-width": "^4.1.0",
-        "strip-ansi": "^6.0.0"
-      },
-      "engines": {
-        "node": ">=10"
-      },
-      "funding": {
-        "url": "https://github.com/chalk/wrap-ansi?sponsor=1"
-      }
-    },
     "node_modules/wrap-ansi-cjs": {
       "name": "wrap-ansi",
       "version": "7.0.0",
+      "dev": true,
       "license": "MIT",
       "dependencies": {
         "ansi-styles": "^4.0.0",
@@ -12521,10 +12037,6 @@
         "url": "https://github.com/chalk/wrap-ansi?sponsor=1"
       }
     },
-    "node_modules/wrappy": {
-      "version": "1.0.2",
-      "license": "ISC"
-    },
     "node_modules/ws": {
       "version": "8.18.1",
       "resolved": "https://registry.npmjs.org/ws/-/ws-8.18.1.tgz",
@@ -12562,14 +12074,6 @@
         "node": ">=16"
       }
     },
-    "node_modules/y18n": {
-      "version": "5.0.8",
-      "resolved": "https://registry.npmjs.org/y18n/-/y18n-5.0.8.tgz",
-      "integrity": "sha512-0pfFzegeDWJHJIAmTLRP2DwHjdF5s7jo9tuztdQxAhINCdvS+3nGINqPd00AphqJR/0LhANUS6/+7SCb98YOfA==",
-      "engines": {
-        "node": ">=10"
-      }
-    },
     "node_modules/yallist": {
       "version": "3.1.1",
       "resolved": "https://registry.npmjs.org/yallist/-/yallist-3.1.1.tgz",
@@ -12583,31 +12087,6 @@
         "node": ">= 6"
       }
     },
-    "node_modules/yargs": {
-      "version": "16.2.0",
-      "resolved": "https://registry.npmjs.org/yargs/-/yargs-16.2.0.tgz",
-      "integrity": "sha512-D1mvvtDG0L5ft/jGWkLpG1+m0eQxOfaBvTNELraWj22wSVUMWxZUvYgJYcKh6jGGIkJFhH4IZPQhR4TKpc8mBw==",
-      "dependencies": {
-        "cliui": "^7.0.2",
-        "escalade": "^3.1.1",
-        "get-caller-file": "^2.0.5",
-        "require-directory": "^2.1.1",
-        "string-width": "^4.2.0",
-        "y18n": "^5.0.5",
-        "yargs-parser": "^20.2.2"
-      },
-      "engines": {
-        "node": ">=10"
-      }
-    },
-    "node_modules/yargs-parser": {
-      "version": "20.2.9",
-      "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-20.2.9.tgz",
-      "integrity": "sha512-y11nGElTIV+CT3Zv9t7VKl+Q3hTQoT9a1Qzezhhl6Rp21gJ/IVTW7Z3y9EWXhuUBC2Shnf+DX0antecpAwSP8w==",
-      "engines": {
-        "node": ">=10"
-      }
-    },
     "node_modules/yocto-queue": {
       "version": "0.1.0",
       "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz",
diff --git a/jbrowse/package.json b/jbrowse/package.json
index 3807eef04..b8823a270 100644
--- a/jbrowse/package.json
+++ b/jbrowse/package.json
@@ -6,25 +6,24 @@
     "setup": "npm ci",
     "build": "npm run build-dev",
     "start": "cross-env NODE_ENV=development webpack serve --config ./config/watch.config.js",
-    "build-no-pkg": "npm run clean && cross-env NODE_ENV=development webpack --config ./config/dev.config.js --progress --profile",
-    "build-dev": "npm run build-no-pkg",
+    "build-dev": "npm run clean && cross-env NODE_ENV=development webpack --config ./config/dev.config.js --progress --profile",
     "build-prod": "npm run clean && cross-env NODE_ENV=production PROD_SOURCE_MAP=source-map webpack --config ./config/prod.config.js --progress --profile",
     "clean": "rimraf resources/web/gen && rimraf resources/web/jbrowse/gen && rimraf resources/views/gen",
-    "prepareCli": "rimraf ./buildCli && rimraf ./resources/external/jb-cli && npm install @jbrowse/cli@1.7.4 --prefix ./buildCli",
-    "jb-pkg": "npm run prepareCli && npx pkg --outdir=./resources/external/jb-cli ./buildCli/node_modules/@jbrowse/cli && rimraf ./buildCli"
+    "jb-sea:fetch": "node ./resources/external/fetch-jbrowse-bundle.mjs",
+    "jb-sea:build": "node ./resources/external/build-sea.mjs ./resources/external/jbrowse.js",
+    "jb-sea": "npm run jb-sea:fetch && npm run jb-sea:build"
   },
   "dependencies": {
     "@gmod/vcf": "^6.0.9",
     "@jbrowse/core": "^3.2.0",
-    "@jbrowse/product-core": "^3.2.0",
     "@jbrowse/plugin-linear-genome-view": "^3.2.0",
     "@jbrowse/plugin-svg": "^3.2.0",
     "@jbrowse/plugin-variants": "^3.2.0",
+    "@jbrowse/product-core": "^3.2.0",
     "@jbrowse/react-linear-genome-view2": "^3.2.0",
     "@labkey/api": "^1.39.0",
     "@labkey/components": "^6.32.2",
     "@mui/x-data-grid": "^7.28.1",
-    "@yao-pkg/pkg": "^6.3.2",
     "assert": "^2.1.0",
     "browserify-zlib": "^0.2.0",
     "buffer": "^6.0.3",
@@ -54,6 +53,8 @@
     "@types/react": "^18.3.0",
     "@types/react-dom": "^18.3.0",
     "rimraf": "^6.0.1",
-    "typescript": "^5.1.6"
+    "tar": "^7.4.3",
+    "typescript": "^5.1.6",
+    "unzipper": "^0.12.3"
   }
 }
diff --git a/jbrowse/resources/external/build-sea.mjs b/jbrowse/resources/external/build-sea.mjs
new file mode 100644
index 000000000..baae7c2f2
--- /dev/null
+++ b/jbrowse/resources/external/build-sea.mjs
@@ -0,0 +1,193 @@
+// Build SEA for all platforms (win/linux/macos) from any host.
+// - Creates sea-prep.blob once from resources/external/jbrowse.js
+// - Downloads official Node runtimes for the same Node version as process.execPath
+// - Injects the blob into each runtime with postject
+// - Writes outputs to resources/external/jb-cli:
+//     cli-win.exe, cli-linux, cli-macos
+// - Cleans up temp files and resources/external/jbrowse.js at the end
+
+import { execFileSync, execSync } from 'node:child_process';
+import {
+  copyFileSync, chmodSync, existsSync, mkdirSync, rmSync, renameSync, writeFileSync
+} from 'node:fs';
+import { join, resolve } from 'node:path';
+import https from 'node:https';
+import { createWriteStream, createReadStream } from 'node:fs';
+import * as unzipper from 'unzipper';
+
+const ROOT = resolve('.');
+const OUTDIR = join(ROOT, 'resources', 'external', 'jb-cli');
+const TMPDIR = join(ROOT, '.sea-tmp');
+const INPUT_JS = join(ROOT, 'resources', 'external', 'jbrowse.js');
+
+const NODE_VERSION = process.versions.node;
+const DIST_BASE = process.env.NODE_DIST_URL || 'https://nodejs.org/dist';
+const TARGETS = [
+  ['win-x64',   'cli-win.exe', 'zip'],
+  ['linux-x64', 'cli-linux',   'tar.xz'],
+  ['darwin-x64','cli-macos',   'tar.xz'],
+  // ['darwin-arm64','cli-macos-arm64','tar.xz'],
+  // ['linux-arm64','cli-linux-arm64','tar.xz'],
+];
+
+const SENTINEL = 'NODE_SEA_FUSE_fce680ab2cc467b6e072b8b5df1996b2';
+const POSTJECT_PKG = 'postject@1.0.0-alpha.6';
+
+function log(s){ console.log(s); }
+function warn(s){ console.warn(s); }
+function fail(e){ console.error(e); process.exit(1); }
+
+function ensureDirs(){
+  mkdirSync(OUTDIR, { recursive: true });
+  mkdirSync(TMPDIR, { recursive: true });
+}
+
+function httpDownload(url, dest){
+  return new Promise((resolveP, rejectP)=>{
+    const file = createWriteStream(dest);
+    https.get(url, res=>{
+      if(res.statusCode && res.statusCode >= 300 && res.statusCode < 400 && res.headers.location){
+        httpDownload(res.headers.location, dest).then(resolveP, rejectP);
+        return;
+      }
+      if(res.statusCode !== 200){
+        rejectP(new Error(`Download failed ${res.statusCode}: ${url}`));
+        return;
+      }
+      res.pipe(file);
+      file.on('finish', ()=>file.close(()=>resolveP(void 0)));
+    }).on('error', err=>{ rejectP(err); });
+  });
+}
+
+function runOrThrow(cmd, args, opts={}){
+  execFileSync(cmd, args, { stdio: 'inherit', ...opts });
+}
+
+function shellOrThrow(command){
+  execSync(command, { stdio: 'inherit', shell: true });
+}
+
+// postject runner with fallbacks
+function runPostject(args){
+  const isWin = process.platform === 'win32';
+  const npxCmd = isWin ? 'npx.cmd' : 'npx';
+  const npmCmd = isWin ? 'npm.cmd' : 'npm';
+  try { runOrThrow(npxCmd, ['--yes', POSTJECT_PKG, ...args]); return; }
+  catch{ warn('[postject] npx failed, trying npm exec…'); }
+  try { runOrThrow(npmCmd, ['exec', '-y', POSTJECT_PKG, '--', ...args]); return; }
+  catch{ warn('[postject] npm exec failed, trying shell npx…'); }
+  try { shellOrThrow(`npx --yes ${POSTJECT_PKG} ${args.map(a=>`"${a}"`).join(' ')}`); return; }
+  catch{ warn('[postject] shell npx failed, trying shell npm exec…'); }
+  shellOrThrow(`npm exec -y ${POSTJECT_PKG} -- ${args.map(a=>`"${a}"`).join(' ')}`);
+}
+
+async function extractZip(zipPath, outDir){
+  if (process.platform === 'win32') {
+    try {
+      shellOrThrow(`powershell -NoProfile -Command "Expand-Archive -Force '${zipPath.replace(/'/g, "''")}' '${outDir.replace(/'/g, "''")}'"`);
+      return;
+    } catch (e) {
+      // Fall through to unzipper if PowerShell isn’t present or fails
+    }
+  } else {
+    // POSIX: try `unzip` if present
+    try {
+      shellOrThrow(`unzip -o "${zipPath}" -d "${outDir}"`);
+      return;
+    } catch (e) {
+      // Fall through to unzipper
+    }
+  }
+
+  await new Promise((resolveP, rejectP) => {
+    const stream = createReadStream(zipPath)
+      .pipe(unzipper.Extract({ path: outDir }));
+
+    stream.on('close', resolveP);
+    stream.on('error', rejectP);
+  });
+}
+
+// extract only bin/node from tar.xz to avoid symlink issues on Windows
+function extractNodeFromTarXz(tarxzPath, outDir, target) {
+  const innerPath = `node-v${NODE_VERSION}-${target}/bin/node`;
+  try { shellOrThrow(`tar -xJf "${tarxzPath}" -C "${outDir}" "${innerPath}"`); }
+  catch { shellOrThrow(`bsdtar -xf "${tarxzPath}" -C "${outDir}" "${innerPath}"`); }
+  return join(outDir, innerPath);
+}
+
+function nodeBinaryPathFromExtract(dir, target){
+  const base = `node-v${NODE_VERSION}-${target}`;
+  if (target.startsWith('win')) return join(dir, base, 'node.exe');
+  return join(dir, base, 'bin', 'node');
+}
+
+function injectForTarget(target, outName, archiveExt, blobPath){
+  const distUrl = `${DIST_BASE}/v${NODE_VERSION}/node-v${NODE_VERSION}-${target}.${archiveExt}`;
+  const dlPath = join(TMPDIR, `node-${target}.${archiveExt}`);
+
+  log(`\n=== Target ${target} ===`);
+  log(`Downloading: ${distUrl}`);
+  return httpDownload(distUrl, dlPath).then(async ()=>{
+    log('Extracting…');
+    let nodePath;
+    if (archiveExt === 'zip') {
+      await extractZip(dlPath, TMPDIR);
+      nodePath = nodeBinaryPathFromExtract(TMPDIR, target);
+    } else {
+      nodePath = extractNodeFromTarXz(dlPath, TMPDIR, target);
+    }
+    if (!existsSync(nodePath)) fail(`node binary not found in ${nodePath}`);
+
+    const workExe = join(TMPDIR, `work-${outName}`);
+    copyFileSync(nodePath, workExe);
+
+    const postjectArgs = target.startsWith('darwin')
+      ? [workExe, 'NODE_SEA_BLOB', blobPath, '--sentinel-fuse', SENTINEL, '--macho-segment-name', 'NODE_SEA']
+      : [workExe, 'NODE_SEA_BLOB', blobPath, '--sentinel-fuse', SENTINEL];
+
+    log('Injecting SEA blob…');
+    runPostject(postjectArgs);
+
+    if (!target.startsWith('win')) chmodSync(workExe, 0o755);
+
+    const finalPath = join(OUTDIR, outName);
+    if (existsSync(finalPath)) rmSync(finalPath, { force: true });
+    renameSync(workExe, finalPath);
+
+    rmSync(dlPath, { force: true });
+    try { rmSync(join(TMPDIR, `node-v${NODE_VERSION}-${target}`), { recursive: true, force: true }); } catch {}
+    log(`Wrote ${finalPath}`);
+  });
+}
+
+function buildBlobOnce(){
+  const cfgPath = join(TMPDIR, 'sea-config.json');
+  const blobPath = join(TMPDIR, 'sea-prep.blob');
+  log('Creating SEA blob…');
+  const cfg = { main: INPUT_JS, output: blobPath, disableExperimentalSEAWarning: true };
+  writeFileSync(cfgPath, JSON.stringify(cfg, null, 2));
+  runOrThrow(process.execPath, ['--experimental-sea-config', cfgPath]);
+  return blobPath;
+}
+
+async function main(){
+  ensureDirs();
+  if (!existsSync(INPUT_JS)) fail(`Missing ${INPUT_JS}. Run your fetch step first.`);
+  rmSync(TMPDIR, { recursive: true, force: true });
+  mkdirSync(TMPDIR, { recursive: true });
+
+  const blob = buildBlobOnce();
+
+  for (const [target, outName, ext] of TARGETS) {
+    await injectForTarget(target, outName, ext, blob);
+  }
+
+  try { rmSync(TMPDIR, { recursive: true, force: true }); } catch {}
+  try { if (existsSync(INPUT_JS)) rmSync(INPUT_JS, { force: true }); } catch {}
+
+  log('\nAll targets built.');
+}
+
+main().catch(fail);
diff --git a/jbrowse/resources/external/fetch-jbrowse-bundle.mjs b/jbrowse/resources/external/fetch-jbrowse-bundle.mjs
new file mode 100644
index 000000000..04623fe0b
--- /dev/null
+++ b/jbrowse/resources/external/fetch-jbrowse-bundle.mjs
@@ -0,0 +1,57 @@
+import { execSync } from 'node:child_process';
+import { existsSync, mkdirSync, copyFileSync, rmSync } from 'node:fs';
+import { join, resolve } from 'node:path';
+
+const ROOT = resolve('.');
+const BUILD = join(ROOT, 'buildCli');
+const OUTDIR = join(ROOT, 'resources', 'external');
+const OUTFILE = join(OUTDIR, 'jbrowse.js');
+
+async function extractTgz(tgzPath, cwd) {
+  try {
+    const mod = await import('tar').catch(() => null);
+    const tar = mod?.default ?? mod;
+    if (tar?.x) {
+      await tar.x({ file: tgzPath, cwd });
+      return;
+    }
+  } catch {
+  }
+  execSync(`tar -xzf "${tgzPath}" -C "${cwd}"`, { stdio: 'inherit', shell: true });
+}
+
+async function main() {
+  if (existsSync(BUILD)) rmSync(BUILD, { recursive: true, force: true });
+  mkdirSync(BUILD, { recursive: true });
+  mkdirSync(OUTDIR, { recursive: true });
+
+  console.log('Packing @jbrowse/cli (latest)…');
+  const out = execSync('npm pack @jbrowse/cli', {
+    cwd: BUILD,
+    stdio: ['ignore', 'pipe', 'inherit'],
+    shell: true,
+  })
+    .toString()
+    .trim();
+
+  const tgz = join(BUILD, out);
+  console.log(`Downloaded: ${tgz}`);
+
+  console.log('Extracting tarball…');
+  await extractTgz(tgz, BUILD);
+
+  const bundled = join(BUILD, 'package', 'bundle', 'index.js');
+  if (!existsSync(bundled)) {
+    throw new Error(`bundle/index.js not found at ${bundled}`);
+  }
+
+  copyFileSync(bundled, OUTFILE);
+  console.log(`Copied bundle to ${OUTFILE}`);
+
+  rmSync(BUILD, { recursive: true, force: true });
+}
+
+main().catch(err => {
+  console.error(err);
+  process.exit(1);
+});
diff --git a/jbrowse/src/org/labkey/jbrowse/JBrowseManager.java b/jbrowse/src/org/labkey/jbrowse/JBrowseManager.java
index c1039d844..1db0ab1d3 100644
--- a/jbrowse/src/org/labkey/jbrowse/JBrowseManager.java
+++ b/jbrowse/src/org/labkey/jbrowse/JBrowseManager.java
@@ -239,7 +239,7 @@ public void testJBrowseCli() throws Exception
             SimpleScriptWrapper wrapper = new SimpleScriptWrapper(_log);
             wrapper.setThrowNonZeroExits(false);
 
-            String output = wrapper.executeWithOutput(Arrays.asList(exe.getPath(), "help"));
+            String output = wrapper.executeWithOutput(Arrays.asList(exe.getPath(), "--help"));
             if (wrapper.getLastReturnCode() != 0)
             {
                 _log.error("Non-zero exit from testJBrowseCli: " + wrapper.getLastReturnCode());
diff --git a/singlecell/resources/chunks/AppendMetadata.R b/singlecell/resources/chunks/AppendMetadata.R
index f14a25f65..d67d25fea 100644
--- a/singlecell/resources/chunks/AppendMetadata.R
+++ b/singlecell/resources/chunks/AppendMetadata.R
@@ -4,9 +4,16 @@ if (!file.exists(netRc)) {
     stop(paste0('Unable to find file: ', netRc))
 }
 
-invisible(Rlabkey::labkey.setCurlOptions(NETRC_FILE = netRc))
+invisible(Rlabkey::labkey.setCurlOptions(NETRC_FILE = netRc, timeout = 60, timeout_ms = 60000, connecttimeout = 20, connecttimeout_ms = 20000))
 Rdiscvr::SetLabKeyDefaults(baseUrl = serverBaseUrl, defaultFolder = defaultLabKeyFolder)
 
+curlOpt <- curl::curl_options('timeout')
+logger::log_info('Curl options:')
+for (x in names(curlOpt)) {
+    logger::log_info(paste0(x, ': ', curlOpt[x]))
+}
+rm(curlOpt)
+
 for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
diff --git a/singlecell/resources/chunks/ApplyKnownClonotypicData.R b/singlecell/resources/chunks/ApplyKnownClonotypicData.R
new file mode 100644
index 000000000..d73e4ef1e
--- /dev/null
+++ b/singlecell/resources/chunks/ApplyKnownClonotypicData.R
@@ -0,0 +1,20 @@
+netRc <- paste0(Sys.getenv('USER_HOME'), '/.netrc')
+if (!file.exists(netRc)) {
+    print(list.files(Sys.getenv('USER_HOME')))
+    stop(paste0('Unable to find file: ', netRc))
+}
+
+invisible(Rlabkey::labkey.setCurlOptions(NETRC_FILE = netRc))
+Rdiscvr::SetLabKeyDefaults(baseUrl = serverBaseUrl, defaultFolder = defaultLabKeyFolder)
+
+for (datasetId in names(seuratObjects)) {
+    printName(datasetId)
+    seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
+
+    seuratObj <- ApplyKnownClonotypicData(seuratObj)
+    saveData(seuratObj, datasetId)
+
+    # Cleanup
+    rm(seuratObj)
+    gc()
+}
\ No newline at end of file
diff --git a/singlecell/resources/chunks/CalculateTcrRepertoireStats.R b/singlecell/resources/chunks/CalculateTcrRepertoireStats.R
new file mode 100644
index 000000000..a365c1bcb
--- /dev/null
+++ b/singlecell/resources/chunks/CalculateTcrRepertoireStats.R
@@ -0,0 +1,21 @@
+netRc <- paste0(Sys.getenv('USER_HOME'), '/.netrc')
+if (!file.exists(netRc)) {
+  print(list.files(Sys.getenv('USER_HOME')))
+  stop(paste0('Unable to find file: ', netRc))
+}
+
+invisible(Rlabkey::labkey.setCurlOptions(NETRC_FILE = netRc))
+Rdiscvr::SetLabKeyDefaults(baseUrl = serverBaseUrl, defaultFolder = defaultLabKeyFolder)
+
+for (datasetId in names(seuratObjects)) {
+  printName(datasetId)
+  seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
+
+  outputFile <- gsub(seuratObjects[[datasetId]], pattern = '.rds', replacement = '.tcrStats.txt')
+  df <- Rdiscvr::CalculateAndStoreTcrRepertoireStats(seuratObj, outputFile = outputFile)
+
+  # Cleanup
+  rm(seuratObj)
+  rm(df)
+  gc()
+}
\ No newline at end of file
diff --git a/singlecell/resources/chunks/PredictTcellActivation.R b/singlecell/resources/chunks/PredictTcellActivation.R
new file mode 100644
index 000000000..7b18f1922
--- /dev/null
+++ b/singlecell/resources/chunks/PredictTcellActivation.R
@@ -0,0 +1,12 @@
+for (datasetId in names(seuratObjects)) {
+  printName(datasetId)
+  seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
+
+  seuratObj <- RIRA::PredictTcellActivation(seuratObj)
+
+  saveData(seuratObj, datasetId)
+
+  # Cleanup
+  rm(seuratObj)
+  gc()
+}
\ No newline at end of file
diff --git a/singlecell/resources/chunks/StudyMetadata.R b/singlecell/resources/chunks/StudyMetadata.R
index b64a2c66e..f5fb694ff 100644
--- a/singlecell/resources/chunks/StudyMetadata.R
+++ b/singlecell/resources/chunks/StudyMetadata.R
@@ -4,9 +4,16 @@ if (!file.exists(netRc)) {
     stop(paste0('Unable to find file: ', netRc))
 }
 
-invisible(Rlabkey::labkey.setCurlOptions(NETRC_FILE = netRc))
+invisible(Rlabkey::labkey.setCurlOptions(NETRC_FILE = netRc, timeout = 60, timeout_ms = 60000, connecttimeout = 20, connecttimeout_ms = 20000))
 Rdiscvr::SetLabKeyDefaults(baseUrl = serverBaseUrl, defaultFolder = defaultLabKeyFolder)
 
+curlOpt <- curl::curl_options('timeout')
+logger::log_info('Curl options:')
+for (x in names(curlOpt)) {
+    logger::log_info(paste0(x, ': ', curlOpt[x]))
+}
+rm(curlOpt)
+
 for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
diff --git a/singlecell/resources/chunks/UpdateSeuratPrototype.R b/singlecell/resources/chunks/UpdateSeuratPrototype.R
index a30396d81..f5b41a24b 100644
--- a/singlecell/resources/chunks/UpdateSeuratPrototype.R
+++ b/singlecell/resources/chunks/UpdateSeuratPrototype.R
@@ -7,6 +7,12 @@ if (!file.exists(netRc)) {
 invisible(Rlabkey::labkey.setCurlOptions(NETRC_FILE = netRc))
 Rdiscvr::SetLabKeyDefaults(baseUrl = serverBaseUrl, defaultFolder = defaultLabKeyFolder)
 
+if (Sys.getenv('SEURAT_MAX_THREADS') != '') {
+  nCores <- Sys.getenv('SEURAT_MAX_THREADS')
+} else {
+  nCores <- 1
+}
+
 for (datasetId in names(seuratObjects)) {
   printName(datasetId)
   seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
@@ -34,6 +40,20 @@ for (datasetId in names(seuratObjects)) {
     seuratObj <- Rdiscvr::ClassifyTNKByExpression(seuratObj)
   }
 
+  if (saveRepertoireStats) {
+    seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
+    outputFile <- gsub(seuratObjects[[datasetId]], pattern = '.rds', replacement = '.tcrStats.txt')
+    df <- Rdiscvr::CalculateAndStoreTcrRepertoireStats(seuratObj, outputFile = outputFile)
+  }
+
+  if (scoreActivation) {
+    seuratObj <- RIRA::PredictTcellActivation(seuratObj)
+  }
+
+  if (recalculateUCells) {
+    seuratObj <- RIRA::CalculateUCellScores(seuratObj, storeRanks = FALSE, assayName = 'RNA', forceRecalculate = TRUE, ncores = nCores)
+  }
+
   saveData(seuratObj, datasetId)
 
   # Cleanup
diff --git a/singlecell/src/org/labkey/singlecell/SingleCellModule.java b/singlecell/src/org/labkey/singlecell/SingleCellModule.java
index 5559f897f..def91fcd7 100644
--- a/singlecell/src/org/labkey/singlecell/SingleCellModule.java
+++ b/singlecell/src/org/labkey/singlecell/SingleCellModule.java
@@ -42,8 +42,10 @@
 import org.labkey.singlecell.pipeline.singlecell.AppendNimble;
 import org.labkey.singlecell.pipeline.singlecell.AppendSaturation;
 import org.labkey.singlecell.pipeline.singlecell.AppendTcr;
+import org.labkey.singlecell.pipeline.singlecell.ApplyKnownClonotypicData;
 import org.labkey.singlecell.pipeline.singlecell.AvgExpression;
 import org.labkey.singlecell.pipeline.singlecell.CalculateGeneComponentScores;
+import org.labkey.singlecell.pipeline.singlecell.CalculateTcrRepertoireStats;
 import org.labkey.singlecell.pipeline.singlecell.CalculateUCellScores;
 import org.labkey.singlecell.pipeline.singlecell.CellBarcodeFilter;
 import org.labkey.singlecell.pipeline.singlecell.CheckExpectations;
@@ -77,6 +79,7 @@
 import org.labkey.singlecell.pipeline.singlecell.PlotAssayFeatures;
 import org.labkey.singlecell.pipeline.singlecell.PlotAverageCiteSeqCounts;
 import org.labkey.singlecell.pipeline.singlecell.PredictScTour;
+import org.labkey.singlecell.pipeline.singlecell.PredictTcellActivation;
 import org.labkey.singlecell.pipeline.singlecell.PrepareRawCounts;
 import org.labkey.singlecell.pipeline.singlecell.RemoveCellCycle;
 import org.labkey.singlecell.pipeline.singlecell.RunCellHashing;
@@ -299,6 +302,9 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new PerformDefaultNimbleAppend.Provider());
         SequencePipelineService.get().registerPipelineStep(new PerformMhcDimRedux.Provider());
         SequencePipelineService.get().registerPipelineStep(new RunTricycle.Provider());
+        SequencePipelineService.get().registerPipelineStep(new ApplyKnownClonotypicData.Provider());
+        SequencePipelineService.get().registerPipelineStep(new CalculateTcrRepertoireStats.Provider());
+        SequencePipelineService.get().registerPipelineStep(new PredictTcellActivation.Provider());
 
         SequenceAnalysisService.get().registerReadsetListener(new SingleCellReadsetListener());
     }
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/ApplyKnownClonotypicData.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/ApplyKnownClonotypicData.java
new file mode 100644
index 000000000..1f6dbf45b
--- /dev/null
+++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/ApplyKnownClonotypicData.java
@@ -0,0 +1,39 @@
+package org.labkey.singlecell.pipeline.singlecell;
+
+import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+import org.labkey.api.singlecell.pipeline.SingleCellStep;
+
+import java.util.List;
+
+public class ApplyKnownClonotypicData extends AbstractRDiscvrStep
+{
+    public ApplyKnownClonotypicData(PipelineContext ctx, ApplyKnownClonotypicData.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("ApplyKnownClonotypicData", "Append Known Clonotype/Antigen Data", "RDiscvr", "This will query the clone_responses table and append a column tagging each cell for matching antigens (based on clonotype)", List.of(
+
+            ), null, null);
+        }
+
+
+        @Override
+        public ApplyKnownClonotypicData create(PipelineContext ctx)
+        {
+            return new ApplyKnownClonotypicData(ctx, this);
+        }
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "ctd";
+    }
+}
+
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CalculateTcrRepertoireStats.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CalculateTcrRepertoireStats.java
new file mode 100644
index 000000000..e802c342a
--- /dev/null
+++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CalculateTcrRepertoireStats.java
@@ -0,0 +1,43 @@
+package org.labkey.singlecell.pipeline.singlecell;
+
+import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+import org.labkey.api.singlecell.pipeline.SingleCellStep;
+
+import java.util.Arrays;
+
+public class CalculateTcrRepertoireStats extends AbstractRDiscvrStep
+{
+    public CalculateTcrRepertoireStats(PipelineContext ctx, CalculateTcrRepertoireStats.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("CalculateTcrRepertoireStats", "Calculate TCR Repertoire Stats", "CellMembrane/tcrdist3", "This will calculate TCR diversity metrics, and save the results in the database.", Arrays.asList(
+
+            ), null, null);
+        }
+
+        @Override
+        public CalculateTcrRepertoireStats create(PipelineContext ctx)
+        {
+            return new CalculateTcrRepertoireStats(ctx, this);
+        }
+    }
+
+    @Override
+    public boolean createsSeuratObjects()
+    {
+        return false;
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "ts";
+    }
+}
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/PredictTcellActivation.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/PredictTcellActivation.java
new file mode 100644
index 000000000..f4e9fdf83
--- /dev/null
+++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/PredictTcellActivation.java
@@ -0,0 +1,37 @@
+package org.labkey.singlecell.pipeline.singlecell;
+
+import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+import org.labkey.api.singlecell.pipeline.SingleCellStep;
+
+import java.util.List;
+
+public class PredictTcellActivation extends AbstractRDiscvrStep
+{
+    public PredictTcellActivation(PipelineContext ctx, PredictTcellActivation.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("PredictTcellActivation", "Predict T cell Activation", "RIRA", "This uses RIRA::PredictTcellActivation to predict TCR-triggered T cells", List.of(), null, null);
+        }
+
+
+        @Override
+        public PredictTcellActivation create(PipelineContext ctx)
+        {
+            return new PredictTcellActivation(ctx, this);
+        }
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "tca";
+    }
+}
+
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java
index 9a9329b96..fad042f96 100644
--- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java
+++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java
@@ -48,6 +48,18 @@ public Provider()
                     {{
                         put("checked", false);
                     }}, false),
+                    SeuratToolParameter.create("recalculateUCells", "Recalculate UCells", "If checked, RIRA::CalculateUCellScores will be re-run", "checkbox", new JSONObject()
+                    {{
+                        put("checked", true);
+                    }}, true),
+                    SeuratToolParameter.create("saveRepertoireStats", "Save TCR Repertoire Stats", "If checked, Rdiscvr::CalculateAndStoreTcrRepertoireStats will be run", "checkbox", new JSONObject()
+                    {{
+                        put("checked", true);
+                    }}, true),
+                    SeuratToolParameter.create("scoreActivation", "Score T Cell Activation", "If checked, RIRA::PredictTcellActivation will be run", "checkbox", new JSONObject()
+                    {{
+                        put("checked", true);
+                    }}, true),
                     SeuratToolParameter.create("keepOriginal", "Keep Copy of Original File", "If checked, the original file will be copied with the file extension '.bk'", "checkbox", new JSONObject()
                     {{
                         put("checked", false);