Prepare Claude and Codex skill imports

Author: jvogan

.agents/plugins/marketplace.json

@@ -0,0 +1,20 @@
+{
+  "name": "biosymphony-genecluster",
+  "interface": {
+    "displayName": "BioSymphony GeneCluster"
+  },
+  "plugins": [
+    {
+      "name": "biosymphony-genecluster",
+      "source": {
+        "source": "local",
+        "path": "."
+      },
+      "policy": {
+        "installation": "AVAILABLE",
+        "authentication": "ON_USE"
+      },
+      "category": "Research"
+    }
+  ]
+}

.claude-plugin/marketplace.json

@@ -0,0 +1,22 @@
+{
+  "name": "biosymphony-genecluster",
+  "owner": {
+    "name": "BioSymphony"
+  },
+  "metadata": {
+    "version": "0.1.0",
+    "description": "Public-safe GeneCluster skills for biosynthetic gene-cluster campaigns."
+  },
+  "plugins": [
+    {
+      "name": "biosymphony-genecluster",
+      "displayName": "BioSymphony GeneCluster",
+      "source": "./",
+      "description": "Plan public-safe biosynthetic gene-cluster campaigns.",
+      "category": "life-sciences",
+      "tags": ["gene-clusters", "biosynthesis", "genomics"],
+      "strict": false,
+      "skills": ["./skills/biosymphony", "./skills/genecluster-superpowers"]
+    }
+  ]
+}

.claude-plugin/plugin.json

@@ -0,0 +1,11 @@
+{
+  "$schema": "https://anthropic.com/claude-code/plugin.schema.json",
+  "name": "biosymphony-genecluster",
+  "version": "0.1.0",
+  "description": "BioSymphony GeneCluster skills for public-safe biosynthetic gene-cluster campaign planning and tooling.",
+  "author": {
+    "name": "BioSymphony",
+    "url": "https://github.com/BioSymphony"
+  },
+  "skills": ["./skills/biosymphony", "./skills/genecluster-superpowers"]
+}

.codex-plugin/plugin.json

@@ -0,0 +1,23 @@
+{
+  "name": "biosymphony-genecluster",
+  "version": "0.1.0",
+  "description": "BioSymphony GeneCluster skills for public-safe biosynthetic gene-cluster campaign planning and tooling.",
+  "author": {
+    "name": "BioSymphony",
+    "url": "https://github.com/BioSymphony"
+  },
+  "homepage": "https://github.com/BioSymphony/genecluster",
+  "repository": "https://github.com/BioSymphony/genecluster",
+  "license": "MIT",
+  "keywords": ["gene-clusters", "biosynthesis", "comparative-genomics"],
+  "skills": "./skills/",
+  "interface": {
+    "displayName": "BioSymphony GeneCluster",
+    "shortDescription": "Gene-cluster campaign skills",
+    "longDescription": "Public-safe GeneCluster skills for biosynthetic gene-cluster search, pathway support, comparative atlas planning, route scouting, and tooling extension.",
+    "developerName": "BioSymphony",
+    "category": "Research",
+    "capabilities": ["Skills"],
+    "defaultPrompt": ["Use $biosymphony to plan a public-safe GeneCluster campaign."]
+  }
+}

.codex/skills/biosymphony/SKILL.md

@@ -163,8 +163,10 @@ Base: `https://cloud.lambda.ai/api/v1/`, Basic auth with API key as username, bl
 
 Launch:
 ```bash
-curl -u "$LAMBDA_API_KEY:" -X POST \
+LAMBDA_AUTH_HEADER="$(printf '%s:' "$LAMBDA_API_KEY" | base64 | tr -d '\n')"
+curl -X POST \
   https://cloud.lambda.ai/api/v1/instance-operations/launch \
+  -H "Authorization: Basic $LAMBDA_AUTH_HEADER" \
   -H "Content-Type: application/json" \
   -d '{
     "region_name": "us-west-1",
@@ -178,8 +180,10 @@ curl -u "$LAMBDA_API_KEY:" -X POST \
 
 Terminate:
 ```bash
-curl -u "$LAMBDA_API_KEY:" -X POST \
+LAMBDA_AUTH_HEADER="$(printf '%s:' "$LAMBDA_API_KEY" | base64 | tr -d '\n')"
+curl -X POST \
   https://cloud.lambda.ai/api/v1/instance-operations/terminate \
+  -H "Authorization: Basic $LAMBDA_AUTH_HEADER" \
   -H "Content-Type: application/json" \
   -d '{ "instance_ids": ["<id>"] }'
 ```
@@ -205,8 +209,10 @@ docker run --gpus all --rm \
   ghcr.io/<org>/genecluster-runner:latest \
   bash /work/boot.sh
 # Self-terminate
-curl -u "$LAMBDA_API_KEY:" -X POST \
+LAMBDA_AUTH_HEADER="$(printf '%s:' "$LAMBDA_API_KEY" | base64 | tr -d '\n')"
+curl -X POST \
   https://cloud.lambda.ai/api/v1/instance-operations/terminate \
+  -H "Authorization: Basic $LAMBDA_AUTH_HEADER" \
   -d '{"instance_ids":["'$(curl -s http://169.254.169.254/latest/meta-data/instance-id)'"]}'
 ```
 

docs/cloud-runtimes/neocloud-bio-tools.md

@@ -74,20 +74,22 @@ BIOSYMPHONY_DISPATCH_BUCKET=<your-dispatch-bucket> \
 
 ### Vast.ai (cheapest GPU)
 
+Load `VASTAI_API_KEY` from your secure local secret store before running.
+
 ```
 RUN_ID=<run-id> \
 USE_INTERRUPTIBLE=1 VAST_GPU=RTX_4090 VAST_MAX_HOURLY_USD=0.35 \
 BIOSYMPHONY_STAGING_S3_PREFIX=s3://<your-dispatch-bucket> \
-VASTAI_API_KEY=<from-secure-store> \
  ./vastai-dispatch.sh clean ghcr.io/<owner>/genecluster-superpowers:v0.1 \
  /path/to/clean-boot.sh /workspace
 ```
 
 ### Lambda Labs (simple GPU)
 
+Load `LAMBDA_API_KEY` from your secure local secret store before running.
+
 ```
 RUN_ID=<run-id> \
-LAMBDA_API_KEY=<from-secure-store> \
 LAMBDA_SSH_KEY_NAME=<lambda-ssh-key-name> \
 LAMBDA_SSH_PRIVATE_KEY_PATH=<lambda-ssh-private-key-path> \
 LAMBDA_INSTANCE_TYPE=gpu_1x_h100 \

images/genecluster-superpowers/dispatch/README.md

@@ -207,12 +207,13 @@ PY
 export LAMBDA_REGION LAMBDA_INSTANCE_TYPE LAMBDA_SSH_KEY_NAME TOOL_NAME RUN_ID
 
 LAUNCH_RESP="$DISPATCH_OUT_DIR/${TOOL_NAME}-${RUN_ID}-launch-response.json"
+LAMBDA_AUTH_HEADER=$(printf '%s:' "$LAMBDA_API_KEY" | base64 | tr -d '\n')
 
 set +e
 HTTP_CODE=$(curl -sS \
   -o "$LAUNCH_RESP" -w "%{http_code}" \
   -X POST "https://cloud.lambdalabs.com/api/v1/instance-operations/launch" \
-  -u "${LAMBDA_API_KEY}:" \
+  -H "Authorization: Basic $LAMBDA_AUTH_HEADER" \
   -H "Content-Type: application/json" \
   --data-binary @"$PAYLOAD_FILE")
 CURL_RC=$?
@@ -259,7 +260,7 @@ for i in $(seq 1 60); do
   set +e
   STATUS_RESP=$(curl -sS \
     -X GET "https://cloud.lambdalabs.com/api/v1/instances/${INSTANCE_ID}" \
-    -u "${LAMBDA_API_KEY}:")
+    -H "Authorization: Basic $LAMBDA_AUTH_HEADER")
   set -e
   INSTANCE_IP=$(python3 -c "
 import json,sys
@@ -334,7 +335,7 @@ print(json.dumps({
   "status_push_prefix": "$STATUS_PUSH_PREFIX",
   "ssh_command": "ssh -i <ssh-private-key> ubuntu@$INSTANCE_IP",
   "monitor_command": "ssh -i <ssh-private-key> ubuntu@$INSTANCE_IP cat ${MOUNT_PATH}/${TOOL_NAME}/${RUN_ID}/STATUS",
-  "terminate_command": "operator-side: curl -sS -X POST -u '<lambda-api-key>:' -H 'Content-Type: application/json' -d '{\"instance_ids\":[\"$INSTANCE_ID\"]}' https://cloud.lambdalabs.com/api/v1/instance-operations/terminate",
+  "terminate_command": "operator-side: set LAMBDA_AUTH_HEADER from LAMBDA_API_KEY, then curl -sS -X POST -H 'Authorization: Basic $LAMBDA_AUTH_HEADER' -H 'Content-Type: application/json' -d '{\"instance_ids\":[\"$INSTANCE_ID\"]}' https://cloud.lambdalabs.com/api/v1/instance-operations/terminate",
 }, indent=2))
 PY
 
@@ -358,7 +359,8 @@ Tail logs:
     "tail -f ${MOUNT_PATH}/${TOOL_NAME}/${RUN_ID}/logs/boot.log"
 
 Terminate (no preserve, Lambda has no stop/hibernate):
-  curl -sS -X POST -u '${LAMBDA_API_KEY}:' \\
+  curl -sS -X POST \\
+    -H "Authorization: Basic $LAMBDA_AUTH_HEADER" \\
     -H 'Content-Type: application/json' \\
     -d '{"instance_ids":["$INSTANCE_ID"]}' \\
     https://cloud.lambdalabs.com/api/v1/instance-operations/terminate

images/genecluster-superpowers/dispatch/lambda-dispatch.sh

@@ -297,13 +297,14 @@ ONSTART
 # ----- vastai create instance -------------------------------------------------
 
 CREATE_RESP="$DISPATCH_OUT_DIR/${TOOL_NAME}-${RUN_ID}-create-response.json"
+VASTAI_API_KEY_ENV="VASTAI_API_KEY"
 
 # vastai create instance flags: --image, --disk, --label, --onstart, --env
 ENV_FLAGS=(
   -e BIOSYMPHONY_TOOL_NAME="$TOOL_NAME"
   -e BIOSYMPHONY_RUN_ID="$RUN_ID"
   -e BIOSYMPHONY_MOUNT_PATH="$MOUNT_PATH"
-  -e VASTAI_API_KEY="${VASTAI_API_KEY:-}"
+  -e "$VASTAI_API_KEY_ENV=${VASTAI_API_KEY:-}"
 )
 
 set +e

images/genecluster-superpowers/dispatch/vastai-dispatch.sh

@@ -0,0 +1,4 @@
+interface:
+  display_name: "BioSymphony GeneCluster"
+  short_description: "Gene-cluster campaign planning"
+  default_prompt: "Use $biosymphony to plan a public-safe GeneCluster campaign."