@cyanheads/ensembl-mcp-server 0.5.0 → 0.5.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/AGENTS.md +15 -12
- package/CLAUDE.md +15 -12
- package/Dockerfile +110 -33
- package/README.md +21 -36
- package/changelog/0.5.x/0.5.1.md +28 -0
- package/dist/mcp-server/tools/definitions/get-homology.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-homology.tool.js +4 -8
- package/dist/mcp-server/tools/definitions/get-homology.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-sequence.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-sequence.tool.js +7 -13
- package/dist/mcp-server/tools/definitions/get-sequence.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-xrefs.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-xrefs.tool.js +1 -3
- package/dist/mcp-server/tools/definitions/get-xrefs.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-gene.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-gene.tool.js +5 -13
- package/dist/mcp-server/tools/definitions/lookup-gene.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/predict-variant.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/predict-variant.tool.js +6 -14
- package/dist/mcp-server/tools/definitions/predict-variant.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/query-region.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/query-region.tool.js +2 -6
- package/dist/mcp-server/tools/definitions/query-region.tool.js.map +1 -1
- package/package.json +11 -10
- package/server.json +10 -24
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"get-sequence.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-sequence.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqBjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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1
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+
{"version":3,"file":"get-sequence.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-sequence.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqBjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsT7B,CAAC"}
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@@ -177,7 +177,7 @@ export const ensemblGetSequence = tool('ensembl_get_sequence', {
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177
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// Ensembl's region endpoint serves genomic DNA only and ignores a type parameter,
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// so a cdna/cds/protein request would come back as genomic — reject it up front.
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if (input.type !== 'genomic') {
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-
throw ctx.fail('type_mismatch', `Region ids are genomic-only — type "${input.type}" is not available for region ${input.id}
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+
throw ctx.fail('type_mismatch', `Region ids are genomic-only — type "${input.type}" is not available for region ${input.id}.`);
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}
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// For the prefixed form the species is the segment before the first colon and
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// the region is everything after it; the bare form takes its species from the
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@@ -186,7 +186,7 @@ export const ensemblGetSequence = tool('ensembl_get_sequence', {
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186
|
const species = input.species?.trim() || (isPrefixedRegion ? input.id.slice(0, firstColon) : undefined);
|
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const region = isPrefixedRegion ? input.id.slice(firstColon + 1) : input.id;
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188
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if (!species) {
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189
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-
throw ctx.fail('missing_species', `Region ${input.id} needs a species — set species (e.g. homo_sapiens) or use the species:chr:start-end id form
|
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189
|
+
throw ctx.fail('missing_species', `Region ${input.id} needs a species — set species (e.g. homo_sapiens) or use the species:chr:start-end id form.`);
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}
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191
191
|
// Both region shapes end in start-end after the last colon. Comparing the digit
|
|
192
192
|
// strings (length, then lexically) stays exact past double precision and linear
|
|
@@ -196,21 +196,17 @@ export const ensemblGetSequence = tool('ensembl_get_sequence', {
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196
196
|
.split('-')
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197
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.map((digits) => digits.replace(/^0+(?=\d)/, ''));
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198
|
if (start.length > end.length || (start.length === end.length && start > end)) {
|
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199
|
-
throw ctx.fail('invalid_region', `Region ${input.id} is reversed: start ${start} is greater than its end ${end}
|
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199
|
+
throw ctx.fail('invalid_region', `Region ${input.id} is reversed: start ${start} is greater than its end ${end}.`);
|
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200
|
}
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|
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201
|
resolved = await service
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|
202
202
|
.getSequenceByRegion(species, region, input.expand_5prime, input.expand_3prime, ctx)
|
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203
|
.catch((err) => {
|
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204
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|
const msg = err instanceof Error ? err.message : String(err);
|
|
205
205
|
if (/cannot request a slice|maximum allowed length|no slice found/i.test(msg)) {
|
|
206
|
-
throw ctx.fail('invalid_region', `Invalid region ${input.id}: ${msg}
|
|
207
|
-
...ctx.recoveryFor('invalid_region'),
|
|
208
|
-
});
|
|
206
|
+
throw ctx.fail('invalid_region', `Invalid region ${input.id}: ${msg}`);
|
|
209
207
|
}
|
|
210
208
|
if (/not found|invalid|no stable id/i.test(msg)) {
|
|
211
|
-
throw ctx.fail('not_found', `Region ${input.id} not found: ${msg}
|
|
212
|
-
...ctx.recoveryFor('not_found'),
|
|
213
|
-
});
|
|
209
|
+
throw ctx.fail('not_found', `Region ${input.id} not found: ${msg}`);
|
|
214
210
|
}
|
|
215
211
|
throw err;
|
|
216
212
|
});
|
|
@@ -230,12 +226,10 @@ export const ensemblGetSequence = tool('ensembl_get_sequence', {
|
|
|
230
226
|
mentionsInOrder(msg, 'type', 'mismatch') ||
|
|
231
227
|
/incompatible/i.test(msg)))) {
|
|
232
228
|
throw ctx.fail('type_mismatch', `Cannot request type "${input.type}" from a gene ID — use a transcript or protein stable ID instead. ` +
|
|
233
|
-
`Call ensembl_lookup_gene with expand_transcripts=true to get transcript IDs
|
|
229
|
+
`Call ensembl_lookup_gene with expand_transcripts=true to get transcript IDs.`);
|
|
234
230
|
}
|
|
235
231
|
if (notFound) {
|
|
236
|
-
throw ctx.fail('not_found', `ID ${input.id} not found in Ensembl
|
|
237
|
-
...ctx.recoveryFor('not_found'),
|
|
238
|
-
});
|
|
232
|
+
throw ctx.fail('not_found', `ID ${input.id} not found in Ensembl.`);
|
|
239
233
|
}
|
|
240
234
|
throw err;
|
|
241
235
|
});
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"get-xrefs.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyBjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;
|
|
1
|
+
{"version":3,"file":"get-xrefs.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyBjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;EAqH1B,CAAC"}
|
|
@@ -77,9 +77,7 @@ export const ensemblGetXrefs = tool('ensembl_get_xrefs', {
|
|
|
77
77
|
.catch((err) => {
|
|
78
78
|
const msg = err instanceof Error ? err.message : String(err);
|
|
79
79
|
if (/not found/i.test(msg)) {
|
|
80
|
-
throw ctx.fail('not_found', `ID "${input.id}" not found in Ensembl
|
|
81
|
-
...ctx.recoveryFor('not_found'),
|
|
82
|
-
});
|
|
80
|
+
throw ctx.fail('not_found', `ID "${input.id}" not found in Ensembl.`);
|
|
83
81
|
}
|
|
84
82
|
throw err;
|
|
85
83
|
});
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"get-xrefs.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,eAAe,GAAG,CAAC,CAAC,MAAM,CAAC;IAC/B,MAAM,EAAE,CAAC;SACN,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,sGAAsG,CACvG;IACH,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;IACtF,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,iFAAiF;QAC/E,+BAA+B,CAClC;IACH,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,oFAAoF,CAAC;IACjG,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;CACzF,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAC,mBAAmB,EAAE;IACvD,KAAK,EAAE,+BAA+B;IACtC,WAAW,EACT,8FAA8F;QAC9F,kGAAkG;QAClG,8FAA8F;QAC9F,gGAAgG;QAChG,iEAAiE;QACjE,qFAAqF;QACrF,6FAA6F;QAC7F,uCAAuC;IACzC,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE,cAAc,EAAE,IAAI,EAAE;IAC9E,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,EAAE,EAAE,CAAC;aACF,MAAM,EAAE;aACR,IAAI,EAAE;aACN,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,2DAA2D;YACzD,mEAAmE;YACnE,kGAAkG,CACrG;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,uEAAuE;YACrE,iEAAiE;YACjE,2DAA2D;YAC3D,gEAAgE;YAChE,+DAA+D,CAClE;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,KAAK,EAAE,CAAC;aACL,KAAK,CACJ,eAAe,CAAC,QAAQ,CACtB,0FAA0F,CAC3F,CACF;aACA,QAAQ,CAAC,uDAAuD,CAAC;QACpE,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,4CAA4C,CAAC;QAC7E,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;KAC1E,CAAC;IACF,UAAU,EAAE;QACV,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,8CAA8C,CAAC;KACvF;IAED,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,iEAAiE;YACvE,QAAQ,EACN,wEAAwE;gBACxE,mFAAmF;SACtF;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,eAAe,EAAE,EAAE,EAAE,EAAE,KAAK,CAAC,EAAE,EAAE,MAAM,EAAE,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC;QACtE,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,MAAM,KAAK,GAAG,MAAM,OAAO;aACxB,YAAY,CAAC,KAAK,CAAC,EAAE,CAAC,IAAI,EAAE,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,EAAE,IAAI,SAAS,EAAE,GAAG,CAAC;aACrE,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;YACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;YAC7D,IAAI,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC3B,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,OAAO,KAAK,CAAC,EAAE,yBAAyB,
|
|
1
|
+
{"version":3,"file":"get-xrefs.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,eAAe,GAAG,CAAC,CAAC,MAAM,CAAC;IAC/B,MAAM,EAAE,CAAC;SACN,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,sGAAsG,CACvG;IACH,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;IACtF,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,iFAAiF;QAC/E,+BAA+B,CAClC;IACH,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,oFAAoF,CAAC;IACjG,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;CACzF,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAC,mBAAmB,EAAE;IACvD,KAAK,EAAE,+BAA+B;IACtC,WAAW,EACT,8FAA8F;QAC9F,kGAAkG;QAClG,8FAA8F;QAC9F,gGAAgG;QAChG,iEAAiE;QACjE,qFAAqF;QACrF,6FAA6F;QAC7F,uCAAuC;IACzC,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE,cAAc,EAAE,IAAI,EAAE;IAC9E,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,EAAE,EAAE,CAAC;aACF,MAAM,EAAE;aACR,IAAI,EAAE;aACN,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,2DAA2D;YACzD,mEAAmE;YACnE,kGAAkG,CACrG;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,uEAAuE;YACrE,iEAAiE;YACjE,2DAA2D;YAC3D,gEAAgE;YAChE,+DAA+D,CAClE;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,KAAK,EAAE,CAAC;aACL,KAAK,CACJ,eAAe,CAAC,QAAQ,CACtB,0FAA0F,CAC3F,CACF;aACA,QAAQ,CAAC,uDAAuD,CAAC;QACpE,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,4CAA4C,CAAC;QAC7E,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;KAC1E,CAAC;IACF,UAAU,EAAE;QACV,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,8CAA8C,CAAC;KACvF;IAED,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,iEAAiE;YACvE,QAAQ,EACN,wEAAwE;gBACxE,mFAAmF;SACtF;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,eAAe,EAAE,EAAE,EAAE,EAAE,KAAK,CAAC,EAAE,EAAE,MAAM,EAAE,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC;QACtE,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,MAAM,KAAK,GAAG,MAAM,OAAO;aACxB,YAAY,CAAC,KAAK,CAAC,EAAE,CAAC,IAAI,EAAE,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,EAAE,IAAI,SAAS,EAAE,GAAG,CAAC;aACrE,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;YACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;YAC7D,IAAI,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC3B,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,OAAO,KAAK,CAAC,EAAE,yBAAyB,CAAC,CAAC;YACxE,CAAC;YACD,MAAM,GAAG,CAAC;QACZ,CAAC,CAAC,CAAC;QAEL,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACvB,MAAM,UAAU,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,wBAAwB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;YAC/E,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,iCAAiC,KAAK,CAAC,EAAE,GAAG,UAAU,IAAI;gBACxD,+DAA+D,CAClE,CAAC;QACJ,CAAC;QACD,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;QAE/B,OAAO,EAAE,KAAK,EAAE,UAAU,EAAE,KAAK,CAAC,MAAM,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC;IAClE,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,EAAE,CAAC;QAC3B,KAAK,CAAC,IAAI,CAAC,2BAA2B,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC;QAC1D,KAAK,CAAC,IAAI,CAAC,cAAc,MAAM,CAAC,UAAU,IAAI,CAAC,CAAC;QAEhD,IAAI,MAAM,CAAC,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC9B,KAAK,CAAC,IAAI,CAAC,4BAA4B,CAAC,CAAC;YACzC,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACpD,CAAC;QAED,oCAAoC;QACpC,MAAM,IAAI,GAAG,IAAI,GAAG,EAA+B,CAAC;QACpD,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,KAAK,EAAE,CAAC;YAC7B,MAAM,EAAE,GAAG,CAAC,CAAC,MAAM,IAAI,SAAS,CAAC;YACjC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBAAE,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC;YACpC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC;QACxB,CAAC;QAED,KAAK,MAAM,CAAC,EAAE,EAAE,OAAO,CAAC,IAAI,IAAI,EAAE,CAAC;YACjC,MAAM,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,EAAE,aAAa,CAAC;YAC9C,KAAK,CAAC,IAAI,CAAC,OAAO,WAAW,IAAI,EAAE,GAAG,WAAW,IAAI,WAAW,KAAK,EAAE,CAAC,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAC7F,KAAK,MAAM,CAAC,IAAI,OAAO,EAAE,CAAC;gBACxB,IAAI,IAAI,GAAG,OAAO,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,SAAS,IAAI,SAAS,IAAI,CAAC;gBAC9D,IAAI,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,SAAS,KAAK,CAAC,CAAC,SAAS;oBAAE,IAAI,IAAI,KAAK,CAAC,CAAC,SAAS,GAAG,CAAC;gBAC5E,IAAI,CAAC,CAAC,WAAW;oBAAE,IAAI,IAAI,KAAK,CAAC,CAAC,WAAW,EAAE,CAAC;gBAChD,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;YACnB,CAAC;YACD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACjB,CAAC;QAED,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
|
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@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"lookup-gene.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-gene.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmEjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
|
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1
|
+
{"version":3,"file":"lookup-gene.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-gene.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmEjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAgQ5B,CAAC"}
|
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@@ -164,9 +164,7 @@ export const ensemblLookupGene = tool('ensembl_lookup_gene', {
|
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164
164
|
input.symbols?.length,
|
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165
165
|
].filter(Boolean).length;
|
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166
166
|
if (inputCount > 1) {
|
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167
|
-
throw ctx.fail('conflicting_input', 'Provide exactly one of: symbol, id, ids, or symbols.'
|
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168
|
-
...ctx.recoveryFor('conflicting_input'),
|
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-
});
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167
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+
throw ctx.fail('conflicting_input', 'Provide exactly one of: symbol, id, ids, or symbols.');
|
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170
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|
}
|
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|
// --- Batch by IDs ---
|
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172
170
|
if (input.ids?.length) {
|
|
@@ -200,12 +198,10 @@ export const ensemblLookupGene = tool('ensembl_lookup_gene', {
|
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|
200
198
|
.catch((err) => {
|
|
201
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|
const msg = err instanceof Error ? err.message : String(err);
|
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200
|
if (/not found|no stable id|no results|no valid lookup/i.test(msg)) {
|
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203
|
-
throw ctx.fail('not_found', `Gene symbol "${input.symbol}" not found in ${speciesStr}
|
|
201
|
+
throw ctx.fail('not_found', `Gene symbol "${input.symbol}" not found in ${speciesStr}.`);
|
|
204
202
|
}
|
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205
203
|
if (/species|invalid|unrecognized/i.test(msg)) {
|
|
206
|
-
throw ctx.fail('invalid_species', `Species "${speciesStr}" not recognized by Ensembl
|
|
207
|
-
...ctx.recoveryFor('invalid_species'),
|
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208
|
-
});
|
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204
|
+
throw ctx.fail('invalid_species', `Species "${speciesStr}" not recognized by Ensembl.`);
|
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205
|
}
|
|
210
206
|
throw err;
|
|
211
207
|
});
|
|
@@ -218,17 +214,13 @@ export const ensemblLookupGene = tool('ensembl_lookup_gene', {
|
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|
218
214
|
.catch((err) => {
|
|
219
215
|
const msg = err instanceof Error ? err.message : String(err);
|
|
220
216
|
if (/not found|no stable id/i.test(msg)) {
|
|
221
|
-
throw ctx.fail('not_found', `Gene ID "${input.id}" not found in Ensembl
|
|
222
|
-
...ctx.recoveryFor('not_found'),
|
|
223
|
-
});
|
|
217
|
+
throw ctx.fail('not_found', `Gene ID "${input.id}" not found in Ensembl.`);
|
|
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218
|
}
|
|
225
219
|
throw err;
|
|
226
220
|
});
|
|
227
221
|
return { gene };
|
|
228
222
|
}
|
|
229
|
-
throw ctx.fail('no_input', 'Provide symbol (with species), id, ids, or symbols.'
|
|
230
|
-
...ctx.recoveryFor('no_input'),
|
|
231
|
-
});
|
|
223
|
+
throw ctx.fail('no_input', 'Provide symbol (with species), id, ids, or symbols.');
|
|
232
224
|
},
|
|
233
225
|
format: (result) => {
|
|
234
226
|
const lines = [];
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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+
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AC,KAAK,EAAE,CAAC,CAAC;gBAC7C,CAAC;YACH,CAAC;QACH,CAAC;QAED,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"predict-variant.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/predict-variant.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA+HjE,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
|
|
1
|
+
{"version":3,"file":"predict-variant.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/predict-variant.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA+HjE,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAmVhC,CAAC"}
|
|
@@ -214,12 +214,10 @@ export const ensemblPredictVariant = tool('ensembl_predict_variant', {
|
|
|
214
214
|
.catch((err) => {
|
|
215
215
|
const msg = err instanceof Error ? err.message : String(err);
|
|
216
216
|
if (/invalid|unrecognized|parse|malformed/i.test(msg)) {
|
|
217
|
-
throw ctx.fail('invalid_notation', `Invalid region+allele notation "${input.variant}": ${msg}
|
|
217
|
+
throw ctx.fail('invalid_notation', `Invalid region+allele notation "${input.variant}": ${msg}`);
|
|
218
218
|
}
|
|
219
219
|
if (/not found|outside/i.test(msg)) {
|
|
220
|
-
throw ctx.fail('not_found', `Variant location not found: ${msg}
|
|
221
|
-
...ctx.recoveryFor('not_found'),
|
|
222
|
-
});
|
|
220
|
+
throw ctx.fail('not_found', `Variant location not found: ${msg}`);
|
|
223
221
|
}
|
|
224
222
|
throw err;
|
|
225
223
|
});
|
|
@@ -231,12 +229,10 @@ export const ensemblPredictVariant = tool('ensembl_predict_variant', {
|
|
|
231
229
|
const msg = err instanceof Error ? err.message : String(err);
|
|
232
230
|
// A well-formed rsID that dbSNP does not know reports "No variant found with ID …".
|
|
233
231
|
if (/not found|no variant|unknown variant/i.test(msg)) {
|
|
234
|
-
throw ctx.fail('not_found', `Variant identifier ${input.variant} not found in dbSNP
|
|
235
|
-
...ctx.recoveryFor('not_found'),
|
|
236
|
-
});
|
|
232
|
+
throw ctx.fail('not_found', `Variant identifier ${input.variant} not found in dbSNP.`);
|
|
237
233
|
}
|
|
238
234
|
if (/invalid|unrecognized|parse|malformed/i.test(msg)) {
|
|
239
|
-
throw ctx.fail('invalid_notation', `Invalid variant identifier "${input.variant}": ${msg}
|
|
235
|
+
throw ctx.fail('invalid_notation', `Invalid variant identifier "${input.variant}": ${msg}`);
|
|
240
236
|
}
|
|
241
237
|
throw err;
|
|
242
238
|
});
|
|
@@ -247,14 +243,10 @@ export const ensemblPredictVariant = tool('ensembl_predict_variant', {
|
|
|
247
243
|
.catch((err) => {
|
|
248
244
|
const msg = err instanceof Error ? err.message : String(err);
|
|
249
245
|
if (/invalid|unrecognized|parse|malformed|hgvs/i.test(msg)) {
|
|
250
|
-
throw ctx.fail('invalid_notation', `Invalid HGVS notation "${input.variant}": ${msg}
|
|
251
|
-
...ctx.recoveryFor('invalid_notation'),
|
|
252
|
-
});
|
|
246
|
+
throw ctx.fail('invalid_notation', `Invalid HGVS notation "${input.variant}": ${msg}`);
|
|
253
247
|
}
|
|
254
248
|
if (/not found/i.test(msg)) {
|
|
255
|
-
throw ctx.fail('not_found', `Variant ${input.variant} not found
|
|
256
|
-
...ctx.recoveryFor('not_found'),
|
|
257
|
-
});
|
|
249
|
+
throw ctx.fail('not_found', `Variant ${input.variant} not found.`);
|
|
258
250
|
}
|
|
259
251
|
throw err;
|
|
260
252
|
});
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"query-region.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/query-region.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyDjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
|
|
1
|
+
{"version":3,"file":"query-region.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/query-region.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyDjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsQ7B,CAAC"}
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@@ -174,14 +174,10 @@ export const ensemblQueryRegion = tool('ensembl_query_region', {
|
|
|
174
174
|
/is not a valid start|is not a valid end|is not a valid chr/i.test(msg) ||
|
|
175
175
|
/no slice found|cannot request a slice|could not decode region/i.test(msg) ||
|
|
176
176
|
/maximum allowed length/i.test(msg)) {
|
|
177
|
-
throw ctx.fail('invalid_region', `Invalid region "${input.region}": ${msg}
|
|
178
|
-
...ctx.recoveryFor('invalid_region'),
|
|
179
|
-
});
|
|
177
|
+
throw ctx.fail('invalid_region', `Invalid region "${input.region}": ${msg}`);
|
|
180
178
|
}
|
|
181
179
|
if (/species|invalid|unrecognized/i.test(msg)) {
|
|
182
|
-
throw ctx.fail('invalid_species', `Species "${input.species}" not recognized
|
|
183
|
-
...ctx.recoveryFor('invalid_species'),
|
|
184
|
-
});
|
|
180
|
+
throw ctx.fail('invalid_species', `Species "${input.species}" not recognized.`);
|
|
185
181
|
}
|
|
186
182
|
throw err;
|
|
187
183
|
});
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/ensembl-mcp-server",
|
|
3
|
-
"version": "0.5.
|
|
3
|
+
"version": "0.5.1",
|
|
4
4
|
"mcpName": "io.github.cyanheads/ensembl-mcp-server",
|
|
5
5
|
"description": "Look up genes, fetch sequences, predict variant consequences, find orthologs, and retrieve cross-database xrefs from Ensembl REST via MCP. STDIO or Streamable HTTP.",
|
|
6
6
|
"type": "module",
|
|
@@ -12,6 +12,7 @@
|
|
|
12
12
|
"files": [
|
|
13
13
|
"changelog/",
|
|
14
14
|
"dist/",
|
|
15
|
+
"!dist/*.mcpb",
|
|
15
16
|
"README.md",
|
|
16
17
|
"LICENSE",
|
|
17
18
|
"CLAUDE.md",
|
|
@@ -82,7 +83,7 @@
|
|
|
82
83
|
}
|
|
83
84
|
],
|
|
84
85
|
"license": "Apache-2.0",
|
|
85
|
-
"packageManager": "bun@1.4.
|
|
86
|
+
"packageManager": "bun@1.4.2",
|
|
86
87
|
"engines": {
|
|
87
88
|
"bun": ">=1.4.0",
|
|
88
89
|
"node": ">=24.0.0"
|
|
@@ -91,19 +92,19 @@
|
|
|
91
92
|
"access": "public"
|
|
92
93
|
},
|
|
93
94
|
"dependencies": {
|
|
94
|
-
"@cyanheads/mcp-ts-core": "^0.13.
|
|
95
|
-
"pino-pretty": "^13.
|
|
95
|
+
"@cyanheads/mcp-ts-core": "^0.13.14",
|
|
96
|
+
"pino-pretty": "^13.2.0",
|
|
96
97
|
"zod": "^4.6.5"
|
|
97
98
|
},
|
|
98
99
|
"devDependencies": {
|
|
99
|
-
"@biomejs/biome": "^2.5.
|
|
100
|
-
"@socketsecurity/bun-security-scanner": "^1.1.
|
|
101
|
-
"@types/node": "^26.6.
|
|
100
|
+
"@biomejs/biome": "^2.5.15",
|
|
101
|
+
"@socketsecurity/bun-security-scanner": "^1.1.3",
|
|
102
|
+
"@types/node": "^26.6.4",
|
|
102
103
|
"depcheck": "^1.4.7",
|
|
103
|
-
"ignore": "^7.0.
|
|
104
|
-
"tsc-alias": "^1.9.
|
|
104
|
+
"ignore": "^7.0.12",
|
|
105
|
+
"tsc-alias": "^1.9.7",
|
|
105
106
|
"typescript": "^7.0.2",
|
|
106
|
-
"vitest": "^5.0.
|
|
107
|
+
"vitest": "^5.0.3"
|
|
107
108
|
},
|
|
108
109
|
"trustedDependencies": ["@socketsecurity/bun-security-scanner"]
|
|
109
110
|
}
|
package/server.json
CHANGED
|
@@ -6,7 +6,7 @@
|
|
|
6
6
|
"url": "https://github.com/cyanheads/ensembl-mcp-server",
|
|
7
7
|
"source": "github"
|
|
8
8
|
},
|
|
9
|
-
"version": "0.5.
|
|
9
|
+
"version": "0.5.1",
|
|
10
10
|
"remotes": [
|
|
11
11
|
{
|
|
12
12
|
"type": "streamable-http",
|
|
@@ -18,18 +18,8 @@
|
|
|
18
18
|
"registryType": "npm",
|
|
19
19
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
20
20
|
"identifier": "@cyanheads/ensembl-mcp-server",
|
|
21
|
-
"runtimeHint": "
|
|
22
|
-
"version": "0.5.
|
|
23
|
-
"packageArguments": [
|
|
24
|
-
{
|
|
25
|
-
"type": "positional",
|
|
26
|
-
"value": "run"
|
|
27
|
-
},
|
|
28
|
-
{
|
|
29
|
-
"type": "positional",
|
|
30
|
-
"value": "start:stdio"
|
|
31
|
-
}
|
|
32
|
-
],
|
|
21
|
+
"runtimeHint": "npx",
|
|
22
|
+
"version": "0.5.1",
|
|
33
23
|
"environmentVariables": [
|
|
34
24
|
{
|
|
35
25
|
"name": "ENSEMBL_BASE_URL",
|
|
@@ -54,19 +44,15 @@
|
|
|
54
44
|
"registryType": "npm",
|
|
55
45
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
56
46
|
"identifier": "@cyanheads/ensembl-mcp-server",
|
|
57
|
-
"runtimeHint": "
|
|
58
|
-
"version": "0.5.
|
|
59
|
-
"
|
|
47
|
+
"runtimeHint": "npx",
|
|
48
|
+
"version": "0.5.1",
|
|
49
|
+
"environmentVariables": [
|
|
60
50
|
{
|
|
61
|
-
"
|
|
62
|
-
"
|
|
51
|
+
"name": "MCP_TRANSPORT_TYPE",
|
|
52
|
+
"description": "Selects the HTTP transport.",
|
|
53
|
+
"format": "string",
|
|
54
|
+
"value": "http"
|
|
63
55
|
},
|
|
64
|
-
{
|
|
65
|
-
"type": "positional",
|
|
66
|
-
"value": "start:http"
|
|
67
|
-
}
|
|
68
|
-
],
|
|
69
|
-
"environmentVariables": [
|
|
70
56
|
{
|
|
71
57
|
"name": "ENSEMBL_BASE_URL",
|
|
72
58
|
"description": "Ensembl REST API base URL. Override to use GRCh37 endpoint or a local mirror.",
|