@bgicli/bgicli 2.2.4 → 2.2.6
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/dist/bgi.js +31 -2
- package/package.json +1 -1
package/dist/bgi.js
CHANGED
|
@@ -13789,7 +13789,8 @@ function toolBash(command, workdir, timeoutMs = 3e4) {
|
|
|
13789
13789
|
} catch (err) {
|
|
13790
13790
|
const e2 = err;
|
|
13791
13791
|
const out = (decodeBuffer(e2.stdout) + "\n" + decodeBuffer(e2.stderr)).trim();
|
|
13792
|
-
|
|
13792
|
+
const cmdLine = (e2.message ?? "Command failed").split("\n")[0];
|
|
13793
|
+
return { output: out, error: cmdLine };
|
|
13793
13794
|
}
|
|
13794
13795
|
}
|
|
13795
13796
|
function toolReadFile(path, maxLines, offset) {
|
|
@@ -14116,6 +14117,34 @@ cat ${SKILLS_DIR}/<skill-id>/SKILL.md
|
|
|
14116
14117
|
|
|
14117
14118
|
---
|
|
14118
14119
|
|
|
14120
|
+
## Environment Awareness
|
|
14121
|
+
|
|
14122
|
+
**\u9996\u6B21\u8FD0\u884C\u4EFB\u4F55 R/Python/\u751F\u4FE1\u5DE5\u5177\u4E4B\u524D\uFF0C\u5148\u68C0\u67E5\u5B83\u662F\u5426\u5DF2\u5B89\u88C5\uFF1A**
|
|
14123
|
+
|
|
14124
|
+
\`\`\`bash
|
|
14125
|
+
# \u68C0\u67E5 R
|
|
14126
|
+
R --version 2>&1 | head -1
|
|
14127
|
+
|
|
14128
|
+
# \u68C0\u67E5 Python
|
|
14129
|
+
python --version 2>&1 || python3 --version 2>&1
|
|
14130
|
+
|
|
14131
|
+
# \u68C0\u67E5\u5E38\u7528\u751F\u4FE1\u5DE5\u5177
|
|
14132
|
+
samtools --version 2>&1 | head -1
|
|
14133
|
+
\`\`\`
|
|
14134
|
+
|
|
14135
|
+
**\u5DE5\u5177\u672A\u5B89\u88C5\u65F6\u7684\u5904\u7406\u89C4\u5219\uFF08\u6309\u4F18\u5148\u7EA7\uFF09\uFF1A**
|
|
14136
|
+
1. \u660E\u786E\u544A\u77E5\u7528\u6237\u8BE5\u5DE5\u5177\u672A\u5B89\u88C5\uFF08\u4E0D\u8981\u7EE7\u7EED\u5047\u8BBE\u53EF\u7528\uFF09
|
|
14137
|
+
2. \u7ED9\u51FA\u5BF9\u5E94\u7CFB\u7EDF\u7684\u5B89\u88C5\u547D\u4EE4\uFF1A
|
|
14138
|
+
- R\uFF1Ahttps://cran.r-project.org/ \uFF0CWindows \u63A8\u8350 \`winget install RProject.R\`
|
|
14139
|
+
- Python\uFF1A\`winget install Python.Python.3\` \u6216 https://www.python.org/downloads/
|
|
14140
|
+
- Conda/Mamba\uFF1A\`winget install Anaconda.Miniconda3\`\uFF08\u751F\u4FE1\u5305\u7BA1\u7406\u9996\u9009\uFF09
|
|
14141
|
+
- samtools/STAR \u7B49\uFF1A\u5728 Linux/macOS \u7528 \`conda install -c bioconda <tool>\`
|
|
14142
|
+
3. \u8BE2\u95EE\u7528\u6237\u662F\u5426\u9700\u8981\u5E2E\u52A9\u5B8C\u6210\u5B89\u88C5\uFF0C\u6216\u6539\u7528\u5176\u4ED6\u5DF2\u5B89\u88C5\u7684\u5DE5\u5177\u66FF\u4EE3
|
|
14143
|
+
|
|
14144
|
+
**\u4E0D\u8981\u5728\u5DE5\u5177\u7F3A\u5931\u65F6\u7EE7\u7EED\u6267\u884C\u4F9D\u8D56\u8BE5\u5DE5\u5177\u7684\u6B65\u9AA4\u3002**
|
|
14145
|
+
|
|
14146
|
+
---
|
|
14147
|
+
|
|
14119
14148
|
## Script Execution Rules
|
|
14120
14149
|
|
|
14121
14150
|
\u{1F6A8} **\u5173\u952E\u89C4\u5219\uFF1A**
|
|
@@ -14697,7 +14726,7 @@ function routeSkill(message) {
|
|
|
14697
14726
|
}
|
|
14698
14727
|
|
|
14699
14728
|
// src/index.ts
|
|
14700
|
-
var VERSION2 = "2.2.
|
|
14729
|
+
var VERSION2 = "2.2.6";
|
|
14701
14730
|
function installBundledData() {
|
|
14702
14731
|
const bundledData = (0, import_path4.join)(__dirname, "..", "data");
|
|
14703
14732
|
if (!(0, import_fs4.existsSync)(bundledData)) return;
|