Update Dockerfile

Dockerfile

@@ -1,11 +1,10 @@
 # TransVar API for HuggingFace Spaces
-# 仓库: https://github.com/pzweuj/TransVar2API
+# 使用 transvar 官方数据库
 
 FROM python:3.9-slim
 
 # 环境变量
 ENV DEBIAN_FRONTEND=noninteractive \
-    TRANSVAR_DB_PATH=/data/transvar_db \
     PYTHONUNBUFFERED=1 \
     PORT=7860
 
@@ -34,36 +33,31 @@ RUN pip3 install --no-cache-dir transvar
 # 修补 transvar 的 localdb.py 以修复 KeyError: 'product' 错误
 RUN python3 /app/scripts/patch_transvar.py
 
-# 创建数据目录
-RUN mkdir -p /data/transvar_db/ucsc_hg38 /data/transvar_db/ucsc_hg19 \
-             /data/transvar_db/ncbi_refseq_hg38 /data/transvar_db/ncbi_refseq_hg19
+# ========== 下载 transvar 官方数据库 ==========
+# hg38 - 下载注释数据库和参考基因组
+RUN echo "Downloading hg38 annotation database..." && \
+    transvar config --download_anno --refversion hg38
 
-# ========== UCSC 数据库 ==========
-WORKDIR /data/transvar_db/ucsc_hg38
-RUN wget -q -O hg38.fa.gz https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz && \
-    gunzip -f hg38.fa.gz && \
-    samtools faidx hg38.fa
-RUN wget -q -O ncbiRefSeq.txt.gz https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz
+RUN echo "Downloading hg38 reference genome..." && \
+    transvar config --download_ref --refversion hg38
 
-WORKDIR /data/transvar_db/ucsc_hg19
-RUN wget -q -O hg19.fa.gz https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz && \
-    gunzip -f hg19.fa.gz && \
-    samtools faidx hg19.fa
-RUN wget -q -O ncbiRefSeq.txt.gz https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ncbiRefSeq.txt.gz
+# hg19 - 下载注释数据库和参考基因组
+RUN echo "Downloading hg19 annotation database..." && \
+    transvar config --download_anno --refversion hg19
 
-# ========== NCBI RefSeq 数据库 (软链接 UCSC 的参考基因组) ==========
-WORKDIR /data/transvar_db/ncbi_refseq_hg38
-RUN ln -sf ../ucsc_hg38/hg38.fa ./hg38.fa && \
-    samtools faidx hg38.fa
-RUN wget -q -O hg38_refseq.gff.gz https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.gff.gz
+RUN echo "Downloading hg19 reference genome..." && \
+    transvar config --download_ref --refversion hg19
 
-WORKDIR /data/transvar_db/ncbi_refseq_hg19
-RUN ln -sf ../ucsc_hg19/hg19.fa ./hg19.fa && \
-    samtools faidx hg19.fa
-RUN wget -q -O hg19_refseq.gff.gz https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.gff.gz
+# 验证数据库
+RUN echo "Verifying databases..." && \
+    echo "hg38 config:" && transvar config --refversion hg38 && \
+    echo "hg19 config:" && transvar config --refversion hg19
+
+# 测试 transvar
+RUN echo "Testing transvar..." && \
+    transvar panno -i "PIK3CA:p.E545K" --refversion hg38 -o /dev/stdout
 
 # 设置启动脚本权限
-WORKDIR /app
 RUN chmod +x /app/scripts/hf_startup.sh
 
 EXPOSE 7860