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10e5a7d 4311660 10e5a7d 4d1536e 10e5a7d 4d1536e 10e5a7d c02b903 10e5a7d c02b903 10e5a7d 4d1536e 10e5a7d 4d1536e 10e5a7d 0249159 10e5a7d 0249159 4311660 0249159 10e5a7d 0249159 28c3864 94fca14 28c3864 4311660 402f825 9c2348a 0249159 7763496 10e5a7d c02b903 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 | # TransVar API for HuggingFace Spaces
# 使用 transvar 官方数据库
FROM python:3.9-slim
# 环境变量
ENV DEBIAN_FRONTEND=noninteractive \
PYTHONUNBUFFERED=1 \
PORT=7860
# 安装系统依赖
RUN apt-get update && apt-get install -y \
wget \
curl \
git \
samtools \
tabix \
build-essential \
zlib1g-dev \
libbz2-dev \
liblzma-dev \
libcurl4-gnutls-dev \
&& rm -rf /var/lib/apt/lists/*
# 从 GitHub 克隆仓库
WORKDIR /app
RUN git clone https://github.com/pzweuj/TransVar2API.git .
# 安装 Python 依赖和 transvar
RUN pip3 install --no-cache-dir -r requirements.txt
RUN pip3 install --no-cache-dir transvar
# ========== 创建数据目录 ==========
RUN mkdir -p /data/hg38 /data/hg19
# ========== 下载参考基因组 ==========
# hg38
WORKDIR /data/hg38
RUN echo "Downloading hg38 reference genome..." && \
wget -q -O hg38.fa.gz https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz && \
gunzip hg38.fa.gz && \
samtools faidx hg38.fa
# hg19
WORKDIR /data/hg19
RUN echo "Downloading hg19 reference genome..." && \
wget -q -O hg19.fa.gz https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz && \
gunzip hg19.fa.gz && \
samtools faidx hg19.fa
# ========== 配置 transvar reference ==========
RUN echo "Configuring hg38 reference..." && \
transvar config -k reference -v /data/hg38/hg38.fa --refversion hg38
RUN echo "Configuring hg19 reference..." && \
transvar config -k reference -v /data/hg19/hg19.fa --refversion hg19
# ========== 下载注释数据库 ==========
RUN echo "Downloading hg38 annotation database..." && \
transvar config --download_anno --refversion hg38
RUN echo "Downloading hg19 annotation database..." && \
transvar config --download_anno --refversion hg19
# 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" --refseq --refversion hg38 -o /dev/stdout
WORKDIR /app
RUN chmod +x /app/scripts/hf_startup.sh
EXPOSE 7860
CMD ["/app/scripts/hf_startup.sh"] |