stat:bioinform:majiq

差别

这里会显示出您选择的修订版和当前版本之间的差别。

到此差别页面的链接

--- stat:bioinform:majiq [2026/04/30 13:39] – 创建 inkit
+++ stat:bioinform:majiq [2026/04/30 13:43] (当前版本) – inkit
@@ 行 14: / 行 14: @@
 https://biociphers.bitbucket.io/majiq-docs/
+```dockerfile
+FROM python:3.12-slim-bookworm
-alias majiq='docker run --rm -e MAJIQ_LICENSE_FILE=/data/majiq_license_academic_official.lic -v "$(pwd)/datamj:/data" -w /data majiq_image majiq'
+ENV DEBIAN_FRONTEND=noninteractive
-alias voila='docker run --rm -e MAJIQ_LICENSE_FILE=/data/majiq_license_academic_official.lic -v "$(pwd)/datamj:/data" -p 5000:5000 -w /data majiq_image voila'
-alias majiq3='docker run --rm -e MAJIQ_LICENSE_FILE=/data/majiq_license_academic_official.lic -v "$(pwd)/datamj:/data" -w /data majiq_image majiq-v3'
+# 1. 安装系统依赖（已增加 libzstd-dev）
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    build-essential \
+    git \
+    libhts-dev \
+    libbz2-dev \
+    zlib1g-dev \
+    liblzma-dev \
+    libzstd-dev \
+    && rm -rf /var/lib/apt/lists/*
- *  放入 ~/majiq_license_academic_official.lic
+ENV HTSLIB_LIBRARY_DIR=/usr/lib/x86_64-linux-gnu
-```
+ENV HTSLIB_INCLUDE_DIR=/usr/include
-gAAAAABlW6-jYooOgeYvzqoEZ9Z6jMLcFAfydEzRxJWwJ7bl9z71xmQCS343USkuLpu88lpTwTOGiGqpJ0uMZV36nto1SCRmdP_LWSugZyS7-E1wDVOzyV8kQcUHzNtPQVMVaLUQXmpYGfXGHEVo-XUPVG3v3waurw==
-```
-```bash
+# 2. 拆分指令以利用缓存 (存档点：下载源码)
-apt install build-essential
+WORKDIR /tmp
-apt install libhts-dev
+RUN git clone https://bitbucket.org/biociphers/majiq_academic.git
-```
+# 3. 存档点：安装 Voila
+WORKDIR /tmp/majiq_academic
+RUN pip install --no-cache-dir ./moccasin
+RUN pip install --no-cache-dir ./voila
+# 4. 存档点：安装 MAJIQ
+RUN pip install --no-cache-dir ./majiq
-majiq build 这是最耗时的一步。它会扫描你的 BAM 文件并识别所有的剪接事件（LSVs）。
+WORKDIR /
-majiq build /data/mm39_115.gff3 -c ./majiq.config -o ./build_output
+RUN rm -rf /tmp/majiq_academic
+RUN majiq --help && voila --version
+CMD ["/bin/bash"]
+```
+#### License
+ *  放入 ~/majiq_license_academic_official.lic
+```majiq_license_academic_official.lic
+gAAAAABlW6-jYooOgeYvzqoEZ9Z6jMLcFAfydEzRxJWwJ7bl9z71xmQCS343USkuLpu88lpTwTOGiGqpJ0uMZV36nto1SCRmdP_LWSugZyS7-E1wDVOzyV8kQcUHzNtPQVMVaLUQXmpYGfXGHEVo-XUPVG3v3waurw==
+```
--v "$(pwd):/data"，所以你在外面（宿主机）看到的文件如果是 ~/project/data/sample1.bam，在配置文件里应该直接写 sample1（如果你就在 data 目录下运行的话），或者相对于 /data 的路径。
 ### Steps v3
 ```bash
+alias majiq='docker run --rm -e MAJIQ_LICENSE_FILE=/data/majiq_license_academic_official.lic -v "$(pwd)/datamj:/data" -w /data majiq_image majiq'
 alias voila='docker run --rm -e MAJIQ_LICENSE_FILE=/data/majiq_license_academic_official.lic -v "$(pwd)/datamj:/data" -p 5000:5000 -w /data majiq_image voila'
 alias majiq3='docker run --rm -e MAJIQ_LICENSE_FILE=/data/majiq_license_academic_official.lic -v "$(pwd)/datamj:/data" -w /data majiq_image majiq-v3'
@@ 行 84: / 行 107: @@
 ```
-### Steps
+### Steps v2
+```bash
 majiq build /data/mm39_115.gff3 -c /data/majiq.config -o /data/build_output
 majiq psi-coverage \
@@ 行 109: / 行 133: @@
 voila view /data/build_output/ --host 0.0.0.0 --port 5000 --enable-type-indexing --psicov-grouping-file /data/majiq.tsv
+```

stat/bioinform/majiq.1777556392.txt.gz · 最后更改: 2026/04/30 13:39 由 inkit