diff --git a/HPC/busco/5.8.3/24.03-lts-sp1/Dockerfile b/HPC/busco/5.8.3/24.03-lts-sp1/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..b6257486d86c53395ea6aaa75d3f89829ca61a84 --- /dev/null +++ b/HPC/busco/5.8.3/24.03-lts-sp1/Dockerfile @@ -0,0 +1,12 @@ +ARG BASE=openeuler/openeuler:24.03-lts-sp1 +FROM ${BASE} + +ARG VERSION=5.8.3 + +RUN yum install -y git python3-pip && \ + yum clean all && \ + pip install pandas bio + +RUN git clone -b ${VERSION} https://gitlab.com/ezlab/busco.git && \ + cd busco/ && \ + python3 -m pip install . \ No newline at end of file diff --git a/HPC/busco/README.md b/HPC/busco/README.md new file mode 100644 index 0000000000000000000000000000000000000000..5eb50cde1a48118a33e0e6fda8592e08eb9f49d1 --- /dev/null +++ b/HPC/busco/README.md @@ -0,0 +1,36 @@ +# Quick reference + +- The official busco container image. + +- Maintained by: [openEuler CloudNative SIG](https://gitee.com/openeuler/cloudnative). + +- Where to get help: [openEuler CloudNative SIG](https://gitee.com/openeuler/cloudnative), [openEuler](https://gitee.com/openeuler/community). +# busco | openEuler +Current busco docker images are built on the [openEuler](https://repo.openeuler.org/). This repository is free to use and exempted from per-user rate limits. + +BUSCO (Benchmarking Universal Single-Copy Orthologs) provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB. + +Learn more on [busco website](https://busco.ezlab.org/). + + +# Supported tags and respective Dockerfile links +The tag of each busco container image is consist of the version of busco and the version of basic image. The details are as follows + +| Tags | Currently | Architectures| +|------|-----------|---------------| +|[5.8.3-oe2403sp1](https://gitee.com/openeuler/openeuler-docker-images/blob/master/HPC/busco/5.8.3/24.03-lts-sp1/Dockerfile)| BUSCO 5.8.3 on openEuler 24.03-LTS-SP1 | amd64, arm64 | + + +# Usage +- Pull the `openeuler/busco` image from `hub.docker.com` + ``` + docker pull openeuler/busco:{Tag} + ``` +- Start a `busco` instance + ``` + docker run -it --name my-busco openeuler/busco:{Tag} + ``` + Now, you can use BUSCO according to [User Guide](https://busco.ezlab.org/) + +# Question and answering +If you have any questions or want to use some special features, please submit an issue or a pull request on [openeuler-docker-images](https://gitee.com/openeuler/openeuler-docker-images). \ No newline at end of file diff --git a/HPC/busco/doc/image-info.yml b/HPC/busco/doc/image-info.yml new file mode 100644 index 0000000000000000000000000000000000000000..d8eaef557c8ef1f760b32a2cc1623646e9629b06 --- /dev/null +++ b/HPC/busco/doc/image-info.yml @@ -0,0 +1,39 @@ +name: busco +category: hpc +description: BUSCO是Benchmarking Universal Single-Copy Orthologs（通用单拷贝同源基因基准）的缩写，基于基因进化（有参比对）评估基因组组装和注释完整性的开源python软件。 +environment: | + 本应用在Docker环境中运行，安装Docker执行如下命令 + ``` + yum install -y docker + ``` +tags: | + busco镜像的Tag由其版本信息和基础镜像版本信息组成，详细内容如下 + + | Tags | Currently | Architectures| + |------|-----------|---------------| + |[5.8.3-oe2403sp1](https://gitee.com/openeuler/openeuler-docker-images/blob/master/HPC/busco/5.8.3/24.03-lts-sp1/Dockerfile)| BUSCO 5.8.3 on openEuler 24.03-LTS-SP1 | amd64, arm64 | +download: | + 拉取镜像到本地 + ``` + docker pull openeuler/busco:{Tag} + ``` +usage: | + - 拉取镜像 + + ``` + docker pull openeuler/busco:{Tag} + ``` + 用户可根据自身需求选择对应版本的{Tag}、容器启动的选项。 + + - 运行容器 + + ``` + docker run -it --name my-busco openeuler/busco:{Tag} + ``` + 容器运行后，按照[BUSCO官方说明](https://busco.ezlab.org/)使用。 + +license: MIT License +similar_packages: + - N/A +dependency: + - pandas diff --git a/HPC/busco/doc/picture/logo.png b/HPC/busco/doc/picture/logo.png new file mode 100644 index 0000000000000000000000000000000000000000..824e7627a84ee7d9cee9aadff0fc6581acb076f3 Binary files /dev/null and b/HPC/busco/doc/picture/logo.png differ diff --git a/HPC/busco/meta.yml b/HPC/busco/meta.yml new file mode 100644 index 0000000000000000000000000000000000000000..a1a1a17b4d1a0df25fc0f1c83e199de58b2eea36 --- /dev/null +++ b/HPC/busco/meta.yml @@ -0,0 +1,2 @@ +5.8.3-oe2403sp1: + path: 5.8.3/24.03-lts-sp1/Dockerfile \ No newline at end of file diff --git a/HPC/eman/2.99.69/24.03-lts-sp1/Dockerfile b/HPC/eman/2.99.69/24.03-lts-sp1/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..f4362d97261d7329b1280499b36a69a6d95a0f97 --- /dev/null +++ b/HPC/eman/2.99.69/24.03-lts-sp1/Dockerfile @@ -0,0 +1,45 @@ +ARG BASE=openeuler/openeuler:24.03-lts-sp1 +FROM ${BASE} + +ARG VERSION=2.99.69 +ARG TARGETARCH +ARG BUILDARCH + +RUN yum install -y \ + git python3-pip wget \ + cmake make gcc g++ libstdc++ libgcc zlib freetype \ + mesa-libGL mesa-libGL-devel mesa-libGLU mesa-libGLU-devel \ + libSM xcb-util-renderutil xcb-util-keysyms xcb-util-image xcb-util-wm + +RUN if [ "$TARGETARCH" = "amd64" ]; then \ + BUILDARCH="x86_64"; \ + elif [ "$TARGETARCH" = "arm64" ]; then \ + BUILDARCH="aarch64"; \ + fi && \ + wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-$BUILDARCH.sh -O miniconda.sh && \ + bash miniconda.sh -b -p /usr/local/miniconda && \ + /usr/local/miniconda/bin/conda init bash + +WORKDIR /opt/ + +RUN git clone -b v${VERSION} https://github.com/cryoem/eman2.git && \ + cd eman2/ && \ + if [ "$TARGETARCH" = "arm64" ]; then \ + sed -i "s/-m64/-mabi=lp64/g" CMakeLists.txt; \ + fi +RUN source /root/.bashrc && \ + conda create -n eman2 -y python=3.7.11 && \ + conda activate eman2 && \ + pip install matplotlib PyOpenGL PyOpenGL_accelerate future && \ + conda install -y -c conda-forge \ + numpy boost ftgl nose gsl fftw hdf5 libtiff bsddb3 \ + qt libxcb=1.13 pyqt=5.12.3 pyqt-impl=5.12.3 pyqt5-sip=4.19.18 pyqtchart=5.12 pyqtwebengine=5.12.1 && \ + mkdir -p /opt/eman2/build && cd /opt/eman2/build && \ + cmake .. -DENABLE_OPTIMIZE_MACHINE=ON && \ + make && make install + +ENV LD_LIBRARY_PATH=/usr/local/miniconda/pkgs/py-boost-1.73.0-py37h839d321_12/lib:$LD_LIBRARY_PATH +ENV QT_QPA_PLATFORM_PLUGIN_PATH=/usr/local/miniconda/envs/eman2/plugins/platforms +ENV QT_QPA_PLATFORM=offscreen + +WORKDIR /usr/local/miniconda/envs/eman2/bin/ diff --git a/HPC/eman/README.md b/HPC/eman/README.md new file mode 100644 index 0000000000000000000000000000000000000000..dd7589550316a71f31df32cbeddd5a62d0a44d45 --- /dev/null +++ b/HPC/eman/README.md @@ -0,0 +1,56 @@ +# Quick reference + +- The official eman container image. +- Maintained by: [openEuler CloudNative SIG](https://gitee.com/openeuler/cloudnative). +- Where to get help: [openEuler CloudNative SIG](https://gitee.com/openeuler/cloudnative), [openEuler](https://gitee.com/openeuler/community). + +# eman | openEuler +Current eman docker images are built on the [openEuler](https://repo.openeuler.org/). This repository is free to use and exempted from per-user rate limits. + +EMAN2 is a broadly based scientific image processing suite (largely greyscale) with a primary focus on processing data from transmission electron microscopes. EMAN's original purpose was performing single particle reconstructions (3-D volumetric models from 2-D cryo-EM images) at the highest possible resolution, but the suite now also offers support for single particle cryo-ET, and tools useful in many other subdisciplines such as helical reconstruction, 2-D crystallography and whole-cell tomography. EMAN2 is capable of processing large data sets (>100,000 particle) very efficiently. + +Learn more on [EMAN2 website](http://eman2.org). + +# Supported tags and respective Dockerfile links +The tag of each eman container image is consist of the version of eman and the version of basic image. The details are as follows + +| Tags | Currently | Architectures| +|------|-----------|---------------| +|[2.99.69-oe2403sp1](https://gitee.com/openeuler/openeuler-docker-images/blob/master/HPC/eman/2.99.69/24.03-lts-sp1/Dockerfile)| EMAN2 2.99.69 on openEuler 24.03-LTS-SP1 | amd64, arm64 | + +# Usage +- Pull the `openeuler/eman` image from `hub.docker.com` + ``` + docker pull openeuler/eman:{Tag} + ``` +- Start a `eman2` instance + ``` + docker run -it --name my-eman openeuler/eman:{Tag} + ``` + To use EMAN2, you should activate `eman2` environment first + ``` + conda activate eman2 + ``` + +- Run `e2speedtest.py` for testing + ``` + /usr/local/miniconda/envs/eman2/bin/e2speedtest.py + ``` + And the result will like + ``` + This could take a few minutes. Please be patient. + Initializing + .................... + .................... + .................... + .................... + .................... + .................... + .................... + .................... + + Your machines speed factor = 2.6758 +- 0.0200 (0.0086 +- 0.00006 sec) + ``` + +# Question and answering +If you have any questions or want to use some special features, please submit an issue or a pull request on [openeuler-docker-images](https://gitee.com/openeuler/openeuler-docker-images). \ No newline at end of file diff --git a/HPC/eman/doc/image-info.yml b/HPC/eman/doc/image-info.yml new file mode 100644 index 0000000000000000000000000000000000000000..c98ec97f00ef23639861bb2caf8b6f33eda87f91 --- /dev/null +++ b/HPC/eman/doc/image-info.yml @@ -0,0 +1,66 @@ +name: eman +category: hpc +description: EMAN2是一个基础广泛的灰度科学图像处理套件，主要专注于处理来自透射电子显微镜的数据。EMAN2能够非常有效地处理大型数据集（>100,000个粒子）。 +environment: | + 本应用在Docker环境中运行，安装Docker执行如下命令 + ``` + yum install -y docker + ``` +tags: | + lumpy-sv镜像的Tag由其版本信息和基础镜像版本信息组成，详细内容如下 + + | Tags | Currently | Architectures| + |------|-----------|---------------| + |[2.99.69-oe2403sp1](https://gitee.com/openeuler/openeuler-docker-images/blob/master/HPC/eman/2.99.69/24.03-lts-sp1/Dockerfile)| EMAN2 2.99.69 on openEuler 24.03-LTS-SP1 | amd64, arm64 | + +download: | + 拉取镜像到本地 + ``` + docker pull openeuler/eman:{Tag} + ``` +usage: | + - 拉取镜像 + + ``` + docker pull openeuler/eman:{Tag} + ``` + 用户可根据自身需求选择对应版本的{Tag}、容器启动的选项。 + + - 运行容器 + + ``` + docker run -it --name my-eman openeuler/eman:{Tag} + ``` + + 使用EMAN2之前, 需要先激活`eman2`环境 + ``` + conda activate eman2 + ``` + + - 测试验证 + 运行`e2speedtest.py`脚本： + ``` + /usr/local/miniconda/envs/eman2/bin/e2speedtest.py + ``` + 正常返回以下内容： + ``` + This could take a few minutes. Please be patient. + Initializing + .................... + .................... + .................... + .................... + .................... + .................... + .................... + .................... + + Your machines speed factor = 2.6758 +- 0.0200 (0.0086 +- 0.00006 sec) + ``` + +license: GPL2、BSD 3-Clause +similar_packages: + - N/A +dependency: + - conda + - python diff --git a/HPC/eman/doc/picture/logo.png b/HPC/eman/doc/picture/logo.png new file mode 100644 index 0000000000000000000000000000000000000000..f0cc09771f132d27666c46319f920680326fabac Binary files /dev/null and b/HPC/eman/doc/picture/logo.png differ diff --git a/HPC/eman/meta.yml b/HPC/eman/meta.yml new file mode 100644 index 0000000000000000000000000000000000000000..81ed465e2bb68a9b3a6f9b13cf2e7cd2b726fedb --- /dev/null +++ b/HPC/eman/meta.yml @@ -0,0 +1,2 @@ +2.99.69-oe2403sp1: + path: 2.99.69/24.03-lts-sp1/Dockerfile \ No newline at end of file diff --git a/HPC/image-list.yml b/HPC/image-list.yml index 2b6995d59adf86e3936e82d607fa5c6e8523a5ac..d2904bd1904f4a5a42950db300dc8f7be9c17c49 100644 --- a/HPC/image-list.yml +++ b/HPC/image-list.yml @@ -13,3 +13,5 @@ images: nemo: nemo lammps: lammps lumpy: lumpy + busco: busco + eman: eman \ No newline at end of file