From c355fbeccdbc5e973bc2f22f2a7b534c743c3a7b Mon Sep 17 00:00:00 2001 From: GuangJie1 Date: Wed, 15 May 2024 16:51:37 +0800 Subject: [PATCH 1/2] bwa: submit docker image --- bwa/0.7.18/22.03-lts-sp3/Dockerfile | 19 +++++++++++ bwa/README.md | 31 ++++++++++++++++++ bwa/doc/image-info.yaml | 49 ++++++++++++++++++++++++++++ bwa/doc/picture/logo.png | Bin 0 -> 1553 bytes bwa/meta.yaml | 2 ++ 5 files changed, 101 insertions(+) create mode 100644 bwa/0.7.18/22.03-lts-sp3/Dockerfile create mode 100644 bwa/README.md create mode 100644 bwa/doc/image-info.yaml create mode 100644 bwa/doc/picture/logo.png create mode 100644 bwa/meta.yaml diff --git a/bwa/0.7.18/22.03-lts-sp3/Dockerfile b/bwa/0.7.18/22.03-lts-sp3/Dockerfile new file mode 100644 index 00000000..74f0c10c --- /dev/null +++ b/bwa/0.7.18/22.03-lts-sp3/Dockerfile @@ -0,0 +1,19 @@ +ARG BASE=openeuler/openeuler:22.03-lts-sp3 +FROM ${BASE} + +ARG VERSION=v0.7.18 +ARG TARGETARCH + +RUN yum -y install make gcc zlib-devel && \ + mkdir -p /tmp/bwa && cd /tmp/bwa && \ + curl -fSL -o bwa.tar.gz https://github.com/lh3/bwa/archive/${VERSION}.tar.gz && \ + tar -xvf bwa.tar.gz -C /tmp/bwa --strip-components=1 && \ + rm -f bwa.tar.gz && \ + make clean && make -j "$(nproc)" && \ + mkdir -p /usr/local/bwa/bin && mv /tmp/bwa/bwa /usr/local/bwa/bin/ && \ + rm -rf /tmp/bwa && \ + yum remove -y make gcc zlib-devel && yum clean all + +ENV PATH=/usr/local/bwa/bin:$PATH + +CMD ["bwa"] \ No newline at end of file diff --git a/bwa/README.md b/bwa/README.md new file mode 100644 index 00000000..7d509b7b --- /dev/null +++ b/bwa/README.md @@ -0,0 +1,31 @@ +# BWA + +# Quick reference + +- The official BWA docker 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) + +# Build reference + +1. Build images and push: +```shell +docker buildx build -t "openeuler/bwa:$VERSION" --platform linux/amd64,linux/arm64 . --push +``` + +We are using `buildx` in here to generate multi-arch images, see more in [Docker Buildx](https://docs.docker.com/buildx/working-with-buildx/) + +2. Run: +```shell +docker run -ti openeuler/bwa:$VERSION +``` + +# Supported tags and respective Dockerfile links + +- 0.7.18.oe2203sp3: bwa v0.7.18, openEuler 22.03-lts-sp3 + +## Operating System +Linux/Unix, ARM64 or x86-64 architecture. + diff --git a/bwa/doc/image-info.yaml b/bwa/doc/image-info.yaml new file mode 100644 index 00000000..1bcb5615 --- /dev/null +++ b/bwa/doc/image-info.yaml @@ -0,0 +1,49 @@ +name: BWA +category: others +description: BWA(Burrow-Wheeler Aligner)是用于将低分叉序列比对到大的参考基因组比如人基因组的软件包。 +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: | + BWA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 + + | Tag | Currently | Architectures | + |----------|-------------|------------------| + |[0.7.18-oe2203sp3](https://gitee.com/openeuler/openeuler-docker-images/blob/master/bwa/0.7.18/22.03-lts-sp3/Dockerfile)| BWA 0.7.18 on openEuler 22.03-LTS-SP3 | amd64, arm64 | + +download: | + 拉取镜像到本地 + ``` + docker pull openeuler/bwa:{Tag} + ``` + +usage: | + - 启动容器 + ``` + docker run -d --name my-bwa openeuler/bwa:{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。 + + - 容器测试 + + 查看运行日志 + ``` + docker logs -f my-bwa + ``` + + 使用shell交互 + ``` + docker exec -it my-bwa /bin/bash + ``` + +license: GPL-3.0 license +similar_packages: + - BLAST（Basic Local Alignment Search Tool）: 用于比对和识别生物序列的工具，广泛用于序列相似性搜索和注释。 + - Bowtie/Bowtie2: 用于高效地比对高通量测序数据的工具，特别适用于短读长的测序数据。 + - BioXFinder: 是目前国内第一个也是国内唯一一个生物信息数据库，由享融智云公司精心研发，主要针对生物科研工作者的综合性生物数据检索及分析平台。 +dependency: + - gcc + - make + - zlib-devel \ No newline at end of file diff --git a/bwa/doc/picture/logo.png b/bwa/doc/picture/logo.png new file mode 100644 index 0000000000000000000000000000000000000000..258a53e898b4eff5053bbb0045d0b423dfe5e86c GIT binary patch literal 1553 zcmeAS@N?(olHy`uVBq!ia0y~yU|a&i985rwk9x*jr^dcJY}yboUQI^^TZ9GY%0awf5>bjVIn808GbFt~F}qS$Yj z{k&p6rgcwkzHu(k5kB`Lp;#|-R{tM`oyz-u_Oj9~jnOMDqu2vX*gu@lCCA$`-aC4l zPMHbC0rcVkJ-Y5KC Date: Wed, 15 May 2024 17:07:04 +0800 Subject: [PATCH 2/2] bwa: modify category type --- bwa/doc/image-info.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bwa/doc/image-info.yaml b/bwa/doc/image-info.yaml index 1bcb5615..218ff40a 100644 --- a/bwa/doc/image-info.yaml +++ b/bwa/doc/image-info.yaml @@ -1,5 +1,5 @@ name: BWA -category: others +category: HPCs description: BWA(Burrow-Wheeler Aligner)是用于将低分叉序列比对到大的参考基因组比如人基因组的软件包。 environment: | 本应用在Docker环境中运行，安装Docker执行如下命令 -- Gitee