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Docker镜像信息

GCModeller以R#语言的软件包的形式提供给客户使用,相应的R#语言的分析环境以Docker镜像的形式进行打包盒发布,Docker的基础镜像为ubuntu 22.04。

dotnet环境:.NET 6
R#语言安装位置:/usr/local/bin
R#程序包安装列表:

索引 包名称 Github
1 GCModeller https://github.com/SMRUCC/GCModeller
2 REnv https://github.com/rsharp-lang/R-sharp
3 ggplot https://github.com/rsharp-lang/ggplot
4 WorkflowRender https://github.com/rsharp-lang/WorkflowRender
5 CellRender https://github.com/SMRUCC/cell-render
6 Erica https://github.com/SMRUCC/Erica

开发环境:Windows Server 2022/WSL2/Docker Desktop

第三方软件安装

在镜像中有第三方软件依赖:

1. NCBI blast+

用于细胞网络结构的同源建模

# /opt/ncbi-blast-2.14.0+

2. meme suite

用于全基因组转录表达调控网络的建立,安装命令记录:

# export PATH=/opt/meme/bin:/opt/meme/libexec/meme-5.5.2:$PATH
./configure --prefix=/opt/meme --enable-build-libxml2 --enable-build-libxslt
# run test
/opt/meme/bin/meme ./upstream_locis.fasta -dna -revcomp -pal -mod zoops -minw 6 -maxw 30 -nmotifs 1000 -evt 1 -minsites 6 -p 16 -maxsize 0 -oc ./meme

3. open mpi

安装Open MPI应用于第三方组件的并行计算环境,在这个镜像之中是直接通过Ubuntu自带的软件源进行安装:

apt-get install openmpi-bin
# for fix the problem:
# fatal error: mpi.h: No such file or directory #include <mpi.h>
apt-get install libopenmpi-dev
谢桂纲
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