简介
平台介绍¶
校级高性能计算平台，由 arm 和 x86 两类芯片架构的CPU节点组成，作业调度系统采用的多瑙（Donau Scheduler）。
公共软件调用¶
module¶
MODULEPATH 配置，在个人账号 ~/.bashrc 文件中，写入下面两行代码，执行 source ~/.bashrc 生效。
export MODULEPATH="/share/software/modulefiles/:$MODULEPATH"
export appdir="/share/software/app/"
$ module av
---------------------------------------------------------- /share/software/modulefiles ----------------------------------------------------------
arm/automake/1.13 arm/cmake/3.30.5 arm/hisat2/2.1.0 arm/minimap2/2.28 arm/star/2.7.11b x86/hifiasm/0.19.9
arm/automake/1.14 arm/curl/8.10.1 arm/htslib/1.21 arm/ncbi-vdb/3.1.1 arm/tassel/5 x86/hisat2/2.1.0
arm/bcftools/1.21 arm/fastp/0.23.4 arm/isal/2.30.0 arm/nextdenovo/2.5.2 arm/vg/1.60.0 x86/htslib/1.21
arm/bedtools/2.31.1 arm/fastqc/0.12.1 arm/java/17.0.11 arm/openblas/0.3.28 arm/zlib/1.3 x86/java/21.0.2
arm/blast/2.16.0 arm/fasttree/2.1.11 arm/jellyfish/2.3.1 arm/openssl/3.3.2 arm/zstd/1.5.6 x86/megahit/1.2.9
arm/boost/1.86.0 arm/gatk/4.6.0.0 arm/libdeflate/1.8 arm/pangenie/3.1.0 x86/bwa/0.7.18 x86/minimap2/2.28
arm/bowtie2/2.5.4 arm/gcc/12.2.0 arm/libpsl/0.21.5 arm/r/4.4.1 x86/bzip2/1.0.6 x86/samtools/1.21
arm/bwa/0.7.18 arm/gsl/2.8 arm/maven/3.9.9 arm/samtools/1.21 x86/cellranger/7.0.0 x86/star/2.7.11b
arm/clapack/3.2.1 arm/hifiasm/0.19.9 arm/megahit/1.2.9 arm/sratools/3.1.1 x86/gatk/4.6.0.0 x86/vg/1.60.0
-------------------------------------------------------- /usr/share/Modules/modulefiles ---------------------------------------------------------
dot module-git module-info modules null use.own
Key:
modulepath
module 更详细的用法见 module 使用。
$ module load arm/bwa/0.7.18
$ bwa
Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.18-r1243-dirty
Contact: Heng Li <hli@ds.dfci.harvard.edu>
Usage: bwa <command> [options]
Command: index index sequences in the FASTA format
mem BWA-MEM algorithm
fastmap identify super-maximal exact matches
pemerge merge overlapping paired ends (EXPERIMENTAL)
aln gapped/ungapped alignment
samse generate alignment (single ended)
sampe generate alignment (paired ended)
bwasw BWA-SW for long queries (DEPRECATED)
shm manage indices in shared memory
fa2pac convert FASTA to PAC format
pac2bwt generate BWT from PAC
pac2bwtgen alternative algorithm for generating BWT
bwtupdate update .bwt to the new format
bwt2sa generate SA from BWT and Occ
Note: To use BWA, you need to first index the genome with `bwa index'.
There are three alignment algorithms in BWA: `mem', `bwasw', and
`aln/samse/sampe'. If you are not sure which to use, try `bwa mem'
first. Please `man ./bwa.1' for the manual.
Singularity 镜像¶
集群公共目录 /share/software/image/arm/ 目录下放了一些在 arm 上打包好的 Singularity 镜像，可以直接调用。注意，arm 镜像不可在 x86 节点上使用。
Singularity 更详细的用法见 Singularity使用。
$ module load arm/singularity/4.1.5
$ singularity exec /share/software/image/arm/bwa-0.7.18.sif bwa
Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.18-r1243-dirty
Contact: Heng Li <hli@ds.dfci.harvard.edu>
Usage: bwa <command> [options]
Command: index index sequences in the FASTA format
mem BWA-MEM algorithm
fastmap identify super-maximal exact matches
pemerge merge overlapping paired ends (EXPERIMENTAL)
aln gapped/ungapped alignment
samse generate alignment (single ended)
sampe generate alignment (paired ended)
bwasw BWA-SW for long queries (DEPRECATED)
shm manage indices in shared memory
fa2pac convert FASTA to PAC format
pac2bwt generate BWT from PAC
pac2bwtgen alternative algorithm for generating BWT
bwtupdate update .bwt to the new format
bwt2sa generate SA from BWT and Occ
Note: To use BWA, you need to first index the genome with `bwa index'.
There are three alignment algorithms in BWA: `mem', `bwasw', and
`aln/samse/sampe'. If you are not sure which to use, try `bwa mem'
first. Please `man ./bwa.1' for the manual.
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