02.服务器现有公共工具‐server ‘lilab2’ in A118 - connshaojunzhang/servers2 GitHub Wiki

lilab2 服务器 ..***.246 (contact: yhliu)

  • OS: Ubuntu 22.04.3 LTS

  • AMD EPYC 7662 64-Core Processor

  • Thread(s) per core: 2

  • Core(s) per socket: 64

  • Socket(s): 2

  • Mem: 1.0T

  • Note：用户账号内，首次使用conda，请：

  • step1 echo "export PATH=/usr/local/anaconda3/bin:$PATH" >> ~/.bashrc ,then source ~/.bashrc；
  • step2 在命令行输入 conda init (如果需要你选择是哪一种shell类型，请选择bash)；
  • step3 退出当前session或者窗口，重新登录即可正常使用已经预装的各类conda环境和工具。
  • 如何查看现有conda环境和环境内工具包？
  • Method 1: conda info --envs
  • conda activate yourenvs
  • conda list (到这里，你应该能想到，更简单的命令：conda list -n yourenvs, yourenvs就是你想查看的conda环境)
  • Method 2：直接看以下内容。

the A118 server

some dependencies

  • Java (openjdk 11.0.20.1)
  • path:/usr/bin/java
  • export JAVA_HOME=/usr/lib/jvm/java-11-openjdk-amd64
  • export JVM_HOME=$JAVA_HOME/jvm
  • export CLASSPATH=$JAVA_HOME/lib:$JVM_HOME/lib:$CLASSPATH
  • export PATH=$JAVA_HOME/bin:$JRE_HOME/bin:$PATH
  • Configuration has been written into /etc/profile. Don't change this configuration of java, because it is suitable for most of tools dependent java.
  • openmpi (Message Passing Interface (MPI) library): added by conda, but you can directly run mpirun command in your account.
  • blast (ncbi-blast-2.15.0): /usr/local/softwares/ncbi-blast-2.15.0/bin
  • ncbi_db:$HOME/data0/dbs/blast_db (full database of nt, nr, taxonomy, uniprot and swissprot).
  • Pfam_db(Pfam-A HMMs in an HMM library searchable with the hmmscan program):$HOME/data0/dbs/blast_db/04_Pfam_db
  • python/python3 (version 3.10):/usr/bin/python3 (/usr/bin/python has been configured by system alternative service. Don't change any python configuration, if you need other versions of python, please contact Administrators).
  • R/Rscript (version 4.3.2): /usr/bin/Rscript (don't change any R configuration).
  • Packages of Python or R can be installed as personal, however, it is recommended to ask the help of Administrators.
  • diamond(2.1.9): /usr/local/softwares/diamond-2.1.9
  • bowtie2(2.5.3):/usr/local/softwares/bowtie2-2.5.3
  • cmake(3.29):/usr/local/softwares/cmake-3.29.0/bin

genomic & phylogenetic tools

  • samtools: /usr/local/softwares/samtools-1.23
  • bedtools (bamToFastq or bedtools bamtofastq): installed by apt, just type the command.
  • genometools: installed comprehensively, just use the relevant command.
  • BamDeal:/usr/local/softwares/BamDeal-0.27/bin
  • Mitochondria assembler and annotation using 3rd sequencing data (Pacbio):
  • MitoHiFi & MitoFinder: installed with docker docker pull ghcr.io/marcelauliano/mitohifi:master (Don't pull any docker image again)
  • If you want to use MitoHiFi, just run as following:
  • docker run -it --mount type=bind,source=/home/username/workdirectory,target=/home/mitohifi/docker ghcr.io/marcelauliano/mitohifi:master bash
  • Then you can cd /home/mitohifi/docker and find your data.
  • You also can run a docker packaged tool in shell script like this:
  • docker run --rm -v ${docker_mountPoint}:/home/docker ${your_img} <command of your tool>
  • or specify the work directory in docker container like this: docker run --rm -v ${docker_mountPoint}:/home/docker -w ${your/work/directory/in/docker/container} ${your_img} <command of your tool>
  • if you encountered "Permission denied" relevant errors, you can run docker as this: docker run --user=root --rm -v ${docker_mountPoint}:/home/docker -w ${your/work/directory/in/docker/container} ${your_img} <command of your tool> (maybe you should contact the administrators and ask to add your account to docker group).
  • RepeatModeler & RepeatMasker (also include RECON, RepeatScout, TRF, RMBlast, CD-HIT, Ninja, LtrHarvest, and LTR_retriever) docker pull dfam/tetools:latest (About how to use a docker packaged tool, please see the above-mentioned). Note: if you have problems when pulling down images from docker hub, you can switch to Singularity, the singularity image name for docker's dfam/tetools:latest is docker://dfam/tetools:latest.

Docker repositories have been stopped in China since 2024-06-24. We build the docker images from its source codes, keeping the tags consistent with the official tags.

  • minimap2:/usr/local/softwares/minimap2-2.28.
  • Hap.py(HapPy):/usr/local/softwares/HapPy-0.1/happy (to use this tool, you should first activate the conda environment happyenv).
  • kmergenie: installed as a python package(root make and python setup.py install, all dependencies are ready), can be used directly (for more information of genome survey, see also the conda envs genomesurvey).
  • MaSuRCA:/usr/local/softwares/MaSuRCA-4.1.1/bin. Try this tool when your genome/assembly is predicted to be with high heterozygosity (e.g., >0.5). While keep in mind that some other steps/other assemblers should be required together with MaSuRCA, and long reads (e.g., 3rd sequencing data) may be also essential for successful assemble of genomes with much higher heterozygosity (e.g., >1). Further polishing steps are unnecessary when using this assembler.
  • iqtree2 (iqtree-2.3.4): /usr/local/softwares/iqtree-2.3.4/bin
  • blobtoolkit (for snail plot): source /usr/local/anaconda3/bin/activate btk.
  • braker (Braker3): source /usr/local/anaconda3/bin/activate braker3.
  • miniprot:/usr/local/softwares/miniprot-0.18-r281.
  • paml(ver. 4.10.9):/usr/local/softwares/paml-4.10.9/bin.
  • csvtk (ver. 0.36.0):/usr/local/softwares/csvtk-0.36.0.
  • ORP(Oyster River Protocol For Transcriptome Assembly): docker pull macmaneslab/orp:2.3.3 (Don't pull again, just use the image).
  • TransDecoder (Find Coding Regions Within Transcripts)
  • path: /usr/local/softwares/TransDecoder-v5.7.1 (all dependencies have been installed)
  • GeneMarkS-T:/usr/local/softwares/GeneMarkS-T
  • STAR(STAR-2.7.11b): /usr/local/softwares/STAR-2.7.11b

  • STAT pre-builded indices can be found at $HOME/data0/dbs/star2_db.

  • hisat2 ( HISAT2 2.2.1): /usr/local/softwares/hisat2-2.2.1

  • hisat2 pre-builded indices can be found at $HOME/data0/dbs/hisat2_db

  • cufflinks (& related tools): /usr/local/softwares/cufflinks-2.2.1
  • RSEM (accurate quantification of gene and isoform expression from RNA-Seq data):/usr/local/softwares/RSEM-1.3.3/bin
  • EBseq also included as a package in RSEM.
  • sra-toolkit(e.g., prefetch and fastq-dump tools):/usr/local/softwares/sratoolkit.3.1.0/bin
  • gffread(0.12.7):/usr/local/softwares/gffread-0.12.7
  • SUPPA(2.3):/usr/local/softwares/SUPPA-2.3
  • cafe5: source /usr/local/anaconda3/bin/activate cafe5.
  • eggnog-mapper: source /usr/local/anaconda3/bin/activate eggnog-mapper.

conda envs

  • mamba create -n annotations -c conda-forge -c bioconda metaeuk trinotate eggnog-mapper
  • mamba create -n assembles -c conda-forge -c anaconda -c bioconda **rcorrector trinity abyss **
  • mamba create -n assembles_3rd -c conda-forge -c bioconda flye hifiasm gfatools nextpolish hicup 3d-dna
  • mamba create -n buscoenv -c bioconda busco quast
  • mamba create -n quastenv -c conda-forge -c bioconda quast transrate (deleted!!)
  • mamba create -n bwa -c bioconda bwa
  • mamba create -n crispresso2 -c bioconda crispresso2 (for crispr editing efficiency calculating)
  • mamba create -n genomesurvey -c conda-forge -c bioconda jellyfish=2.2.10 kmc genomescope2 smudgeplot
  • mamba create -n kmerenv -c bioconda -c conda-forge kat=2.4.2
  • mamba create -n kallisto -c bioconda kallisto
  • Note:the metagenomic tools are installed by other ways, the following installation methods are official (but not work). Users can ask Administrators if want to use those tools
  • mamba create -n metagenomics -c conda-forge -c bioconda -c biobakery kneaddata
  • mamba create -n metaphlan -c bioconda -c biobakery -c conda-forge metaphlan humann
  • mamba create -n mito_phyloanalysis -c conda-forge -c bioconda openmpi phylobayes-mpi mrbayes（this tool has been installed via apt, but need openmpi in this envs）
  • mamba create -n msaenv -c bioconda -c jlsteenwyk mafft bmge phykit clipkit muscle mummer trimal(readal)
  • mamba create -n nextpolish -c conda-forge -c bioconda nextpolish
  • mamba create -n orthofinder -c conda-forge -c bioconda orthofinder.
  • mamba create -n partitionfinder python=2.7 (in this envs, pandas, scipy, scikit-learn, pytables, pyparsing, numpy have been install from conda), and partitionfinder executable *.py files are in /usr/local/softwares/partitionfinder-2.1.1.
  • mamba create -n phylogen -c conda-forge -c bioconda raxml
  • mamba create -n qiime2 -c conda-forge -c bioconda -c qiime2 qiime2
  • mamba create -n redundans -c conda-forge -c bioconda redundans purge_haplotigs
  • mamba create -n rnaseq -c conda-forge -c bioconda picard subread(including featureCounts) htseq rmats
  • mamba create -n seqqc -c conda-forge -c bioconda fastqc fastp trimmomatic bbmap kraken2

  • Kraken2 databases can be found at $HOME/data0/dbs/Kraken2_db

  • mamba create -n tophat2 -c bioconda tophat