一、自行下载安装：

进入kobas官网点击下载，对应的安装包和数据库。

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二、conda 安装(推荐)

conda install -c bioconda  kobas==3.0.3

conda 安装 kobas时报错：python需要用2.7版本

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - kobas==3.0.3 -> python[version='2.7.*|<3|>=2.7,<2.8.0a0']

Your python: python=3.8

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.28=0
  - feature:|@/linux-64::__glibc==2.28=0

Your installed version is: 2.28

重新构建conda环境，采用python 2.7版本即可

conda create -n kobas python=2.7
#使用activate激活环境直接安装
conda activate kobas
conda install -c bioconda  kobas==3.0.3

三、配置kobas

如果没有配置直接运行，会出现以下报错。

(kobas) [user@localhost /data/pipeline/get_Enrichment]$kobas-annotate
Error: configuration file does not exist. Please create the file or provide the options through command line parameters.
Usage: kobas-annotate [-l] -i infile [-t intype] -s species [-o outfile] [-e evalue] [-r rank] [-n nCPUs] [-c coverage] [-z ortholog] [-k kobas_home] [-v blast_home] [-y blastdb] [-q kobasdb] [-p blastp] [-x blastx]

kobas-annotate: error: Option -i must be assigned.

1、下载数据库

下载：sqlite3.tar.gz和seq_pep.tar.gz
链接：ftp://ftp.cbi.pku.edu.cn/pub/KOBAS_3.0_DOWNLOAD/

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2、配置~/.kobasrc文件

将上面下载的数据量路径和blast的路径写进去

[KOBAS]
kobasdb = /data/database/kobas/sqlite3

[BLAST]
blastp = /data/pipeline/scRNA/miniconda/envs/kobas/bin/blastp
blastx = /data/pipeline/scRNA/miniconda/envs/kobas/bin/blastx
blastdb = /data/database/kobas/seq_pep/

四、测试运行

(kobas) [user@localhost /data/pipeline/get_Enrichment]$kobas-run
Usage: run_kobas.py [-l] -i infile [-t intype] -s species [-E evalue] [-R rank] [-N nCPUs] [-C coverage] [-Z ortholog] [-b bgfile] [-d database] [-m method] [-n fdr] [-o outfile] [-c cutoff] [-k kobas_home] [-v blast_home] [-y blastdb] [-q kobasdb] [-p blastp] [-x blastx]

Options:
  -h, --help            show this help message and exit
  -l, --list            list available species, or list available databases
                        for specific species
  -i INFILE, --infile=INFILE
                        input data file
  -t INTYPE, --intype=INTYPE
                        input type (fasta:pro, fasta:nuc, blastout:xml,
                        blastout:tab, id:refseqpro, id:uniprot, id:ensembl,
                        id:ncbigene), default fasta:pro
  -s SPECIES, --species=SPECIES
                        species abbreviation (for example: ko for KEGG
                        Orthology, hsa for Homo sapiens, mmu for Mus musculus,
                        dme for Drosophila melanogaster, ath for Arabidopsis
                        thaliana, sce for Saccharomyces cerevisiae and eco for
                        Escherichia coli K-12 MG1655)
  -E EVALUE, --evalue=EVALUE
                        expect threshold for BLAST, default 1e-5
  -R RANK, --rank=RANK  rank cutoff for valid hits from BLAST result, default
                        5
  -N NCPUS, --nCPUs=NCPUS
                        number of CPUs to be used by BLAST, default 1
  -C COVERAGE, --coverage=COVERAGE
                        subject coverage cutoff for BLAST, default 0
  -Z ORTHOLOG, --ortholog=ORTHOLOG
                        whether only use ortholog for cross-species annotation
                        or not, default NO (If only use ortholog, give species
                        abbr)
  -b BGFILE, --bgfile=BGFILE
                        background file, the output of annotate (3 or 4-letter
                        file name is not allowed), or species abbreviation
                        (for example: hsa for Homo sapiens, mmu for Mus
                        musculus, dme for Drosophila melanogaster, ath for
                        Arabidopsis thaliana, sce for Saccharomyces cerevisiae
                        and eco for Escherichia coli K-12 MG1655), default
                        same species as annotate
  -d DB, --db=DB        databases for selection, 1-letter abbreviation
                        separated by "/": K for KEGG PATHWAY, R for Reactome,
                        B for BioCyc, p for PANTHER, o for OMIM, k for KEGG
                        DISEASE, N for NHGRI GWAS Catalog and G for Gene
                        Ontology, S for Gene Ontology Slim, default
                        K/R/B/p/o/k/N/G/S
  -m METHOD, --method=METHOD
                        choose statistical test method: b for binomial test, c
                        for chi-square test, h for hypergeometric test /
                        Fisher's exact test, and x for frequency list, default
                        hypergeometric test / Fisher's exact test
  -n FDR, --fdr=FDR     choose false discovery rate (FDR) correction method:
                        BH for Benjamini and Hochberg, BY for Benjamini and
                        Yekutieli, QVALUE, and None, default BH
  -o OUTFILE, --outfile=OUTFILE
                        output file for identification result, default stdout
  -c CUTOFF, --cutoff=CUTOFF
                        the gene number in a term is not less than the cutoff,
                        default 5
  -k KOBAS_HOME, --kobashome=KOBAS_HOME
                        Optional parameter. To set path to kobas_home, which
                        is parent directory of sqlite3/ and seq_pep/ , default
                        value is read from ~/.kobasrcwhere you set before
                        running kobas. If you set this parameter, it means you
                        set "kobasdb" and "blastdb" in this following
                        directory. e.g. "-k /home/user/kobas/", means that you
                        set kobasdb = /home/user/kobas/sqlite3/ and blastdb =
                        /home/user/kobas/seq_pep/
  -v BLAST_HOME, --blasthome=BLAST_HOME
                        Optional parameter. To set parent directory of blastx
                        and blastp. If you set this parameter, it means you
                        set "blastx" and "blastp" in this following directory.
                        Default value is read from ~/.kobasrc where you set
                        before running kobas
  -y BLASTDB, --blastdb=BLASTDB
                        Optional parameter. To set path to sep_pep/, default
                        value is read from ~/.kobasrc where you set before
                        running kobas
  -q KOBASDB, --kobasdb=KOBASDB
                        Optional parameter. To set path to sqlite3/, default
                        value is read from ~/.kobasrc where you set before
                        running kobas, e.g. "-q /kobas_home/sqlite3/"
  -p BLASTP, --blastp=BLASTP
                        Optional parameter. To set path to blastp program,
                        default value is read from ~/.kobasrc where you set
                        before running kobas
  -x BLASTX, --blastx=BLASTX
                        Optional parameter. To set path to  blasx program,
                        default value is read from ~/.kobasrc where you set
                        before running kobas