本例为root安装后，多用户共享环境的方法，若user只为自己安装，解决方法是一样的，此时忽略root前缀。
1. 通过conda安装
root用户运行如下命令安装：
[root@localhost ~]# /opt/anaconda/bin/conda create -n busco -c bioconda busco
user 调用时报错：
(base) [yanqing_zhang@localhost ~]$ conda activate busco
(busco) [yanqing_zhang@localhost ~]$ run
run_busco runcon runlevel run-parts run_with_lock
run_BUSCO.py runJemboss.sh run-ncbi-converter runuser runxlrd.py
(busco) [yanqing_zhang@localhost ~]$ run_BUSCO.py
ERROR No section [busco] found in /opt/anaconda/envs/busco/bin/../config/config.ini. Please make sure both the file and this section exist, see userguide.
google查找报错原因，conda安装时，config.ini文件不在config文件夹内，
亦可参见：https://github.com/bioconda/bioconda-recipes/issues/5429
解决办法：生成config.ini文件到该目录
①. 直接下载：下载链接 https://gitlab.com/ezlab/busco/raw/master/config/config.ini.default?inline=false
[root@localhost ~]# wget https://gitlab.com/ezlab/busco/raw/master/config/config.ini.default?inline=false -O config.ini.default
②. 脚本生成：
[root@localhost ~]# generate_busco_config.py > config.ini
[root@localhost ~]# BUSCO_CONFIG_FILE=config.ini run_busco
2. 本例中选择方案①
进入文件缺失目录
[root@localhost config]# cd /opt/anaconda/envs/busco/bin/../config/
wget下载config.ini.default文件
[root@localhost config]# wget https://gitlab.com/ezlab/busco/raw/master/config/config.ini.default?inline=false -O config.ini.default
--2019-07-10 16:08:07-- https://gitlab.com/ezlab/busco/raw/master/config/config.ini.default?inline=false
Resolving gitlab.com (gitlab.com)... 35.231.145.151
Connecting to gitlab.com (gitlab.com)|35.231.145.151|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 2199 (2.1K) [text/plain]
Saving to: ‘config.ini.default’
100%[==============================================================================================================>] 2,199 --.-K/s in 0s
2019-07-10 16:08:10 (415 MB/s) - ‘config.ini.default’ saved [2199/2199]
另存一份config.ini.default为config.ini，并更改拥有者和权限
[root@localhost config]# cp config.ini.default config.ini
[root@localhost config]# chown anaconda:anaconda config.ini.default config.ini
[root@localhost config]# chmod 755 config.ini.default config.ini
[root@localhost config]# ll -htr
total 16K
drwxr-xr-x. 99 anaconda anaconda 4.0K Jul 10 13:00 species
drwxr-xr-x. 2 anaconda anaconda 225 Jul 10 13:00 cgp
drwxr-xr-x. 2 anaconda anaconda 284 Jul 10 13:00 extrinsic
drwxr-xr-x. 2 anaconda anaconda 4.0K Jul 10 13:00 model
drwxr-xr-x. 2 anaconda anaconda 65 Jul 10 13:00 profile
-rwxr-xr-x. 1 anaconda anaconda 2.2K Jul 10 16:08 config.ini.default
-rwxr-xr-x. 1 anaconda anaconda 2.2K Jul 10 16:08 config.ini
回到 user 界面使用，即可成功调用run_BUSCO.py
(busco) [yanqing_zhang@localhost ~]$ run_BUSCO.py --help
usage: python BUSCO.py -i [SEQUENCE_FILE] -l [LINEAGE] -o [OUTPUT_NAME] -m [MODE] [OTHER OPTIONS]
Welcome to BUSCO 3.0.1: the Benchmarking Universal Single-Copy Ortholog assessment tool.
For more detailed usage information, please review the README file provided with this distribution and the BUSCO user guide.
optional arguments:
-i FASTA FILE, --in FASTA FILE
Input sequence file in FASTA format. Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set.
-c N, --cpu N Specify the number (N=integer) of threads/cores to use.
-o OUTPUT, --out OUTPUT
Give your analysis run a recognisable short name. Output folders and files will be labelled with this name. WARNING: do not provide a path
-e N, --evalue N E-value cutoff for BLAST searches. Allowed formats, 0.001 or 1e-03 (Default: 1e-03)
-m MODE, --mode MODE Specify which BUSCO analysis mode to run.
There are three valid modes:
- geno or genome, for genome assemblies (DNA)
- tran or transcriptome, for transcriptome assemblies (DNA)
- prot or proteins, for annotated gene sets (protein)
-l LINEAGE, --lineage_path LINEAGE
Specify location of the BUSCO lineage data to be used.
Visit http://busco.ezlab.org for available lineages.
-f, --force Force rewriting of existing files. Must be used when output files with the provided name already exist.
-r, --restart Restart an uncompleted run. Not available for the protein mode
-sp SPECIES, --species SPECIES
Name of existing Augustus species gene finding parameters. See Augustus documentation for available options.
--augustus_parameters AUGUSTUS_PARAMETERS
Additional parameters for the fine-tuning of Augustus run. For the species, do not use this option.
Use single quotes as follow: '--param1=1 --param2=2', see Augustus documentation for available options.
-t PATH, --tmp_path PATH
Where to store temporary files (Default: ./tmp/)
--limit REGION_LIMIT How many candidate regions (contig or transcript) to consider per BUSCO (default: 3)
--long Optimization mode Augustus self-training (Default: Off) adds considerably to the run time, but can improve results for some non-model organisms
-q, --quiet Disable the info logs, displays only errors
-z, --tarzip Tarzip the output folders likely to contain thousands of files
--blast_single_core Force tblastn to run on a single core and ignore the --cpu argument for this step only. Useful if inconsistencies when using multiple threads are noticed
-v, --version Show this version and exit
-h, --help Show this help message and exit