busco-software
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busco-software [2015/09/13 08:19] – [Installation] aorth | busco-software [2021/12/28 11:33] – aorth | ||
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====== BUSCO ====== | ====== BUSCO ====== | ||
- | |||
BUSCO (Benchmarking Universal Single-Copy Orthologs) assesses genome assembly and annotation completeness with single-copy ortholog. | BUSCO (Benchmarking Universal Single-Copy Orthologs) assesses genome assembly and annotation completeness with single-copy ortholog. | ||
===== Information ===== | ===== Information ===== | ||
- | * Latest Version: | + | * Latest Version: |
* Added: August, 2015 | * Added: August, 2015 | ||
- | * Link: http:// | + | |
+ | | ||
===== Usage ===== | ===== Usage ===== | ||
Line 13: | Line 13: | ||
See versions of BUSCO which are available: | See versions of BUSCO which are available: | ||
< | < | ||
+ | |||
+ | Load one version into your environment and run it: | ||
+ | < | ||
+ | |||
+ | After loading the module, consult the built-in help: | ||
+ | |||
+ | < | ||
+ | |||
+ | See the BUSCO documentation for more information about how to use it: https:// | ||
+ | |||
+ | Note: BUSCO utilizes Augustus and requires you to make a copy of the Augustus configuration for each of your runs as well as set up an environment variable pointing to it, ie: | ||
+ | |||
+ | < | ||
+ | $ export AUGUSTUS_CONFIG_PATH=/ | ||
===== Installation ====== | ===== Installation ====== | ||
Notes from the sysadmin during installation: | Notes from the sysadmin during installation: | ||
- | < | + | < |
- | $ tar -xvf BUSCO_v1.1b1.tar.gz | + | $ git clone https://gitlab.com/ezlab/busco.git |
- | $ cd BUSCO_v1.1b1 | + | $ cd busco |
- | $ ln -s BUSCO_v1.1b1.py BUSCO_v1.1b.py | + | $ git checkout 4.0.6 |
- | $ chmod +x BUSCO_v1.1b1.py | + | $ sudo mkdir /export/ |
- | $ sudo mkdir -p / | + | $ sudo chown aorth / |
- | $ sudo cp -r . / | + | $ python3 |
- | + | $ source / | |
- | ===== Running ===== | + | $ pip install --upgrade setuptools pip |
- | After loading the module, consult the built-in help: | + | $ python setup.py install |
+ | $ module load R/3.6 | ||
+ | $ mkdir / | ||
+ | $ export R_LIBS=/ | ||
+ | $ Rscript -e ' | ||
+ | $ module load blast/ | ||
+ | $ ./ | ||
+ | $ sudo cp config/ | ||
+ | $ sudo chown -R root: | ||
- | < | + | Consult the [[https:// |
busco-software.txt · Last modified: 2023/03/21 12:37 by aorth