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busco-software [2015/09/13 08:18]
aorth [Information] 		busco-software [2020/05/12 15:13]
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: v1.1b+  * Latest Version: 4.0.6
   * Added: August, 2015   * Added: August, 2015
-  * Link: http://busco.ezlab.org/#software+  * Updated: May, 2020 
 +  * Link: https://busco.ezlab.org
  
 ===== Usage ===== ===== Usage =====
Line 13: Line 13:
 See versions of BUSCO which are available: See versions of BUSCO which are available:
 <code>$ module avail BUSCO</code> <code>$ module avail BUSCO</code>
 +
 +Load one version into your environment and run it:
 +<code>$ module load BUSCO/4.0.6</code>
 +
 +After loading the module, consult the built-in help:
 +
 +<code>$ busco -h</code>
 +
 +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:
 +
 +<code>$ cp -r /export/apps/augustus/3.2.3/config /var/scratch/aorth-augustus-config
 +$ export AUGUSTUS_CONFIG_PATH=/var/scratch/aorth-augustus-config</code>
  
 ===== Installation ====== ===== Installation ======
 Notes from the sysadmin during installation: Notes from the sysadmin during installation:
  
-<code>http://busco.ezlab.org/files/BUSCO_v1.1b1.tar.gz +<code>$ cd /tmp 
-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/apps/BUSCO/4.0.6 
-sudo mkdir -p /export/apps/BUSCO/v1.1b/ +$ sudo chown aorth /export/apps/BUSCO/4.0.6 
-sudo cp -r . /export/apps/BUSCO/v1.1b/</code> +$ python3 -m venv /export/apps/BUSCO/4.0.6 
- +$ source /export/apps/BUSCO/4.0.6/bin/activate 
-===== Running ===== +$ pip install --upgrade setuptools pip 
-After loading the module, consult the built-in help:+$ module load R/3.6 
 +$ mkdir /export/apps/BUSCO/4.0.6/r-libs 
 +$ export R_LIBS=/export/apps/BUSCO/4.0.6/r-libs 
 +$ Rscript -e 'install.packages("ggplot2", repos="https://cran.rstudio.com")' 
 +$ module load blast/2.2.31+ augustus/3.2.3 hmmer/3.2.1 sepp/4.3.8 prodigal/2.6.3 
 +$ ./scripts/busco_configurator.py config/config.ini config/myconfig.ini 
 +$ sudo cp config/myconfig.ini  /export/apps/BUSCO/4.0.6/ 
 +$ sudo chown -R root:root /export/apps/BUSCO/4.0.6</code>
  
-<code>$ BUSCO_v1.1b.py --help</code>+Consult the [[https://busco.ezlab.org/busco_userguide.html|BUSCO user guide]] for more installation and usage tips.
busco-software.txt · Last modified: 2020/05/12 15:45 by aorth

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