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checkm-software [2020/03/12 16:17] aorthcheckm-software [2020/03/12 16:45] (current) aorth
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 $ pip install checkm-genome==1.1.2 $ pip install checkm-genome==1.1.2
 $ wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz $ wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
-sudo mkdir -p /export/apps/checkm/1.1.2/data+$ mkdir -p /export/apps/checkm/1.1.2/data
 $ tar xf checkm_data_2015_01_16.tar.gz -C /export/apps/checkm/1.1.2/data $ tar xf checkm_data_2015_01_16.tar.gz -C /export/apps/checkm/1.1.2/data
 $ find /export/apps/checkm/1.1.2/data -type d -exec chmod 755 {} \; $ find /export/apps/checkm/1.1.2/data -type d -exec chmod 755 {} \;
 $ find /export/apps/checkm/1.1.2/data -type f -exec chmod 644 {} \; $ find /export/apps/checkm/1.1.2/data -type f -exec chmod 644 {} \;
 +$ checkm data setRoot /export/apps/checkm/1.1.2/data
 $ sudo chown -R root:root /export/apps/checkm/1.1.2</code> $ sudo chown -R root:root /export/apps/checkm/1.1.2</code>
  
-Note that the ''checkm data setRoot'' command expects to be able to write to the site-wide configuration so I update the data path after installation:+Test the installation with:
  
-<code>sudo sed -i -e 's|/srv/db/checkm_data/1.0.0|/export/apps/checkm/1.1.2/data|' /export/apps/checkm/1.1.2/lib64/python3.6/site-packages/checkm/DATA_CONFIG</code>+<code>$ checkm test /tmp/test-checkm</code>
checkm-software.1584029857.txt.gz · Last modified: 2020/03/12 16:17 by aorth