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--- checkm-software [2020/03/12 15:13]
aorth
+++ checkm-software [2020/03/12 16:45] (current)
aorth
@@ Line 28: / Line 28: @@
 $ pip install --upgrade pip setuptools
 $ pip install checkm-genome==1.1.2
-$ sudo chown -R root:root /export/apps/checkm/1.1.2
 $ 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
-$ sudo tar xf checkm_data_2015_01_16.tar.gz -C /export/apps/checkm/1.1.2/data</code>
+$ 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 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>
-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>

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