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qiime2-software [2019/09/28 23:28]
aorth [Usage]
qiime2-software [2019/09/28 23:33] (current)
aorth
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 $ sudo chown -R root:root /​export/​apps/​qiime2/​2019.7</​code>​ $ sudo chown -R root:root /​export/​apps/​qiime2/​2019.7</​code>​
  
-QIIME2 has over 200 dependencies and is essentially impossible to install without the use of [[https://​conda.io/​miniconda.html|Miniconda]] (it is not even published on PyPy anymore, so installing it with pip is not an option). My strategy is to install Conda somewhere globally and then use it to install QIIME2. After the installation is done I think we don't technically need Conda itself anymore, as all binaries seem to be linked against libraries in the qiime2/​2019.7 directory.+QIIME2 has over 200 dependencies and is essentially impossible to install without the use of [[https://​conda.io/​miniconda.html|Miniconda]] (it is not even published on PyPy anymore, so installing it with pip is not an option). My strategy is to install Conda somewhere globally and then use it to install QIIME2. After the installation is done I think we don't technically need Conda itself anymore, as all binaries seem to be linked against libraries in the qiime2/​2019.7 directory. Furthermore,​ I first installed qiime2/​2019.7 in a chroot on the local file system and then rsynced it over to the network applications directory. This is MUCH faster, but more importantly,​ it avoids random "​permission denied"​ errors I was getting when installing on the network file system.
  
 To create the [[https://​github.com/​ilri/​hpc-environment-modules/​tree/​master/​qiime2|modulefile]] I compared the output ''​env''​ before and after loading the Qiime2 environment with Conda. To create the [[https://​github.com/​ilri/​hpc-environment-modules/​tree/​master/​qiime2|modulefile]] I compared the output ''​env''​ before and after loading the Qiime2 environment with Conda.
qiime2-software.txt · Last modified: 2019/09/28 23:33 by aorth