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qiime2-software [2019/09/28 23:33]
aorth
qiime2-software [2019/12/15 13:11] (current)
aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 2019.7+  * Version: 2019.10
   * Added: May, 2018   * Added: May, 2018
-  * Updated: ​September, 2019+  * Updated: ​December, 2019
   * Link: https://​qiime2.org/​   * Link: https://​qiime2.org/​
  
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 Load a particular version into your environment and run it: Load a particular version into your environment and run it:
  
-<​code>​$ module load qiime2/​2019.7+<​code>​$ module load qiime2/​2019.10
 $ qiime --help</​code>​ $ qiime --help</​code>​
  
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 <​code>​$ mkdir -p /​var/​tmp/​chroot/​qiime2 <​code>​$ mkdir -p /​var/​tmp/​chroot/​qiime2
 $ rpm --rebuilddb --root=/​var/​tmp/​chroot/​qiime2 $ rpm --rebuilddb --root=/​var/​tmp/​chroot/​qiime2
 +$ wget https://​hpc.ilri.cgiar.org/​mirror/​centos/​7/​os/​x86_64/​Packages/​centos-release-7-7.1908.0.el7.centos.x86_64.rpm
 $ sudo rpm --root=/​var/​tmp/​chroot/​qiime2 -i centos-release-7-7.1908.0.el7.centos.x86_64.rpm $ sudo rpm --root=/​var/​tmp/​chroot/​qiime2 -i centos-release-7-7.1908.0.el7.centos.x86_64.rpm
 $ sudo yum --installroot=/​var/​tmp/​chroot/​qiime2 install -y rpm-build yum wget vim $ sudo yum --installroot=/​var/​tmp/​chroot/​qiime2 install -y rpm-build yum wget vim
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 # eval "​$(/​export/​apps/​qiime2/​conda/​bin/​conda shell.bash hook)" # eval "​$(/​export/​apps/​qiime2/​conda/​bin/​conda shell.bash hook)"
 # conda update -n base conda # conda update -n base conda
-# wget https://​data.qiime2.org/​distro/​core/​qiime2-2019.7-py36-linux-conda.yml +# wget https://​data.qiime2.org/​distro/​core/​qiime2-2019.10-py36-linux-conda.yml 
-# conda env create -p /​export/​apps/​qiime2/​2019.--file qiime2-2019.7-py36-linux-conda.yml +# conda env create -p /​export/​apps/​qiime2/​2019.10 --file qiime2-2019.10-py36-linux-conda.yml 
-source ​activate qiime2-2019.7 +conda activate ​/​export/​apps/​qiime2/2019.10 
-# env > conda-qiime2-2019.7+# env > conda-qiime2-2019.10
 # exit # exit
-$ sudo mkdir -p /​export/​apps/​qiime2/​2019.7 +$ sudo mkdir -p /​export/​apps/​qiime2/​2019.10 
-$ sudo chown aorth /​export/​apps/​qiime2/​2019.7 +$ sudo chown aorth /​export/​apps/​qiime2/​2019.10 
-$ rsync -av /​var/​tmp/​chroot/​qiime2/​export/​apps/​qiime2/​2019.7/ /​export/​apps/​qiime2/​2019.7 +$ rsync -av /​var/​tmp/​chroot/​qiime2/​export/​apps/​qiime2/​2019.10/ /​export/​apps/​qiime2/​2019.10 
-$ sudo chown -R root:root /​export/​apps/​qiime2/​2019.7</​code>​+$ sudo chown -R root:root /​export/​apps/​qiime2/​2019.10 
 +$ sudo umount /​var/​tmp/​chroot/​qiime2/​dev /​var/​tmp/​chroot/​qiime2/​proc /​var/​tmp/​chroot/​qiime2/​sys</​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.directory. Furthermore,​ I first installed qiime2/​2019.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.+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/​2019.10 directory. Furthermore,​ I first installed qiime2/​2019.10 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: 2019/12/15 13:11 by aorth