Differences

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--- qiime2-software [2018/05/21 06:54] – created aorth
+++ qiime2-software [2018/07/22 16:21] – aorth
@@ Line 1: / Line 1: @@
 ====== QIIME2 ======
-QIIME™ (canonically pronounced chime) stands for Quantitative Insights Into Microbial Ecology. QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.
+QIIME™ (canonically pronounced chime) stands for Quantitative Insights Into Microbial Ecology. QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QIIME2 is a completely new and different version than QIIME1.
 ===== Information =====
-  * Version: 2018.4
+  * Version: 2018.6
   * Added: May, 2018
+  * Updated: July, 2018
   * Link: https://qiime2.org/
 ===== Usage =====
-See versions of qiime2 which are available:
+See versions of qiime2 that are available:
 <code>$ module avail qiime2</code>
-Load a particular version:
+Load a particular version into your environment and run it:
-<code>$ module load qiime2/2018.4</code>
+<code>$ module load qiime2/2018.6
+$ qiime --help</code>
 ===== Installation ======
-Notes from the sysadmin during installation. Install Conda somewhere globally, but not used by anyone, then use that Conda to install Qiime2:
+Notes from the sysadmin during installation:
 <code>$ cd /tmp
@@ Line 26: / Line 28: @@
 $ bash Miniconda3-latest-Linux-x86_64.sh -p /export/apps/qiime2/conda
 $ source /export/apps/qiime2/conda/bin/activate
-$ wget https://data.qiime2.org/distro/core/qiime2-2018.4-py35-linux-conda.yml
+$ conda update -n base conda
-$ conda env create -p /export/apps/qiime2/2018.4 --file qiime2-2018.4-py35-linux-conda.yml
+$ wget https://data.qiime2.org/distro/core/qiime2-2018.6-py35-linux-conda.yml
-$ conda activate /export/apps/qiime2/2018.4
+$ conda env create -p /export/apps/qiime2/2018.6 --file qiime2-2018.6-py35-linux-conda.yml
+$ conda activate /export/apps/qiime2/2018.6
 $ sudo chown -R root:root /export/apps/qiime2
 $ qiime --help</code>
-Qiime2 has 240 dependencies and is extremely tricky 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.
+Qiime2 has 240 dependencies and is extremely tricky 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, but but I will keep it around for ease of upgrading and installing future versions.
+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.