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.