38,760
edits
QIIME/en: Difference between revisions
Jump to navigation
Jump to search
Updating to match new version of source page
(Updating to match new version of source page) |
(Updating to match new version of source page) |
||
| Line 5: | Line 5: | ||
<b>Note</b>: As of February 2020, due to various issues generated by Conda environments on our HPC systems, <b>installation using Anaconda or Miniconda is no longer supported</b>. | <b>Note</b>: As of February 2020, due to various issues generated by Conda environments on our HPC systems, <b>installation using Anaconda or Miniconda is no longer supported</b>. | ||
== QIIME2 as a module == | |||
QIIME2 is now available in our environment using a module which wraps around a container. You can run | |||
{{Command|module spider qiime2}} | |||
to find which versions we have available. | |||
After loading the module, you can run | |||
{{Command|qiime --help}} | |||
{{Callout | |||
|title=Note | |||
|content=Since the <tt>qiime</tt> command is in fact calling a container, you may have to define the environment variable <tt>APPTAINER_BIND</tt> to bind specific folders within the container to access your data. For example: <tt>APPTAINER_BIND=/home qiime ...</tt> | |||
}} | |||
==Installation == | ==Installation == | ||
QIIME2 can be installed using [[Apptainer]] or [[EasyBuild]]. Apptainer is strongly preferred since it does not generate many thousands of files in your /home directory, potentially causing you to exceed the disk quota limit on the number of files. | QIIME2 can be installed using [[Apptainer]] or [[EasyBuild]]. Apptainer is strongly preferred since it does not generate many thousands of files in your /home directory, potentially causing you to exceed the disk quota limit on the number of files. | ||
{{Outdated}} | |||
=== Using Apptainer === | === Using Apptainer === | ||