Amphora2: Difference between revisions

Latest revision as of 17:35, 10 June 2022

Description

An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.

AMPHORA2 is free software: you may redistribute it and/or modify its under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or any later version.

Environment Modules

Run module spider amphora2 to find out what environment modules are available for this application.

System Variables

HPC_AMPHORA2_DIR - installation directory
HPC_AMPHORA2_BIN - executable directory
HPC_AMPHORA2_DOC - documentation directory
HPC_AMPHORA2_EXE - test data directory
HPC_AMPHORA2_TAX- taxonomy data directory
HPC_AMPHORA2_TREE - tree data directory

Citation

If you publish research that uses amphora2 you have to cite it as follows:

Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28(7):1033-1034

@@ Line 23: / Line 23: @@
 <!--Modules-->
-==Required Modules==
+==Environment Modules==
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-===Serial===
-* {{#var:app}}
-<!--
-===Parallel (OpenMP)===
-* intel
-* {{#var:app}}
-===Parallel (MPI)===
-* intel
-* openmpi
-* {{#var:app}}
--->
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
-* HPC_{{#uppercase:{{#var:app}}}}_BIN - executable directory
+* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
-* HPC_{{#uppercase:{{#var:app}}}}_DOC - documentation directory
+* HPC_{{uc:{{#var:app}}}}_DOC - documentation directory
-* HPC_{{#uppercase:{{#var:app}}}}_EXE - test data directory
+* HPC_{{uc:{{#var:app}}}}_EXE - test data directory
-* HPC_{{#uppercase:{{#var:app}}}}_TAX- taxonomy data directory
+* HPC_{{uc:{{#var:app}}}}_TAX- taxonomy data directory
-* HPC_{{#uppercase:{{#var:app}}}}_TREE - tree data directory
+* HPC_{{uc:{{#var:app}}}}_TREE - tree data directory
 <!--Configuration-->
@@ Line 77: / Line 66: @@
 If you publish research that uses {{#var:app}} you have to cite it as follows:
-Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28(7):1033-1034
+[https://www.ncbi.nlm.nih.gov/pubmed/22332237 Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28(7):1033-1034]
 |}}