paup
Table of Content
About
PAUP (Phylogenetic Analysis Using Parsimony) is a widely used software package for the inference of evolutionary trees.
Versions and Availability
Module Names for paup on qb
| Machine | Version | Module Name |
|---|---|---|
| qb2 | 4.0 | paup/4.0 |
▶ Module FAQ?
The information here is applicable to LSU HPC and LONI systems.
Shells
A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.
/bin/bash
System resource file: /etc/profile
When one access the shell, the following user files are read in if they exist (in order):
- ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
- ~/.bashrc (interactive login only)
- ~/.profile
When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.
The default value of the environmental variable, PATH, is set automatically using SoftEnv. See below for more information.
/bin/tcsh
The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.
Modules
Modules is a utility which helps users manage the complex business of setting up their shell environment in the face of potentially conflicting application versions and libraries.
Default Setup
When a user logs in, the system looks for a file named .modules in their home directory. This file contains module commands to set up the initial shell environment.
Viewing Available Modules
The command
$ module avail
displays a list of all the modules available. The list will look something like:
--- some stuff deleted --- velvet/1.2.10/INTEL-14.0.2 vmatch/2.2.2 ---------------- /usr/local/packages/Modules/modulefiles/admin ----------------- EasyBuild/1.11.1 GCC/4.9.0 INTEL-140-MPICH/3.1.1 EasyBuild/1.13.0 INTEL/14.0.2 INTEL-140-MVAPICH2/2.0 --- some stuff deleted ---
The module names take the form appname/version/compiler, providing the application name, the version, and information about how it was compiled (if needed).
Managing Modules
Besides avail, there are other basic module commands to use for manipulating the environment. These include:
add/load mod1 mod2 ... modn . . . Add modules rm/unload mod1 mod2 ... modn . . Remove modules switch/swap mod . . . . . . . . . Switch or swap one module for another display/show . . . . . . . . . . List modules loaded in the environment avail . . . . . . . . . . . . . . List available module names whatis mod1 mod2 ... modn . . . . Describe listed modules
The -h option to module will list all available commands.
Module is currently available only on SuperMIC.
Usage
paup requires an input file to define the type of analysis to perform and the data sources to examine.
Use soft-dbq to determine the executable's name:
$ soft-dbq +paup-4.0
This is all the information associated with
the key or macro +paup-4.0.
-------------------------------------------
Name: +paup-4.0
Description: @type: Application/Biology @name: paup @version: 4.0
@about: tools for inferring and interpreting phylogenetic trees
Flags: none
Groups: none
Exists on: Linux
-------------------------------------------
On the Linux architecture,
the following will be done to the environment:
The following environment changes will be made:
PATH = ${PATH}:/usr/local/packages/paup/4.0
$ ls /usr/local/packages/paup/4.0
paup4b10-opt-linux-a
$ paup4b10-opt-linux-a -h
P A U P *
Portable version 4.0b10 for Unix
Mon Mar 31 15:40:51 2014
-----------------------------NOTICE-----------------------------
This is a beta-test version. Please report any crashes,
apparent calculation errors, or other anomalous results.
There are no restrictions on publication of results obtained
with this version, but you should check the WWW site
frequently for bug announcements and/or updated versions.
See the README file on the distribution media for details.
----------------------------------------------------------------
Usage: paup4b10-opt-linux-a [options...] [input-file-name] [-l log-file-name]
Options: -a Append to log-file if already exists
-r Replace log-file if already exists
-n Run in "non-interactive" mode (no prompts)
-u Don't buffer standard output
-f Ignore file-locking
Resources
Last modified: August 21 2017 10:47:37.