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paup

About

PAUP (Phylogenetic Analysis Using Parsimony) is a widely used software package for the inference of evolutionary trees.

Versions and Availability

Softenv Keys for paup on philip
Machine Version Softenv Key
philip 4.0 +paup-4.0
▶ Softenv 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):

  1. ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
  2. ~/.bashrc (interactive login only)
  3. ~/.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.

Softenv

SoftEnv is a utility that is supposed to help users manage complex user environments with potentially conflicting application versions and libraries.

System Default Path

When a user logs in, the system /etc/profile or /etc/csh.cshrc (depending on login shell, and mirrored from csm:/cfmroot/etc/profile) calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh to set up the default path via the SoftEnv database.

SoftEnv looks for a user's ~/.soft file and updates the variables and paths accordingly.

Viewing Available Packages

The command softenv will provide a list of available packages. The listing will look something like:

$ softenv
These are the macros available:
*   @default
These are the keywords explicitly available:
+amber-8                       Applications: 'Amber', version: 8 Amber is a
+apache-ant-1.6.5              Ant, Java based XML make system version: 1.6.
+charm-5.9                     Applications: 'Charm++', version: 5.9 Charm++
+default                       this is the default environment...nukes /etc/
+essl-4.2                      Libraries: 'ESSL', version: 4.2 ESSL is a sta
+gaussian-03                   Applications: 'Gaussian', version: 03 Gaussia
... some stuff deleted ...
Managing SoftEnv

The file ~/.soft in the user's home directory is where the different packages are managed. Add the +keyword into your .soft file. For instance, ff one wants to add the Amber Molecular Dynamics package into their environment, the end of the .soft file should look like this:

+amber-8

@default

To update the environment after modifying this file, one simply uses the resoft command:

% resoft

The command soft can be used to manipulate the environment from the command line. It takes the form:

$ soft add/delete +keyword

Using this method of adding or removing keywords requires the user to pay attention to possible order dependencies. That is, best results require the user to remove keywords in the reverse order in which they were added. It is handy to test out individual keys, but can lead to trouble if changing multiple keys. Changing the .soft file and issuing the resoft is the recommended way of dealing with multiple changes.

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: November 12 2014 09:49:09.