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paup

About

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

Version and Availability

▶ Display Softenv Keys for paup all clusters
Machine Version Softenv Key
philip 4.0 +paup-4.0
▶ Softenv FAQ?

The information here is applicable to LSU HPC and LONI systems.

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

Using the softenv command, a user may view the list of available packages. Currently, it can not be ensured that the packages shown are actually available or working on the particular machine. Every attempt is made to present an identical environment on all of the LONI clusters, but sometimes this is not the case.

Example,

$ 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
....
Listing of Available Packages

See Packages Available via SoftEnv on LSU HPC and LONI.

For a more accurate, up to date list, use the softenv command.

Caveats

Currently there are some caveats to using this tool.

  1. packages might be out of sync between what is listed and what is actually available
  2. resoft and soft utilities are not; to update the environment for now, log out and login after modifying the ~/.soft file.
Availability

softenv is available on all LSU HPC and LONI clusters to all users in both interactive login sessions (i.e., just logging into the machine) and the batch environment created by the PBS job scheduler on Linux clusters and by loadleveler on AIX clusters..

Packages Availability

This information can be viewed using the softenv command:

% softenv
Managing Environment with 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

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: March 31 2014 16:06:29.