Difference between revisions of "Available Software on the OBCP Cluster"
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| Line 14: | Line 14: | ||
* ''Parallel'': BEAGLE threading | * ''Parallel'': BEAGLE threading | ||
* ''Notes'': | * ''Notes'': | ||
| + | |||
=== BEAUti === | === BEAUti === | ||
* ''Filename'': beauti | * ''Filename'': beauti | ||
| Line 19: | Line 20: | ||
* ''Parallel'': No | * ''Parallel'': No | ||
* ''Notes'': This program is a BEAST plugin | * ''Notes'': This program is a BEAST plugin | ||
| + | |||
=== MrBayes === | === MrBayes === | ||
* ''Filename'': mb | * ''Filename'': mb | ||
| Line 24: | Line 26: | ||
* ''Parallel'': MPI-enabled | * ''Parallel'': MPI-enabled | ||
* ''Notes'': This version of MrBayes as well as 3.1.x do not operate properly on operating systems using the newer Linux kernels. An attempt to address this problem with the authors was fruitless. | * ''Notes'': This version of MrBayes as well as 3.1.x do not operate properly on operating systems using the newer Linux kernels. An attempt to address this problem with the authors was fruitless. | ||
| + | |||
| + | === MUSCLE === | ||
| + | * ''Filename'': muscle | ||
| + | * ''Version'': 3.8.31 | ||
| + | * ''Parallel'': No | ||
| + | * ''Notes'': | ||
| + | |||
=== pyRAD === | === pyRAD === | ||
* ''Filename'': pyRAD | * ''Filename'': pyRAD | ||
| Line 29: | Line 38: | ||
* ''Parallel'': No | * ''Parallel'': No | ||
* ''Notes'': | * ''Notes'': | ||
| + | |||
=== RaxML === | === RaxML === | ||
* ''Filename'': raxml | * ''Filename'': raxml | ||
| Line 34: | Line 44: | ||
* ''Parallel'': Pthreads threading | * ''Parallel'': Pthreads threading | ||
* ''Notes'': | * ''Notes'': | ||
| + | |||
=== RaxML Light === | === RaxML Light === | ||
* ''Filename'': raxmlLight | * ''Filename'': raxmlLight | ||
| Line 39: | Line 50: | ||
* ''Parallel'': Pthreads threading | * ''Parallel'': Pthreads threading | ||
* ''Notes'': | * ''Notes'': | ||
| + | |||
=== SNAPP === | === SNAPP === | ||
* ''Filename'': snapp | * ''Filename'': snapp | ||
| Line 44: | Line 56: | ||
* ''Parallel'': BEAGLE threading | * ''Parallel'': BEAGLE threading | ||
* ''Notes'': This program is a BEAST plugin | * ''Notes'': This program is a BEAST plugin | ||
| + | |||
=== USEARCH === | === USEARCH === | ||
* ''Filename'': usearch | * ''Filename'': usearch | ||
| Line 56: | Line 69: | ||
* ''Parallel'': Pthreads threading | * ''Parallel'': Pthreads threading | ||
* ''Notes'': | * ''Notes'': | ||
| + | |||
=== GENSCAN === | === GENSCAN === | ||
* ''Filename'': genscan | * ''Filename'': genscan | ||
| Line 61: | Line 75: | ||
* ''Parallel'': No | * ''Parallel'': No | ||
* ''Notes'': | * ''Notes'': | ||
| + | |||
=== Oases === | === Oases === | ||
* ''Filename'': oases | * ''Filename'': oases | ||
| Line 66: | Line 81: | ||
* ''Parallel'': OpenMP threading | * ''Parallel'': OpenMP threading | ||
* ''Notes'': Default parameters were used. Oases (as with Velvet) should be compiled within your home directory with the specific compilation parameters (max k-mer length, # of read categories, etc.) tailored to your reads at hand. | * ''Notes'': Default parameters were used. Oases (as with Velvet) should be compiled within your home directory with the specific compilation parameters (max k-mer length, # of read categories, etc.) tailored to your reads at hand. | ||
| + | |||
| + | === SAMtools === | ||
| + | * ''Filename'': samtools | ||
| + | * ''Version'': 0.1.19+ | ||
| + | * ''Parallel'': No | ||
| + | * ''Notes'': | ||
| + | |||
=== Trimmomatic === | === Trimmomatic === | ||
* ''Filename'': java -jar /usr/local/bin/trimmomatic.jar | * ''Filename'': java -jar /usr/local/bin/trimmomatic.jar | ||
| Line 71: | Line 93: | ||
* ''Parallel'': Java threading | * ''Parallel'': Java threading | ||
* ''Notes'': | * ''Notes'': | ||
| + | |||
=== Velvet === | === Velvet === | ||
* ''Filename'': velveth & velvetg | * ''Filename'': velveth & velvetg | ||
| Line 102: | Line 125: | ||
* ''Parallel'': MPI-enabled | * ''Parallel'': MPI-enabled | ||
* ''Notes'': This is a beta version | * ''Notes'': This is a beta version | ||
| + | |||
| + | === RTD === | ||
| + | * ''Filename'': multiple executables | ||
| + | * ''Version'': 06-10-2013 | ||
| + | * ''Parallel'': GNU parallel | ||
| + | * ''Notes'': | ||
=== Stacks === | === Stacks === | ||
Revision as of 17:14, 30 July 2013
Available Software on the OBCP Cluster
This section of the wiki is designed to help a user locate particular software that is present on the OBCP cluster. Send any software requests to Joe Cora.
Contents
Introduction
Standard software packages that are present on most Linux operating systems like Python, Perl, R, etc. are already installed on the OBCP cluster. Some software are designed to be run in parallel by using the message passing interface (MPI) and/or through thread support built into the software. For more information on running programs in parallel, visit the Multiple Processor Runs on the OBCP Cluster page.
Phylogenetic Software
BEAST
- Filename: beast
- Version: 2.0.1
- Parallel: BEAGLE threading
- Notes:
BEAUti
- Filename: beauti
- Version: 2.0.1
- Parallel: No
- Notes: This program is a BEAST plugin
MrBayes
- Filename: mb
- Version: 3.2.1
- Parallel: MPI-enabled
- Notes: This version of MrBayes as well as 3.1.x do not operate properly on operating systems using the newer Linux kernels. An attempt to address this problem with the authors was fruitless.
MUSCLE
- Filename: muscle
- Version: 3.8.31
- Parallel: No
- Notes:
pyRAD
- Filename: pyRAD
- Version: 1.4a
- Parallel: No
- Notes:
RaxML
- Filename: raxml
- Version: 7.3.1
- Parallel: Pthreads threading
- Notes:
RaxML Light
- Filename: raxmlLight
- Version: 1.0.8
- Parallel: Pthreads threading
- Notes:
SNAPP
- Filename: snapp
- Version: 1.1.1
- Parallel: BEAGLE threading
- Notes: This program is a BEAST plugin
USEARCH
- Filename: usearch
- Version: 6.0.307
- Parallel: threading
- Notes:
Genomic Software
CASAVA
- Filename: multiple executables
- Version: 1.8.2
- Parallel: Pthreads threading
- Notes:
GENSCAN
- Filename: genscan
- Version: ??
- Parallel: No
- Notes:
Oases
- Filename: oases
- Version: 0.2
- Parallel: OpenMP threading
- Notes: Default parameters were used. Oases (as with Velvet) should be compiled within your home directory with the specific compilation parameters (max k-mer length, # of read categories, etc.) tailored to your reads at hand.
SAMtools
- Filename: samtools
- Version: 0.1.19+
- Parallel: No
- Notes:
Trimmomatic
- Filename: java -jar /usr/local/bin/trimmomatic.jar
- Version: 0.30
- Parallel: Java threading
- Notes:
Velvet
- Filename: velveth & velvetg
- Version: 1.2.09
- Parallel: OpenMP threading
- Notes: Default parameters were used with the exception of enabling OpenMP. Velvet should be compiled within your home directory with the specific compilation parameters (max k-mer length, # of read categories, etc.) tailored to your reads at hand.
Population Genetic/Genomic Software
BP&P
- Filename: bpp
- Version: 2.1b
- Parallel: No
- Notes:
IMa2
- Filename: IMa2
- Version: 8.27.12
- Parallel: No
- Notes: version is the date of release (August 27, 2012)
Migrate-N
- Filename: migrate-n
- Version: 3.3.1
- Parallel: MPI-enabled
- Notes:
Migrate-N (beta)
- Filename: migrate-n-beta
- Version: 3.4.4
- Parallel: MPI-enabled
- Notes: This is a beta version
RTD
- Filename: multiple executables
- Version: 06-10-2013
- Parallel: GNU parallel
- Notes:
Stacks
- Filename: multiple executables
- Version: 0.99998
- Parallel: OpenMP threading
- Notes:
