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[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]][[Category:Bioinformatics Database]] ...prot_sprot -parse_seqids -out uniprot_sprot -logfile uniprot_sprot.blast+.log

[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]] Rosetta is a software suite for macromolecular modeling. Please see https://www.rosettacommons.or

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]] ..., and genomic annotations." more details at [http://www.broadinstitute.org/software/igv/ IGV]

[[Category:Sapelo2]][[Category:Software]][[Category:Other]] #SBATCH --output=%x.%j.out # Standard output log

#SBATCH --output=%x.%j.out # Standard output log #SBATCH --error=%x.%j.err # Standard error log

[[Category:Sapelo2]][[Category:Software]][[Category:Other]] From http://magma.maths.usyd.edu.au/magma/: "Magma is a large, well-supported software package designed for computations in algebra, number theory, algebraic geom

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]] #SBATCH --output=log.%j.out # Standard output log

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]] #SBATCH --output=%x.%j.out # Standard output log

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]] <nowiki>#</nowiki>SBATCH --output=log.%j.out<br>

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]] #SBATCH --output=%x.%j.out # Standard output log

[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]] #SBATCH --output=%x.%j.out # Standard output log

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]] Please see http://merenlab.org/software/

[[Category:Sapelo2]][[Category:Software]][[Category:Tools]] Please log on a Sapelo2 transfer node xfer-irods.gacrc.uga.edu to use iCommands, for e

[[Category:Sapelo2]][[Category:Software]][[Category:Other]] Please see https://jgi.doe.gov/data-and-tools/software-tools/meraculous/: "Meraculous is a whole genome assembler for Next Generat

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]] #SBATCH --output=%x.%j.out # Standard output log

...st have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including L ...st have an ssh software and a connection to the UGA campus network. An ssh software is included in recent releases of Unix based operating systems (including L

[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]] $EBROOTORCA/bin/orca example.inp > example.${SLURM_JOB_ID}.log

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]] #SBATCH --output=log.%j.out

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]] #SBATCH --output=log.%j.out # Standard output log

...ent. Outlined here is an explanation of each of these three categories of software and how to use them. =Getting Help Using Software=

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]] #SBATCH --output=log.%j.out

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]] Please see https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]] ...oguserplotX=FILE[,FILE2] For sequence 'X' open one or more userplots, take log(data)

...container. Outlined here is an explanation of each of both categories of software and how to use them. =Getting Help Using Software=

[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]] #SBATCH --output=%x.%j.out # Standard output log

...container. Outlined here is an explanation of each of both categories of software and how to use them. =Getting Help Using Software=

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]] -v/--verbose log-friendly verbose processing (no progress bar) [ default: FALSE ]

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]] <nowiki>#</nowiki>SBATCH --output=log.%j.out<br>

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]] ...on of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to proces

This code works as a modification of the popular phylogenetics software package [[MrBayes]] Log -- Logs screen output to a file

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]] #SBATCH --output=log.%j.out

[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]] #SBATCH --output=%x.%j.out # Standard output log

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]] -a = <int>: min (a)NCHOR length (default = 1.1*Log(S))

...eing released for the existing operating system and newer versions of some software applications are not supported by the current OS version. * The compiler toolchains and many software packages will be updated to newer versions.

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]] #SBATCH --output=log.%j.out

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]] <nowiki>#</nowiki>SBATCH --output=log.%j.out<br>

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]] [https://ab.inf.uni-tuebingen.de/software/diamond DIAMOND]

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]] -G alpha ( N(t) = N0*exp(-alpha*t) . alpha = -log(Np/Nr)/t

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]] Efficient phylogenomic software by maximum likelihood. More information: http://www.iqtree.org/

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]] "The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequ

During the Oct.24-28 maintenance window, GACRC implemented the Slurm software *Log out then log back in and submit your job

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]] <nowiki>#</nowiki>SBATCH --output=log.%j.out<br>

[Category:Sapelo2old]][[Category:Software]][[Category:Bioinformatics]] ...Qualities are logit (log p/1-p) rather than phred (log p) scores [phred]

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]] --log= Path to standard logging destination (if given, captures both STD

#SBATCH --output=testserial.%j.out # Standard output log #SBATCH --error=testserial.%j.err # Standard error log

...ware on your local machine and a connection to the UGA campus network. ssh software is included in recent releases of Unix based operating systems (including L ...others. So you would need to check which login node you landed on and then log back into it directly. To check the name of the login node, you can run the

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]] [http://ccb.jhu.edu/software/stringtie/ StringTie]

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]] ...incorperated in Mothur. In addition to improving the flexibility of these software, a number of other features including calculators and visualization tools a

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]] -m INT minimal chaining score (matching bases minus log gap penalty) [40]

...perations for a VMWare cluster are managed by a physical machine that runs software named vCenter. vCenter is composed of an application, the Virtual Infrastru # Log into Virtual Center using Remote Desktop

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]] ...-variant_index_parameter <variant_index_parameter>] [-l <logging_level>] [-log <log_to_file>]

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]] A. Stamatakis, please see http://sco.h-its.org/exelixis/web/software/raxml/index.html

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]] -e set model optimization precision in log likelihood units for final

...notified via e-mail. The applicant’s UGA MyID and password will be used to log into the requested GACRC resources. ...notified via e-mail. The Affiliate’s UGA MyID and password will be used to log into the requested GACRC resources.

..., users will need to install the [http://filezilla-project.org/ FileZilla] software on the local machine. After installation, start FileZilla and follow these ...e and Sapelo2, users will need to install the [http://winscp.net/ WinSCP] software on the local machine. After installation, when you click the WinSCP shortcu

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]] --[no]alsologtostderr: also log to stderr?

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]] outStd Log

===How to install software (general)=== Loading internal null logger. Install Log::Log4perl for logging messages

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]] genotype likelihood is no more than log(N) from the highest

[[Category:Sapelo2]][[Category:Software]][[Category:Other]][[Category:Programming]][[Category:Graphics]] ...duces an error, call the <code>getDebugLog</code> method to view the error log file. When submitting independent jobs, with multiple tasks, specify the t

...e at the [[Software on Sapelo2]] page and on the teaching cluster at the [[Software on Teaching Cluster]] page. ...t requires extra documentation not covered in [[Software on Sapelo2]] or [[Software on Teaching Cluster]].

Below is a partial list of software packages installed on Sapelo2, Teaching (we are in the process of adding wi ...installed there. For information on software installed there, please see [[Software on sap2test]].

[[Category:Sapelo2old]][[Category:Software]][[Category:Bioinformatics]] File to which the program log should be redirected