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|{{#vardefine:app|r-index}} |{{#vardefine:url|https://github.com/alshai/r-index}}

==Example of script used to test application installation== #SBATCH --job-name=impute5_test

...mmend using RStudio through [[Open OnDemand]] as the main GUI interface to R| warn}} To run RStudio Server in a job on HiPerGator and connect to the session from a web browser on your local c

[[R|back to the main R page]] # Load the R MPI package if it is not already loaded.

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct cod

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:app|R}} |{{#vardefine:url|http://www.r-project.org/}}

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|{{#vardefine:job|}} <!--JOB SCRIPTS--> Tax4Fun is a open-source R package that predicts the functional capabilities of microbial communities

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> SAIGE is an R package developed with Rcpp for genome-wide association tests in large-scal

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> ...atistic for making inference about population admixture described in Loh P-R, Lipson M, Patterson N, Moorjani P, Pickrell JK, Reich D, and Berger B. Inf

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|1}} <!--Enable job script wiki page link--> ...' The module load command should also be included in your batch submission script since your compiled Matlab executable must also find the appropriate dynami

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

...H. Gohlke, R. Luo, K.M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods. The Amber biomolecular simulation programs. J. Computat. Chem. 26, <!--Job scripts-->

# Command-line batch Job Submission: See the next section. ...This means that if you want to use more than one processor for a Gaussian job, you are limited to the number of processors in a single machine. You canno

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> r) Rename remote

|{{#vardefine:job|1}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> ...ncing technology paired with Mission Bio’s microfluidic platform (Tapestri(R)).

|{{#vardefine:job|}} <!--JOB SCRIPTS--> cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data. Most of the scripts only requir

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

== Job script used for testing application installation == #SBATCH --job-name=rnaframework_2.7.2_test

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> ...rom high-throughput microsatellite sequences. MEGASAT is written in Perl & R and includes a simple graphical user interface for Windows and Mac OS X sys

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

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|{{#vardefine:job|}} <!--JOB SCRIPTS--> PhiSpy is a computer program written in C++, Python and R to identify prophages in a complete bacterial genome sequences.

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> Run fastGear in your job script as

|{{#vardefine:job|}} <!--JOB SCRIPTS--> mapDamage2 is a computational framework written in Python3 and R, which tracks and quantifies DNA damage patterns among ancient DNA sequenci

|{{#vardefine:job|}} <!--JOB SCRIPTS--> ...lly gives transparent access to well-known toolboxes such as scikit-learn, R, and Deeplearning4j.

|{{#vardefine:job|}} <!--JOB SCRIPTS--> ...ependent yet fully integrated parts. The first part (Giotto Analyzer) is a R package that provides utilities and step-by-step instructions about the dif

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> $ chmod -R +x .

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

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|{{#vardefine:job|}} <!--JOB SCRIPTS--> Create dynamic content with Python, R, Julia, and Observable.

|{{#vardefine:job|}} <!--JOB SCRIPTS--> ...segregant analysis by deep sequencing. The core function is programmed by R language. For the detailed description of the method, please see the origin

|{{#vardefine:job|}} <!--JOB SCRIPTS--> Supports integration with Python and R

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

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|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> The R package 'DeepGS' can be used to perform genomic selection (GS), which is a

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> ...nes for working with ribosomal DNA sequence data generated with the PacBio(R) SMRT sequencing. rDnaTools works by wrapping existing tools from microbial

|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> picard CreateSequenceDictionary R=example.fa O=example.dict

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> ...by SimpleElastix, making it available in languages like C++, Python, Java, R, Ruby, C# and Lua.

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

...lso available (“sh”, “csh”, “perl”, “python”, “lisp”, “fish”, “cmake”, or “r”). See documentation for details.

|{{#vardefine:url|https://www.r-ccs.riken.jp/labs/cbrt/}} |{{#vardefine:job|}} <!--JOB SCRIPTS-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

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|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

...notebooks, consoles, or terminals with multiple custom kernels and several job resource request profiles, which we can expand on request to satisfy your n * The dropdown menu lists the available job profile options for the resource request for your Jupyter Server. As with a

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> ...language, Java including Android, Lua, Modula-3, OCAML, Octave, Scilab and R. Also several interpreted and compiled Scheme implementations (Guile, MzSch

* Create a job script with the appropriate resources to run the server * The job script should load the ParaView module and launch the "pvserver" component:

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

...ccessful jobs make sure to specify a valid MPI SLURM job layout in the job script and to match the requested CPU cores to the number passed to auto3dem. For {{#if: {{#var: pbs}}|==PBS Script Examples==

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> ...iling of NGS libraries has been developed as a collection of C++, Perl and R scripts.

<span style="font-size: 12pt"> '''[[Jupyter_Notebooks| Jupyter (Python, R)]]''' | [[Galaxy|Galaxy Genomics Framework]] | [[Open OnDemand|OnDemand (Ma ...M_Job_Arrays|Job Arrays]] | [[GPU_Access|GPU Access]] | [[SLURM_Job_States|Job States]] | [[SLURM Partition Limits|Time Limits]]</span>

|{{#vardefine:job|}} <!--JOB SCRIPTS--> ...ided for the rice genome (TIGR7/MSU7 version). You may use the lib-test.pl script to compare the annotation performance of your method/library to the already

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> ...n set up in a manner that does not require you to invoke Python to run the script. If you are following the examples in the authors' tutorial, '''drop the "

|{{#vardefine:job|}} <!--JOB SCRIPTS--> <!--Job Scripts-->

# You may detach the screen at any time and then use screen -r to reattach at a later time. # Once the <code>bedpostx</code> script has finished running turn the screen log off with

...default, which will fill up memory disks on HPG2 nodes and cause node and job failures. Our qiime modules will automatically create a 'tmp' directory ins ...8-thread parallel QIIME job use the following resource request in your job script:

|{{#vardefine:job|1}} <!--JOB SCRIPTS--> <!--Job Scripts-->

...blue how you want to execute the job and it takes care of the rest. Python job scripts give you unlimited flexibility to create custom initialization rout {{#if: {{#var: pbs}}|==PBS Script Examples==

|{{#vardefine:job|1}} <!--JOB SCRIPTS--> <!--Job Scripts-->

|{{#vardefine:job|}} <!--JOB SCRIPTS--> ...variable for you, and this is an excellent option. See example submission script. Another convenient variable you could use is $PBS_O_WORKDIR, something lik

|{{#vardefine:job|1}} <!--JOB SCRIPTS--> ...r computing system. It provides high-level APIs in Java, Scala, Python and R, and an optimized engine that supports general execution graphs. It also su