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1.1. Description¶

Pmset −a displaysleep 10 disksleep 10 sleep 30 womp 1 Restores the system’s energy settings to their default values. For a system with an attached and supported UPS, this instructs the system to perform an emergency shutdown when UPS battery drains to below 40%. On serebii week re max ahmed jafri commercial indoor air quality meter the mighty clouds of joy order my steps plusoptix vision screener manual.

Sentieon® Genomics software is a set of software tools that performanalysis of genomic data obtained from DNA sequencing.

1.2. Benefits and Value¶

The Sentieon® Genomics software enables rapid and accurate analysis ofnext-generation sequence data. The Sentieon® DNAseq pipelines enablegermline variant calling on hundreds of thousands of samplessimultaneously. The Sentieon® TNseq pipelines enable accurate calling ofsomatic variants in paired tumor-normal samples or in an unpaired tumorsamples. The Sentieon® Genomics software produces more accurate resultsthan other tools on third-party benchmarks with results obtained in onetenth the time of comparable pipelines.

1.3. Platform Requirements¶

Sentieon® Genomics software is designed to run on Linux and otherPOSIX-compatible platforms.

For Linux systems, we recommended using the following Linuxdistributions or higher: RedHat/CentOS 6.5, Debian 7.7, OpenSUSE-13.2,or Ubuntu-14.04. Sentieon® Genomics software has not been tested on olderreleases, and may not work.

For Apple OSX systems, OSX 10.9 (Mavericks) or higher is recommended.

Sentieon® Genomics software requires at least 16GB of memory, although werecommend using 64 GB of memory. The alignment step is typically themost memory consuming stage; you can check section Section 7.2.3 for ways tocontrol the memory used in alignment.

Sentieon® Genomics software processes file data at speeds around20-30MB/s per core using a state of the art server. In order to takeadvantage of the maximum speed that the software can provide, werecommend that you use high-speed SSD hard drives in your system,preferably two identical drives in a high speed RAID 0 striped volumeconfiguration. When using a RAID 0 configuration, it is advised to usethe drives to only store intermediate files, and move out any final resultsor important information out of those hard drives; this way, your server shouldhave additional storage space to store the results.

Sentieon® Genomics software requires that your system have either python2.6.x,python2.7.x, or python3.x. You can check the version of the default python in yoursystem by running:

If neither python2.6.x, python2.7.x, or python3.x is not the default python version in yoursystem, you will need to install it and set an environmental variable totell the software where the python binary is located

1.4. Installation procedure for a Linux Based system¶

In order to install the Sentieon® Genomics software in a Linux basedsystem, you need to follow these installation instructions:

Obtain the software release package. The software release package isnamed sentieon-genomics-202010.03.tar.gz, where 202010.03 is therelease version.
Obtain the license file from Sentieon®. The license file has extension .lic.The Sentieon® license control is based on a lightweight floating license serverprocess running on a node, and serving licenses though TCP. In a HPC cluster,the license server process is typically running in a special non-computing nodeon the cluster periphery that has unrestricted access to the outside world throughHTTPS, and serves the licenses to the rest of the nodes in the cluster by listeningto a specific TCP port that needs to be open within the cluster. The license serverneeds to have external https access to validate the license, while the computingclient nodes do not need to have access to the internet. You need to provideSentieon® with the hostname (FQDN or IP) and port where you plan on deploying thelicense server.
Upload the software release package and license file to your server.
Decompress the release package with the command below. This willcreate a folder named sentieon-genomics-202010.03.

Copy the license file to the directory that stores the license files(LICENSE_DIR). If you are running a license server process, startthe license server.

Set an environment variable in your system to indicate where thelicense is located (either LICSRVR_HOST:LICSRVR_PORT if you areusing a license server or LICENSE_DIR/LICENSE_FILE.lic if you areusing a license file)
We recommend that you add this line to the shell scripts you use torun the Sentieon® software, or to your shell profile:

1.5. Installation procedure for an Apple OSX system¶

In order to install the Sentieon® Genomics software in a Mac OSX basedsystem, you need to follow these installation instructions:

Obtain the software release package. The software release package isnamed mac-sentieon-genomics-202010.03.tar.gz, where 202010.03 is therelease version.
Obtain the license file. The license file has extension .lic.
Upload the software release package and license file to yourcomputer.
Decompress the release package with the command below. This willcreate a folder named mac-sentieon-genomics-202010.03.

Copy the license file to the directory that stores the license files(LICENSE_DIR).
Set the environment variable in your system to indicate where thelicense is located (LICENSE_DIR/LICENSE_FILE.lic). We recommendthat you add these lines to you shell profile ~/.bash_profile:

1.5.1. Using the software on an Apple OSX system¶

When using Sentieon® Genomics software on a laptop using Apple OSX werecommend that you disable the energy saving capabilities of yourcomputer, or temporarily change them while running commands.

To disable the energy saving capabilities of your computer:

Open the system preferences.
Select Energy Saver.
Make sure you check the option to “Prevent computer from sleepingautomatically when display is off”, as shown inFig. 1.1.

Alternatively, you can temporarily disable the energy savingcapabilities of your computer by running the command from a Terminal:

1.6. Useful environmental variables when using the software¶

When using Sentieon® Genomics software there are certain environmental variablesthat may be useful or are required:

SENTIEON_LICENSE: tells the software where the license is located. This variableis required.

SENTIEON_PYTHON: tells the software the location of the python binary. This variableis useful when python2.6.x, python2.7.x, or python3.x is not the default python version in your system.

SENTIEON_TMPDIR: tells the software where to store the intermediate temporary files. Thisvariable is recommended and should point to a fast storage location to prevent the softwarefrom being I/O limited; this is specially important when using a slow NFS storage for input/output.When using this variable, the software will create a unique temporary subfolder in SENTIEON_TMPDIRfor each command, which will reduce contention if multiple commands output to the same folder.

Environmental settings to use jemalloc memory allocation: use the settings bellow to have thesoftware use jemalloc instead of the standard OS memory allocation library. This is recommended in systemswith large memory, or large number of CPUs (more than 32 vCPU). In the code below SENTIEON_INSTALL_DIRpoints to the location of the Sentieon® software package.

1.7. Keywords¶

Bioinformatics, DNA sequencing, Genomics.

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1.1. Description¶

1.2. Benefits and Value¶

1.3. Platform Requirements¶

1.4. Installation procedure for a Linux Based system¶

1.5. Installation procedure for an Apple OSX system¶

1.5.1. Using the software on an Apple OSX system¶

1.6. Useful environmental variables when using the software¶

1.7. Keywords¶

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