Difference between revisions of "Tutorials"
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==Running Tutorials on Your Computer== | ==Running Tutorials on Your Computer== | ||
| − | + | Starting Fall 2019 we adopt [https://www.docker.com/ docker] to run our course material . We have created various [https://hub.docker.com/u/statisticalgenetics docker repositories] with source material freely available from [https://github.com/statgenetics/statgen-courses github] for users to readily setup and reproduce our tutorials on their own computers. These docker images can also be used as production tool to run relevant software on your computer (Mac, Linux or Windows) for your own data analysis. | |
In this document we will focus on discussing how to set it up and run course tutorials on your computer, using these docker images and optionally a utility script we created to streamline various docker commands. | In this document we will focus on discussing how to set it up and run course tutorials on your computer, using these docker images and optionally a utility script we created to streamline various docker commands. | ||
===Pre-requisites=== | ===Pre-requisites=== | ||
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Software you need to install on your computer are <code>SoS</code> (a workflow system to run our course utility script) and <code>docker</code>. | Software you need to install on your computer are <code>SoS</code> (a workflow system to run our course utility script) and <code>docker</code>. | ||
====Mac and Linux users==== | ====Mac and Linux users==== | ||
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<code>SoS</code> requires Python 3.6+ to run. It is recommended that you install [https://docs.conda.io/en/latest/miniconda.html Miniconda] to run Python 3 if you don't have it already. Once you have Python 3 installed, simply type <code>pip install sos</code> to install <code>SoS</code>, or, check out [https://vatlab.github.io/sos-docs/running.html here for alternative installation methods] if you have troubles with that command. To install <code>docker</code> from command line please follow our instructions [http://statgen.us/lab-wiki/orientation/jupyter-setup.html#install-docker here]. Alternatively Mac users can download docker app for Mac and install from a graphical interface. | <code>SoS</code> requires Python 3.6+ to run. It is recommended that you install [https://docs.conda.io/en/latest/miniconda.html Miniconda] to run Python 3 if you don't have it already. Once you have Python 3 installed, simply type <code>pip install sos</code> to install <code>SoS</code>, or, check out [https://vatlab.github.io/sos-docs/running.html here for alternative installation methods] if you have troubles with that command. To install <code>docker</code> from command line please follow our instructions [http://statgen.us/lab-wiki/orientation/jupyter-setup.html#install-docker here]. Alternatively Mac users can download docker app for Mac and install from a graphical interface. | ||
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you should see some meaningful output. | you should see some meaningful output. | ||
| − | ==== Windows users==== | + | ====Windows users==== |
| − | + | Running these tutorials in Windows is currently not supported. Although in principle these docker images will also work in Windows, this has not yet been tested out and we are unable to provide sure instructions to setting it up. The utility script "statgen-setup" that we provide will certainly need adjustments (though minor) to work with Windows. | |
| − | Running these tutorials in Windows is currently not supported. Although in principle these docker images will also work in Windows, this has not yet been tested out and we are unable to provide sure instructions to setting it up. The utility script "statgen-setup" that we provide will certainly need adjustments (though minor) to work with Windows. | + | |
===Tutorial specific instructions=== | ===Tutorial specific instructions=== | ||
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==Annotation== | ==Annotation== | ||
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation | + | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.docx Functional Annotation Exercise <nowiki>[DOCX]</nowiki>] |
* [[Commands in Annotation Exercise|Exercise Commands]] | * [[Commands in Annotation Exercise|Exercise Commands]] | ||
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==Cochran Armitage Trend Test== | ==Cochran Armitage Trend Test== | ||
| − | * [ | + | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/Armitage_sample_size.pdf CATT Exercise <nowiki>[PDF]</nowiki>] |
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==Gemini== | ==Gemini== | ||
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The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions]. | The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions]. | ||
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==Genehunter== | ==Genehunter== | ||
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==GWAS: Data Quality Control== | ==GWAS: Data Quality Control== | ||
| − | * [ | + | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_data_QC.docx Exercise <nowiki>[PDF]</nowiki>] |
* [[GWAS Data QC Exercise|Exercise Commands]] | * [[GWAS Data QC Exercise|Exercise Commands]] | ||
| − | + | To run the exercise from docker image provided, | |
| − | To | + | |
| + | <pre>statgen-setup login --tutorial plink | ||
| + | </pre> | ||
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| + | The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions]. | ||
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==GWAS: Association Analysis Controlling for Population Substructure== | ==GWAS: Association Analysis Controlling for Population Substructure== | ||
| − | * [ | + | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_Substructure.docx Exercise <nowiki>[PDF]</nowiki>] |
* [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]] | * [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]] | ||
| − | + | To run the exercise from docker image provided, | |
| − | To | + | |
| − | <pre> | + | <pre>statgen-setup login --tutorial plink |
| − | The | + | </pre> |
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| + | The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions]. | ||
==Homozygosity Mapper== | ==Homozygosity Mapper== | ||
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* [http://statgen.us/files/tutorials/Homozygosity_mapping_exercise_part_1.pdf Exercise Part I] | * [http://statgen.us/files/tutorials/Homozygosity_mapping_exercise_part_1.pdf Exercise Part I] | ||
* [http://statgen.us/files/tutorials/Homozygosity_mapping_exercise_part_2.pdf Exercise Part II] | * [http://statgen.us/files/tutorials/Homozygosity_mapping_exercise_part_2.pdf Exercise Part II] | ||
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==IGV== | ==IGV== | ||
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* [https://github.com/statgenetics/statgen-courses/blob/master/handout/IGV.docx IGV exercise <nowiki>[DOCX]</nowiki>] | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/IGV.docx IGV exercise <nowiki>[DOCX]</nowiki>] | ||
* [http://statgen.us/files/igv_exercise.zip Exercise files (VCF and BAM)] | * [http://statgen.us/files/igv_exercise.zip Exercise files (VCF and BAM)] | ||
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The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions]. | The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions]. | ||
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Revision as of 04:00, 25 February 2020
Contents
- 1 Running Tutorials on Your Computer
- 2 Alohomora
- 3 Annotation
- 4 Annovar MEndelian
- 5 Cochran Armitage Trend Test
- 6 Gemini
- 7 Genehunter
- 8 GWAS: Data Quality Control
- 9 GWAS: Association Analysis Controlling for Population Substructure
- 10 Homozygosity Mapper
- 11 IGV
- 12 Linkage/FastLinkage
- 13 Population Genetics
- 14 PSEQ
- 15 Regression
- 16 RV-TDT
- 17 SEQLinkage
- 18 SEQSpark
- 19 SLINK
- 20 SUPERLINK
- 21 Variant Association Tools
Running Tutorials on Your Computer
Starting Fall 2019 we adopt docker to run our course material . We have created various docker repositories with source material freely available from github for users to readily setup and reproduce our tutorials on their own computers. These docker images can also be used as production tool to run relevant software on your computer (Mac, Linux or Windows) for your own data analysis.
In this document we will focus on discussing how to set it up and run course tutorials on your computer, using these docker images and optionally a utility script we created to streamline various docker commands.
Pre-requisites
Software you need to install on your computer are SoS (a workflow system to run our course utility script) and docker.
Mac and Linux users
SoS requires Python 3.6+ to run. It is recommended that you install Miniconda to run Python 3 if you don't have it already. Once you have Python 3 installed, simply type pip install sos to install SoS, or, check out here for alternative installation methods if you have troubles with that command. To install docker from command line please follow our instructions here. Alternatively Mac users can download docker app for Mac and install from a graphical interface.
Finally please download our utility script src/statgen-setup to your PATH and change it to executable, eg, chmod +x ~/bin/statgen-setup if you put it under ~/bin which is part of your PATH. To verify your setup, type:
statgen-setup -h
you should see some meaningful output.
Windows users
Running these tutorials in Windows is currently not supported. Although in principle these docker images will also work in Windows, this has not yet been tested out and we are unable to provide sure instructions to setting it up. The utility script "statgen-setup" that we provide will certainly need adjustments (though minor) to work with Windows.
Tutorial specific instructions
Material and instructions for specific exercise are listed in each section below (only those using statgen-setup command are relevant to our docker based tutorials). They provide links to materials and a minimal set of commands to use for launching and running an exercise. For advanced options and other features provided by our utility script please read here our complete documentation to the utility script.
Alohomora
Annotation
To run the exercise from docker image provided,
statgen-setup login --tutorial annovar
The "statgen-setup" script is available here and can be installed following these instructions.
Annovar MEndelian
Cochran Armitage Trend Test
Gemini
To run the exercise from docker image provided,
statgen-setup login --tutorial gemini
The "statgen-setup" script is available here and can be installed following these instructions.
Genehunter
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install genehunter-tutorial
The exercise's files will then be installed in the folder /home/shared/genehunter. You can run from there or copy the files into your user's home directory and proceed with the exercise.
GWAS: Data Quality Control
To run the exercise from docker image provided,
statgen-setup login --tutorial plink
The "statgen-setup" script is available here and can be installed following these instructions.
GWAS: Association Analysis Controlling for Population Substructure
To run the exercise from docker image provided,
statgen-setup login --tutorial plink
The "statgen-setup" script is available here and can be installed following these instructions.
Homozygosity Mapper
IGV
To run the exercise from docker image provided,
statgen-setup login --tutorial igv
The "statgen-setup" script is available here and can be installed following these instructions.
Linkage/FastLinkage
To run the exercise from docker image provided,
statgen-setup login --tutorial mlink
The "statgen-setup" script is available here and can be installed following these instructions.
Population Genetics
To run the exercise from docker image provided,
statgen-setup login --tutorial popgen
The "statgen-setup" script is available here and can be installed following these instructions.
PSEQ
To run the exercise from docker image provided,
statgen-setup login --tutorial pseq
The "statgen-setup" script is available here and can be installed following these instructions.
Regression
To run the exercise from docker image provided,
statgen-setup login --tutorial regression
The "statgen-setup" script is available here and can be installed following these instructions.
RV-TDT
Installing Packages
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install rvtdt-tutorial
The exercise's files will then be installed in the folder /home/shared/rvtdt. You can run from there or copy the files into your user's home directory and proceed with the exercise.
SEQLinkage
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install seqlinkage-tutorial
The exercise's files will then be installed in the folder /home/shared/seqlinkage. You can run from there or copy the files into your user's home directory and proceed with the exercise.
SEQSpark
Installing Packages
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install seqspark-tutorial
The exercise's files will then be installed in the folder /home/shared/seqspark. You can run from there or copy the files into your user's home directory and proceed with the exercise.In order for the commands to work correctly, you don't need to reboot, but you should log out and log back in to make sure that the computer's environment is correctly configured.
SLINK
To run the exercise from docker image provided,
statgen-setup login --tutorial slink
The "statgen-setup" script is available here and can be installed following these instructions.
SUPERLINK
Variant Association Tools
To run the exercise from docker image provided,
statgen-setup login --tutorial vat
The "statgen-setup" script is available here and can be installed following these instructions.
