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Please work through the tutorial and add your comments on the bottom of this page. Or send comments per email to upendra@cyverseto support@cyverse.org. Thank you. 

Part 1: Connect to an instance of an Atmosphere Image (Virtual Machine)

Step 1. Go to https://atmo.iplantcollaborativecyverse.org and log in with your CyVerse credentials.

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Step 2. Create a new project (faststructure) and add some description after log-in.

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Step 3. Click on the Launch New Instance button and search for fastStructure-1.0 image.

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Step 3. Select the image fastStructure and click 4. Click Launch Instance. It will take 102-15 5 minutes for the cloud instance to be launched. 

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Note: Instances can be configured for different amounts of CPU, memory, and storage depending on user needs.  This tutorial can be accomplished with the small medium1 instance size, medium1 (4 CPUs, 8 GB memory, 80 GB root)  

Part 2: Set up a fastStructure run using the Terminal window

Step 1.

• Open the Terminal on mac.  Add the ssh details along with your IP address to connect the instance through the terminal

$ ssh <username>@Ipaddress

• Using or using webshell

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Step 2. Get oriented. 

1. You will find fastStructure software in "/opt" folder. All the dependencies for running fastStructure are located in "/opt/fastStructure" but you need to change the permissions before using it 

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$ ls /opt/fastStructure-1.0/test

testdata.bed  testoutput_logistic.3.log    testoutput_logistic.3.varP  testoutput_simple.3.meanP  testoutput_simple.3.varQ
testdata.bim  testoutput_logistic.3.meanP  testoutput_logistic.3.varQ  testoutput_simple.3.meanQ
testdata.fam  testoutput_logistic.3.meanQ  testoutput_simple.3.log     testoutput_simple.3.varP

The testdata.bed file (with corresponding test.fam and test.bim) contains genotypes sampled for 200 individuals at 500 SNP loci. There are also other testdata outpuut files. Let's copy the files

$ cd ~
$ cp -R /opt/fastStructure-1.0/test .
$ rm test/*output*
$ ls test
testdata.bed  testdata.bim  testdata.fam

Step 4. Set up a fastStructure test run.  Executing  Executing the code with the provided test data should generate a log file identical to the ones in test/, as a first check that the source code has been downloaded and compiled correctly. The algorithm scales linearly with number of samples, number of loci and value of K; the expected runtime for a new dataset can be computed from the runtime in the above log file.

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$ python /opt/fastStructure-1.0/structure.py -K 2 --input=test/testdata --output=test/testoutput_simple --full --seed=100
$ python /opt/fastStructure-1.0/structure.py -K 3 --input=test/testdata --output=test/testoutput_simple --full --seed=100
$ python /opt/fastStructure-1.0/structure.py -K 4 --input=test/testdata --output=test/testoutput_simple --full --seed=100

$ ls test
testdata.bed             testoutput_simple.2.meanP  testoutput_simple.3.log    testoutput_simple.3.varQ   testoutput_simple.4.varP
testdata.bim             testoutput_simple.2.meanQ  testoutput_simple.3.meanP  testoutput_simple.4.log    testoutput_simple.4.varQ
testdata.fam             testoutput_simple.2.varP   testoutput_simple.3.meanQ  testoutput_simple.4.meanP
testoutput_simple.2.log  testoutput_simple.2.varQ   testoutput_simple.3.varP   testoutput_simple.4.meanQ

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$ python /opt/fastStructure-1.0/distruct.py -K 2 --input=test/testoutput_simple --output=test/testoutput_simple_distruct_K2.pdf
$ python /opt/fastStructure-1.0/distruct.py -K 3 --input=test/testoutput_simple --output=test/testoutput_simple_distruct_K3.pdf
$ python /opt/fastStructure-1.0/distruct.py -K 4 --input=test/testoutput_simple --output=test/testoutput_simple_distruct_K4.pdf

$ ls
testdata.bed               testoutput_simple.2.varP   testoutput_simple.3.varQ   testoutput_simple_distruct_K2.pdf
testdata.bim               testoutput_simple.2.varQ   testoutput_simple.4.log    testoutput_simple_distruct_K3.pdf
testdata.fam               testoutput_simple.3.log    testoutput_simple.4.meanP  testoutput_simple_distruct_K4.pdf
testoutput_simple.2.log    testoutput_simple.3.meanP  testoutput_simple.4.meanQ
testoutput_simple.2.meanP  testoutput_simple.3.meanQ  testoutput_simple.4.varP
testoutput_simple.2.meanQ  testoutput_simple.3.varP   testoutput_simple.4.varQ

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Step 7. Downloading the files using cyberduck.

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