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== STEP 1 : Setup GotCloud ==
== STEP 1 : Setup GotCloud ==
=== Step 1c: Setup Environment ===
=== Step 1a: Setup Environment ===
To facilitate running this tutorial, set environment variables:
To facilitate running this tutorial, set environment variables:
* GCHOME to the path to the base directory of your gotcloud instalation
* GCHOME to the path to the base directory of your gotcloud instalation
setenv GCOUT ~/gotcloudTutorial
setenv GCOUT ~/gotcloudTutorial
=== Step 1a: Install GotCloud ===
=== Step 1b: Install GotCloud ===
In order to run this tutorial, you need to make sure you have GotCloud is installed on your system.
In order to run this tutorial, you need to make sure you have GotCloud is installed on your system.
=== Step 1b: Install Example Dataset ===
=== Step 1c: Install Example Dataset ===
Our dataset consists of 60 individuals from GBR sequenced by the 1000 Genomes Project. These individuals have been sequenced to an average depth of about 4x.
Our dataset consists of 60 individuals from GBR sequenced by the 1000 Genomes Project. These individuals have been sequenced to an average depth of about 4x.
== STEP 5 : Run GotCloud Association Analysis Pipeline ==
== STEP 5 : Run GotCloud Association Analysis Pipeline ==
/net/fantasia/home/hmkang/bin/epacts/bin/epacts single --vcf gotcloud/test_data/UMAKE_OUT/vcfs/chr20/chr20.filtered.vcf.gz --ped gotcloud/test_data/gotcloudExample/test.GBR60.ped --out EPACTS_TEST --test q.linear --run -1 --top 1 --chr 20
