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| | | |
| We will use 3 different directories for this tutorial: | | We will use 3 different directories for this tutorial: |
− | # path to the directory where gotcloud is installed, default ~/gotcloud/ | + | # path to the directory where gotcloud is installed, default ~/gotcloud-latest/ |
| # path to the directory where the example data is installed, default ~/gotcloudExample | | # path to the directory where the example data is installed, default ~/gotcloudExample |
| # path to your output directory, default ~/gotcloudTutorialOut/ | | # path to your output directory, default ~/gotcloudTutorialOut/ |
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| | | |
| Otherwise, you can install it in your own directory: | | Otherwise, you can install it in your own directory: |
− | # Change to the directory where you want gotcloud/ installed | + | # Change to the directory where you want gotcloud-latest/ installed |
− | # Download the gotcloud tar from the ftp site. | + | # Download the gotcloud tar. |
| # Extract the tar | | # Extract the tar |
| # Build (compile) the source | | # Build (compile) the source |
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| cd ~ | | cd ~ |
| wget https://github.com/statgen/gotcloud/archive/latest.tar.gz # Download | | wget https://github.com/statgen/gotcloud/archive/latest.tar.gz # Download |
− | tar xf latest.tgz # Extracts into gotcloud/ | + | tar xf latest.tar.gz # Extracts into gotcloud-latest/ |
| cd gotcloud-latest/src; make # Build source | | cd gotcloud-latest/src; make # Build source |
| | | |
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| Run the variant calling pipeline: | | Run the variant calling pipeline: |
| cd ~ | | cd ~ |
− | gotcloud/gotcloud snpcall --conf gotcloudExample/[[GBR60vc.conf]] --outdir gotcloudTutorialOut --numjobs 2 --region 20:42900000-43200000 --baseprefix gotcloudExample | + | gotcloud-latest/gotcloud snpcall --conf gotcloudExample/[[GBR60vc.conf]] --outdir gotcloudTutorialOut --numjobs 2 --region 20:42900000-43200000 --baseprefix gotcloudExample |
| | | |
| Upon successful completion of the variant calling pipeline (about 2-4 minutes), you will see the following message: | | Upon successful completion of the variant calling pipeline (about 2-4 minutes), you will see the following message: |
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| Run the LD-aware genotype refinement pipeline: | | Run the LD-aware genotype refinement pipeline: |
| cd ~ | | cd ~ |
− | gotcloud/gotcloud ldrefine --conf gotcloudExample/[[GBR60vc.conf]] --outdir gotcloudTutorialOut --numjobs 2 --baseprefix gotcloudExample | + | gotcloud-latest/gotcloud ldrefine --conf gotcloudExample/[[GBR60vc.conf]] --outdir gotcloudTutorialOut --numjobs 2 --baseprefix gotcloudExample |
| | | |
| Upon successful completion of this pipeline (about 3-10 minutes), you will see the following message: | | Upon successful completion of this pipeline (about 3-10 minutes), you will see the following message: |