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Jump to navigationJump to search→STEP 2 : Run GotCloud Alignment Pipeline
Run the alignment pipeline (the example aligns 2 samples) :
Run the alignment pipeline (the example aligns 2 samples) :
cd ~
cd ~
gotcloud/gotcloud align --conf gotcloudExample/[[#Alignment Configuration File|GBR2align.conf]] --outdir [[#Alignment Output Directory|gotcloudTutorialOut]] --baseprefix gotcloudExample
gotcloud-latest/gotcloud align --conf gotcloudExample/[[#Alignment Configuration File|GBR2align.conf]] --outdir [[#Alignment Output Directory|gotcloudTutorialOut]] --baseprefix gotcloudExample
Upon successful completion of the alignment pipeline (about 1-3 minutes), you will see the following message:
Upon successful completion of the alignment pipeline (about 1-3 minutes), you will see the following message:
