* Fixed links

[arvados.git] / doc / user / tutorials / tutorial-gatk-variantfiltration.textile

diff --git a/doc/user/tutorials/tutorial-gatk-variantfiltration.textile b/doc/user/tutorials/tutorial-gatk-variantfiltration.textile
index 5083d7470b2b787bef39453dcda7fd0f79683061..06ca3fb18b19be39f8e2a4e9efbcb18f4788e8ab 100644 (file)
--- a/doc/user/tutorials/tutorial-gatk-variantfiltration.textile
+++ b/doc/user/tutorials/tutorial-gatk-variantfiltration.textile
@@ -9,18 +9,12 @@ h1. Tutorial: GATK VariantFiltration
 
 Here you will use the GATK VariantFiltration program to assign pass/fail scores to variants in a VCF file.
 
+*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.basedoc}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.basedoc}}/user/getting_started/check-environment.html*
+
 <!-- _This should be motivated better using a specific biomedical research or diagnostic question that involves this analysis_ -->
 
 <!-- From conversation with Ward:  We should link to a discussion of the personal genome project and explain that it a freely available dataset that any researcher can use, which makes it appropriate to be used in these examples._ -->
 
-h3. Prerequisites
-
-* Log in to a VM "using SSH":ssh-access.html
-* Put an "API token":api-tokens.html in your @ARVADOS_API_TOKEN@ environment variable
-* Put the API host name in your @ARVADOS_API_HOST@ environment variable
-
-If everything is set up correctly, the command @arv -h user current@ will display your account information.
-
 h3. Get the GATK binary distribution.
 
 <!-- _Perhaps separate out this and the next sections and link to it so the user only