Notes on new user documentation

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

diff --git a/doc/user/tutorial-gatk-variantfiltration.textile b/doc/user/tutorial-gatk-variantfiltration.textile
index 39ed4973f6ac4bb33e8333eb114b1d1f73624f0e..0a5a9a4e5e45c3a49ec09aa0009e35a84081a031 100644 (file)
--- a/doc/user/tutorial-gatk-variantfiltration.textile
+++ b/doc/user/tutorial-gatk-variantfiltration.textile
@@ -9,6 +9,13 @@ h1. Tutorial: GATK VariantFiltration
 
 Here you will use the GATK VariantFiltration program to assign pass/fail scores to variants in a VCF file.
 
+_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
@@ -19,8 +26,16 @@ If everything is set up correctly, the command @arv -h user current@ will displa
 
 h3. Get the GATK binary distribution.
 
+_Perhaps separate out this and the next sections and link to it so the user only
+has to do this if they really don't have GATK installed.  Also provide
+a way to determine if they do have it._
+
 Download the GATK binary tarball[1] -- e.g., @GenomeAnalysisTK-2.6-4.tar.bz2@ -- and copy it to your Arvados VM.
 
+_Is it necessary to copy it to the Arvados VM first, you could put it into
+keep from your desktop and/or use the workbench?  Also if we are
+telling them to copy it to the VM, maybe we should mention scp?_
+
 Store it in Keep.
 
 <pre>
@@ -29,6 +44,8 @@ arv keep put --in-manifest GenomeAnalysisTK-2.6-4.tar.bz2
 
 &darr;
 
+_Make the itty bitty down arrows bigger, and maybe center them_
+
 <pre>
 c905c8d8443a9c44274d98b7c6cfaa32+94+K@qr1hi
 </pre>
@@ -88,6 +105,8 @@ Note the job UUID in the API response.
 
 h3. Monitor job progress
 
+_This was already covered in tutorial1_
+
 There are three ways to monitor job progress:
 
 # Go to Workbench, drop down the Compute menu, and click Jobs. The job you submitted should appear at the top of the list. Hit "Refresh" until it finishes.
@@ -99,6 +118,9 @@ curl -s -H "Authorization: OAuth2 $ARVADOS_API_TOKEN" \
   https://{{ site.arvados_api_host }}/arvados/v1/jobs/JOB_UUID_HERE/log_tail_follow
 </pre>
 
+
+_That's it?  Say something about the output we're going to get_
+
 h3. Notes
 
 fn1. Download the GATK tools &rarr; http://www.broadinstitute.org/gatk/download