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.
 
 
 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
 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.
 
 
 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.
 
 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>
 Store it in Keep.
 
 <pre>


@@ -29,6 +44,8 @@ arv keep put --in-manifest GenomeAnalysisTK-2.6-4.tar.bz2
 
 &darr;
 
 
 &darr;
 

+_Make the itty bitty down arrows bigger, and maybe center them_
+

 <pre>
 c905c8d8443a9c44274d98b7c6cfaa32+94+K@qr1hi
 </pre>
 <pre>
 c905c8d8443a9c44274d98b7c6cfaa32+94+K@qr1hi
 </pre>


@@ -88,6 +105,8 @@ Note the job UUID in the API response.
 
 h3. Monitor job progress
 
 
 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.
 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>
 
   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
 h3. Notes
 
 fn1. Download the GATK tools &rarr; http://www.broadinstitute.org/gatk/download