Arvados

Updated http://doc.arvados.org/user/tutorials/running-external-program.html with more escapes in the bwa read group -- https://cloud.curoverse.com/pipeline_instances/qr1hi-d1hrv-iwjstz139qzrkdq

Notes on #7565:

Step 2 - Creating a Public Key

Define what type if key to generate. SSH-2 RSA is by default. Other options are SSH-1 (RSA) and SSH-2 DSA.

branch 7015-update-user-guide is up for review on c31abb

I went through the entire user guide and either filed bugs on things that didn't work as expected (attached to the this ticket) or fixed the documentation. I'm not sure what else I can do here, its possible I missed some things but I tried to do a thorough read/test of everything.

I made sure the Develop a new pipeline section works as extended as specified in the description. I made one change in note #7 that I think people were running into.

Bryan Cosca wrote:

I went through the entire user guide and either filed bugs on things that didn't work as expected (attached to the this ticket)…

Thanks. I'm going to break these off the ticket so that we can track them through Redmine backlogs, and make sure they get addressed appropriately. I'll add relationships so we remember where they came from, though.

reviewing c31abb2aa1a1e4493ee1f3ed2d63163cf7b4cafb

doc/user/index.html.textile.liquid line 13 has an extra space at the end. delete it before merging.

there changes aren't that big. and LGTM...

I trust that the triple escape "\\\" is OK in doc/_includes/_tutorial_bwa_sortsam_pipeline.liquid:

-                    "@RG\\tID:group_id\\tPL:illumina\\tSM:sample_id",
+                    "@RG\\\tID:group_id\\\tPL:illumina\\\tSM:sample_id",

ready for merge in my opinion