Merge branch 'origin-3609-arv-run' into master closes #3609

Conflicts:
	sdk/cli/bin/arv

diff --combined doc/_config.yml
index aa64748bb234c581a191c382179e20a5790a3321,b03a18dff549dbdcbc8ab75d74cfba6a2ce6e959..0b1645fc0c7ab9bdc489a78e5cc390d73a750d98
--- 1/doc/_config.yml
--- 2/doc/_config.yml
+++ b/doc/_config.yml
@@@ -32,6 -32,7 +32,7 @@@ navbar
        - user/topics/keep.html.textile.liquid
      - Run a pipeline on the command line:
        - user/topics/running-pipeline-command-line.html.textile.liquid
+       - user/topics/arv-run.html.textile.liquid
        - user/reference/sdk-cli.html.textile.liquid
      - Develop a new pipeline:
        - user/tutorials/intro-crunch.html.textile.liquid
@@@ -39,10 -40,7 +40,10 @@@
        - user/tutorials/tutorial-firstscript.html.textile.liquid
        - user/tutorials/tutorial-submit-job.html.textile.liquid
        - user/topics/tutorial-parallel.html.textile.liquid
 +      - user/topics/arv-docker.html.textile.liquid
 +    - Reference:
        - user/topics/run-command.html.textile.liquid
 +      - user/reference/job-pipeline-ref.html.textile.liquid
        - user/examples/crunch-examples.html.textile.liquid
      - Query the metadata database:
        - user/topics/tutorial-trait-search.html.textile.liquid
@@@ -128,16 -126,9 +129,16 @@@
      - Docker:
        - install/install-docker.html.textile.liquid
      - Manual installation:
 -      - install/install-keep.html.textile.liquid
 -      - install/install-sso.html.textile.liquid
 +      - install/install-manual-overview.html.textile.liquid
 +      - install/install-manual-prerequisites.html.textile.liquid
        - install/install-api-server.html.textile.liquid
        - install/install-workbench-app.html.textile.liquid
 +      - install/install-shell-server.html.textile.liquid
        - install/create-standard-objects.html.textile.liquid
 +      - install/install-keepstore.html.textile.liquid
 +      - install/install-keepproxy.html.textile.liquid
        - install/install-crunch-dispatch.html.textile.liquid
 +      - install/install-compute-node.html.textile.liquid
 +    - Software prerequisites:
 +      - install/install-manual-prerequisites-ruby.html.textile.liquid
 +      - install/install-sso.html.textile.liquid

diff --combined sdk/cli/bin/arv
index 35de7c629ff67ff993676057a603ea8119bf1825,6f56a089b6a82e4cacf7a4008a04b69456bb1cc5..77affe909384cbefd6e5ea5dc0cae02cf252f5e3
--- 1/sdk/cli/bin/arv
--- 2/sdk/cli/bin/arv
+++ b/sdk/cli/bin/arv
@@@ -113,7 -113,7 +113,8 @@@ def init_confi
    end
  end
  
- subcommands = %w(copy create edit keep pipeline tag ws)
 -subcommands = %w(create edit keep pipeline run tag ws)
++
++subcommands = %w(copy create edit keep pipeline run tag ws)
  
  def check_subcommands client, arvados, subcommand, global_opts, remaining_opts
    case subcommand
@@@ -121,8 -121,6 +122,8 @@@
      arv_create client, arvados, global_opts, remaining_opts
    when 'edit'
      arv_edit client, arvados, global_opts, remaining_opts
 +  when 'copy', 'tag', 'ws'
 +    exec `which arv-#{subcommand}`.strip, *remaining_opts
    when 'keep'
      @sub = remaining_opts.shift
      if ['get', 'put', 'ls', 'normalize'].index @sub then
@@@ -149,6 -147,12 +150,12 @@@
        puts "Available methods: run"
      end
      abort
+   when 'run'
+     exec `which arv-run`.strip, *remaining_opts
+   when 'tag'
+     exec `which arv-tag`.strip, *remaining_opts
+   when 'ws'
+     exec `which arv-ws`.strip, *remaining_opts
    end
  end
  
@@@ -300,7 -304,7 +307,7 @@@ def arv_edit client, arvados, global_op
        begin
          result = client.execute(:api_method => eval(api_method),
                                  :parameters => {"uuid" => uuid},
 -                                :body => { rsc.singularize => dumped },
 +                                :body_object => { rsc.singularize => dumped },
                                  :authenticated => false,
                                  :headers => {
                                    authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
@@@ -671,7 -675,7 +678,7 @@@ whe
  else
    result = client.execute(:api_method => eval(api_method),
                            :parameters => request_parameters,
 -                          :body => request_body,
 +                          :body_object => request_body,
                            :authenticated => false,
                            :headers => {
                              authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']