[ARVADOS] updated: 1.3.0-3013-ga7631a1cc

Git user git at public.arvados.org
Tue Aug 25 18:45:45 UTC 2020


Summary of changes:
 build/run-tests.sh                                 |   2 +-
 doc/_config.yml                                    |  28 +--
 doc/_includes/_0_filter_py.liquid                  |  35 ----
 doc/_includes/_alert-incomplete.liquid             |  11 --
 doc/_includes/_alert_stub.liquid                   |  11 --
 doc/_includes/_arv_copy_expectations.liquid        |  12 --
 doc/_includes/_concurrent_hash_script_py.liquid    |  88 ---------
 doc/_includes/_crunch1only_begin.liquid            |   8 -
 doc/_includes/_example_docker.liquid               |  34 ----
 doc/_includes/_install_compute_docker.liquid       |   2 +-
 doc/_includes/_install_git.liquid                  |   9 -
 doc/_includes/_install_rails_reconfigure.liquid    |  17 --
 doc/_includes/_install_ruby_and_bundler_sso.liquid |  69 -------
 doc/_includes/_install_runit.liquid                |  19 --
 doc/_includes/_pipeline_deprecation_notice.liquid  |   9 -
 doc/_includes/_run_command_foreach_example.liquid  |  46 -----
 doc/_includes/_run_command_simple_example.liquid   |  43 -----
 doc/_includes/_run_md5sum_py.liquid                |  24 ---
 doc/_includes/_ssh_addkey.liquid                   |   6 +-
 .../_tutorial_bwa_sortsam_pipeline.liquid          |  78 --------
 doc/_includes/_tutorial_cluster_name.liquid        |   9 -
 doc/_includes/_tutorial_expectations.liquid        |   2 +-
 doc/_includes/_tutorial_hash_script_py.liquid      |  50 -----
 ...1only_end.liquid => _tutorial_hello_cwl.liquid} |   8 +-
 doc/_includes/_tutorial_submit_job.liquid          |  25 ---
 doc/_includes/_what_is_cwl.liquid                  |   2 +-
 doc/architecture/federation.html.textile.liquid    |   2 +-
 .../pipeline_templates/gatk-exome-fq-snp.json      | 175 -----------------
 doc/examples/pipeline_templates/rtg-fq-snp.json    |  76 --------
 doc/examples/ruby/list-active-nodes.rb             |  16 --
 ...opy_pipeline_from_curoverse.html.textile.liquid |  68 -------
 doc/sdk/java-v2/example.html.textile.liquid        |   2 +-
 doc/sdk/python/cookbook.html.textile.liquid        |  24 +--
 doc/sdk/python/events.html.textile.liquid          |   2 +-
 doc/sdk/ruby/example.html.textile.liquid           |   2 +-
 .../firstpipeline.html.textile.liquid              |  94 ---------
 .../getting_started/nextsteps.html.textile.liquid  |  12 --
 .../publicproject.html.textile.liquid              | 133 -------------
 .../getting_started/sharedata.html.textile.liquid  | 102 ----------
 doc/start/index.html.textile.liquid                | 133 -------------
 doc/user/cwl/bwa-mem/bwa-mem-input-mixed.yml       |   6 +-
 doc/user/cwl/bwa-mem/bwa-mem-input-uuids.yml       |   6 +-
 doc/user/cwl/bwa-mem/bwa-mem.cwl                   |   6 +-
 doc/user/cwl/cwl-run-options.html.textile.liquid   |  24 +--
 doc/user/cwl/cwl-runner.html.textile.liquid        | 190 ++++++++++++------
 doc/user/cwl/cwl-style.html.textile.liquid         |   2 +-
 doc/user/cwl/cwl-versions.html.textile.liquid      |   4 +-
 .../check-environment.html.textile.liquid          |  10 +-
 .../ssh-access-unix.html.textile.liquid            |  22 ++-
 .../ssh-access-windows.html.textile.liquid         |  14 +-
 .../vm-login-with-webshell.html.textile.liquid     |   4 +
 .../getting_started/workbench.html.textile.liquid  |  12 +-
 doc/user/index.html.textile.liquid                 |   2 +-
 doc/user/topics/arv-copy.html.textile.liquid       |  91 +++------
 doc/user/topics/arv-docker.html.textile.liquid     | 155 +++++----------
 doc/user/topics/keep.html.textile.liquid           |   2 +-
 ...rial-gatk-variantfiltration.html.textile.liquid | 173 -----------------
 doc/user/topics/tutorial-job1.html.textile.liquid  | 214 ---------------------
 .../add-new-repository.html.textile.liquid         |   2 +-
 .../git-arvados-guide.html.textile.liquid          |  36 +---
 ...l-keep-collection-lifecycle.html.textile.liquid |  44 +++--
 .../tutorial-keep-get.html.textile.liquid          |  93 ++++-----
 ...torial-keep-mount-gnu-linux.html.textile.liquid |  21 +-
 .../tutorial-keep-mount-os-x.html.textile.liquid   |  10 +-
 ...tutorial-keep-mount-windows.html.textile.liquid |   4 +-
 .../tutorials/tutorial-keep.html.textile.liquid    |  61 +++---
 ...tutorial-workflow-workbench.html.textile.liquid |  16 +-
 .../writing-cwl-workflow.html.textile.liquid       | 120 +-----------
 lib/config/config.default.yml                      |   2 +-
 lib/config/generated_config.go                     |   2 +-
 tools/copy-tutorial/copy-tutorial.sh               |  25 +++
 71 files changed, 507 insertions(+), 2354 deletions(-)
 delete mode 100644 doc/_includes/_0_filter_py.liquid
 delete mode 100644 doc/_includes/_alert-incomplete.liquid
 delete mode 100644 doc/_includes/_alert_stub.liquid
 delete mode 100644 doc/_includes/_arv_copy_expectations.liquid
 delete mode 100644 doc/_includes/_concurrent_hash_script_py.liquid
 delete mode 100644 doc/_includes/_crunch1only_begin.liquid
 delete mode 100644 doc/_includes/_example_docker.liquid
 delete mode 100644 doc/_includes/_install_git.liquid
 delete mode 100644 doc/_includes/_install_rails_reconfigure.liquid
 delete mode 100644 doc/_includes/_install_ruby_and_bundler_sso.liquid
 delete mode 100644 doc/_includes/_install_runit.liquid
 delete mode 100644 doc/_includes/_pipeline_deprecation_notice.liquid
 delete mode 100644 doc/_includes/_run_command_foreach_example.liquid
 delete mode 100644 doc/_includes/_run_command_simple_example.liquid
 delete mode 100644 doc/_includes/_run_md5sum_py.liquid
 delete mode 100644 doc/_includes/_tutorial_bwa_sortsam_pipeline.liquid
 delete mode 100644 doc/_includes/_tutorial_cluster_name.liquid
 delete mode 100644 doc/_includes/_tutorial_hash_script_py.liquid
 rename doc/_includes/{_crunch1only_end.liquid => _tutorial_hello_cwl.liquid} (50%)
 delete mode 100644 doc/_includes/_tutorial_submit_job.liquid
 delete mode 100644 doc/examples/pipeline_templates/gatk-exome-fq-snp.json
 delete mode 100644 doc/examples/pipeline_templates/rtg-fq-snp.json
 delete mode 100755 doc/examples/ruby/list-active-nodes.rb
 delete mode 100644 doc/install/copy_pipeline_from_curoverse.html.textile.liquid
 delete mode 100644 doc/start/getting_started/firstpipeline.html.textile.liquid
 delete mode 100644 doc/start/getting_started/nextsteps.html.textile.liquid
 delete mode 100644 doc/start/getting_started/publicproject.html.textile.liquid
 delete mode 100644 doc/start/getting_started/sharedata.html.textile.liquid
 delete mode 100644 doc/start/index.html.textile.liquid
 delete mode 100644 doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
 delete mode 100644 doc/user/topics/tutorial-job1.html.textile.liquid
 create mode 100755 tools/copy-tutorial/copy-tutorial.sh

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commit a7631a1ccb6e2a6925d00a06562e171c4ce4ea2f
Merge: bd8bdd900 8a41cc44e
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Tue Aug 25 14:45:29 2020 -0400

    Merge branch '15964-fix-docs' refs #15964
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>


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