[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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