[ARVADOS] updated: 2bd85647821f5cb27034218fcd0efc9de9f7c3a0
git at public.curoverse.com
git at public.curoverse.com
Mon Jul 7 15:07:18 EDT 2014
Summary of changes:
apps/workbench/app/helpers/provenance_helper.rb | 54 ++++----
.../collections/_show_chooser_preview.html.erb | 2 +-
.../app/views/collections/_show_files.html.erb | 2 +
crunch_scripts/arvados-bcbio-nextgen.py | 136 +++++++++++++++++++++
crunch_scripts/run-command | 43 +++++--
.../running-external-program.html.textile.liquid | 2 +-
.../tutorial-firstscript.html.textile.liquid | 2 +-
.../tutorial-new-pipeline.html.textile.liquid | 2 +-
docker/bcbio-nextgen/Dockerfile | 47 +++++++
docker/build_tools/Makefile | 16 ++-
.../{bwa-samtools => java-bwa-samtools}/Dockerfile | 3 +-
docker/jobs/Dockerfile | 6 +-
sdk/cli/bin/arv-run-pipeline-instance | 2 +-
sdk/cli/bin/crunch-job | 25 ++--
services/api/Gemfile | 2 +-
services/api/Gemfile.lock | 6 +-
services/api/app/models/job.rb | 18 ++-
services/api/lib/load_param.rb | 6 +-
services/api/script/crunch-dispatch.rb | 2 +-
.../arvados/v1/commits_controller_test.rb | 4 +-
.../api/test/functional/arvados/v1/git_setup.rb | 27 ----
.../arvados/v1/job_reuse_controller_test.rb | 4 +-
.../functional/arvados/v1/jobs_controller_test.rb | 4 +-
services/api/test/helpers/git_test_helper.rb | 30 +++++
.../api/test/integration/crunch_dispatch_test.rb | 4 +-
.../test/integration/serialized_encoding_test.rb | 4 +-
services/api/test/integration/websocket_test.rb | 2 +-
services/api/test/unit/job_test.rb | 89 ++++++++++----
services/keep/src/keep/keep.go | 4 +-
services/keep/src/keep/volume.go | 3 +-
services/keep/src/keep/volume_unix.go | 7 +-
31 files changed, 415 insertions(+), 143 deletions(-)
create mode 100755 crunch_scripts/arvados-bcbio-nextgen.py
create mode 100644 docker/bcbio-nextgen/Dockerfile
rename docker/{bwa-samtools => java-bwa-samtools}/Dockerfile (90%)
delete mode 100644 services/api/test/functional/arvados/v1/git_setup.rb
create mode 100644 services/api/test/helpers/git_test_helper.rb
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Those revisions listed above that are new to this repository have
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commit 2bd85647821f5cb27034218fcd0efc9de9f7c3a0
Merge: 137c264 5968d7e
Author: radhika <radhika at curoverse.com>
Date: Mon Jul 7 15:00:25 2014 -0400
Merge branch 'master' into 3140-project-content-tabs
commit 137c26497b8bf7454da2e62842e038f69569604b
Merge: 3b7eb34 58c4c90
Author: radhika <radhika at curoverse.com>
Date: Mon Jul 7 14:58:01 2014 -0400
Merge branch 'master' into 3140-project-content-tabs
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