[ARVADOS] updated: a1fc48d0bdba5062da9d8ea57e2cda805421aab8
git at public.curoverse.com
git at public.curoverse.com
Mon Jul 7 13:53:04 EDT 2014
Summary of changes:
.../_show_advanced_cli_example.html.erb | 4 +
.../_show_advanced_curl_example.html.erb | 1 +
.../_show_advanced_python_example.html.erb | 1 +
.../app/views/projects/_index_projects.html.erb | 11 +-
crunch_scripts/arvados-bcbio-nextgen.py | 136 +++++++++++++++++++++
crunch_scripts/run-command | 43 +++++--
doc/api/methods/jobs.html.textile.liquid | 20 +++
doc/install/install-docker.html.textile.liquid | 47 ++++++-
.../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 +-
docker/mkimage-debootstrap.sh | 2 +
sdk/cli/bin/arv-run-pipeline-instance | 16 +--
sdk/cli/bin/crunch-job | 25 ++--
sdk/python/bin/arv-ls | 3 +-
sdk/python/tests/test_arv_put.py | 5 +-
services/api/Gemfile | 2 +-
services/api/Gemfile.lock | 8 +-
.../app/controllers/arvados/v1/links_controller.rb | 26 ++++
services/api/app/models/arvados_model.rb | 19 +++
services/api/app/models/blob.rb | 2 +-
services/api/app/models/job.rb | 18 ++-
services/api/app/models/link.rb | 36 +++---
services/api/app/models/user.rb | 11 ++
services/api/config/routes.rb | 1 +
services/api/lib/load_param.rb | 6 +-
.../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 +-
services/api/test/integration/permissions_test.rb | 89 ++++++++++++++
.../test/integration/serialized_encoding_test.rb | 4 +-
services/api/test/integration/websocket_test.rb | 2 +-
services/api/test/unit/job_test.rb | 89 ++++++++++----
services/api/test/unit/link_test.rb | 4 +
services/api/test/unit/permission_test.rb | 103 ++++++++++++++++
services/keep/src/keep/keep.go | 6 +-
services/keep/src/keep/volume.go | 3 +-
services/keep/src/keep/volume_unix.go | 7 +-
45 files changed, 751 insertions(+), 150 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
via a1fc48d0bdba5062da9d8ea57e2cda805421aab8 (commit)
via 10543be10e5db9721a638d46e40bacc17d7599fe (commit)
via c0cda7d557efe50ab2e817a0bb920e8f1c8f73f7 (commit)
via 4a25da032d4de7452c498b9720ce0e294bd03816 (commit)
via 1875ddb761e4ae2909d2afe0718f3d0ad5f3ce0f (commit)
via c5c5bc06270222f811fa75bc714fa912882ae279 (commit)
via 847459b3c257aba65df3e0cbf6777f7148542af2 (commit)
via e9c0ab574e6bae899556e82d4ba0da439a976093 (commit)
via 280e17d8c95b5488e6cfabb7304c8b95e1102dfb (commit)
via e0f9e708b23c656ae7625438ff76a131da8746eb (commit)
via 6caf9c476d842c59883ca7087182fde2445bd712 (commit)
via 45f70bea3eb3760d5a7572625c63c9d079b1cd77 (commit)
via b7de0ac72fe6e5270d58940f782e630789391f05 (commit)
via 2833e72b9373d50b232d248b04e8154fbdc220ff (commit)
via 69b45719b95e59c3293fd8a6003d72c4d0b9d9c7 (commit)
via c0ccea12dac59b30d3d86977aa70531e7b0126b5 (commit)
via 7dec0933c112ce80f5ccda3e223158b94d5bce4d (commit)
via 338b0f4cd1b7d2ad4b3cca061184fe814617bb8f (commit)
via 1cf15bae4e5236084c338fb557c749533adce679 (commit)
via 66efe78cdf4c28222a0e96ad4d614dce10f344ff (commit)
via ff6dfcb1b9bc2ed25466baffb8cacbf5daf49b57 (commit)
via df7ddbe4c94700abe695d8799b8fc1db1b48d02d (commit)
via 888c00d55b2a8beb463c35d5b91818adbba1609d (commit)
via a4daf2cf097005a45ea7727a3c6e33abba8c39d4 (commit)
via f88096f61cd024b8d072d23f6c51f4d4cc0db451 (commit)
via 0ff12afbbf1eed7673d6a9a724f626643cc78ff0 (commit)
via 3657c576451610bc6e7f269cbf4f13cb18ff35ba (commit)
via ee99af104e445cabbe6a0389b9f3d1ac170ce6d5 (commit)
via ce69b2c94aeb8f897f41fbeaabfed3f3c55495d5 (commit)
via 5759cf04d9a87c1e0cb70ae0785ace15af6ee491 (commit)
via d0284f9f1af01be566d671e875f31b12eeca1960 (commit)
via 5126d94fd644a657243e5ec80d5ef1fc250f8b76 (commit)
via 10071dfd716b0131dfd5cd6d782422beef950f61 (commit)
via 350c01c50d131eaf01f52eb660ed8e63835177d6 (commit)
via c2278f1529e9c6d0488920ec924684208f56e6ee (commit)
via 22060b240f43ee4301032ba395ddd6ce59b4b581 (commit)
via 0b8f1f94be9f49e7a65f5ca84fe563918861be24 (commit)
via 02226bdb54db7b8db0468409f6495b6daf82ad71 (commit)
via c806ef1d33a260fb736ab0268fbe993314256a4a (commit)
via d62d420af90a635da0593fd1e9bc5650b57ba2bd (commit)
via a9980e0967507a3d74a12f93d82f8330c8ce3009 (commit)
via 4a040b5eb8e506a51376582093ad4e4c223450db (commit)
via 42acc196ca8f5908f3cc214d5f715eb1db82c7a8 (commit)
via f4d92dbb53d31a3577f0b52a7b54c92762090cdc (commit)
via ec0278bcf9affbbe9f88c413116f6aaa2713e0f6 (commit)
via 004bbae6c7ddfb8c952270781974591407502279 (commit)
via c0f1da371e57752ac48d314264fdd445a05192cb (commit)
via 9060fbf9984b5e05081931c4c30846fd304ebced (commit)
via f888eee63ff962201154114efae87f3342ec2aa7 (commit)
via f99d19546774d0204249affe0961000043a2ad11 (commit)
via fa3fbd543823400c58d14df2e800a4a447bd3ee0 (commit)
via 5f5ef11b0cfc6f6125e9e5316933156049c43b76 (commit)
via ae7e9e24a464aea23e60b914a527390bff579a7a (commit)
via 4689df784ce9702958361952b80f24076ea92039 (commit)
via 01f05d1fd88b17f88eb671984c8ceab49e6ef3d4 (commit)
via 678f9f5f58048d5d378bdcc5f55a62c9305dcbc6 (commit)
via da4c5f6695602d612b657f209f705d04fae5eb38 (commit)
via f007a9c4cf2a5c32cddf1a5d1fa652b7acb05380 (commit)
via bf688c8ccafa66caaa7694f770e69635f5f89249 (commit)
via 31351d3a55ca31c97a6f098a897a1179caacd701 (commit)
via 945bebae56ec2fb5faef965cbf55fc8309e8df11 (commit)
via 2d7610520e4d1ab289899821bf4d885b77a1e327 (commit)
via 3650b57d77642a75fc7f21d339732c2d39431c39 (commit)
via bbc3324f62acfda616c3ef867331bddcdc4f5114 (commit)
via 97c9b2b49f94735c6d4d5b62b772089ef7e0e3bf (commit)
via 7b23dea6aaf66492ddb0e204cf0eae4b159f2a1c (commit)
via f76bc1b30f5bfc32722d2639e609c12531dc8319 (commit)
via 3cc2c876251849002c1377c4631222c26545508d (commit)
via c56584d3bb97bc8e6652ac0d8cdd6c60b57f18ed (commit)
via 497851073641c8486ece1a0e5066aeca6e51f7a8 (commit)
via 99a349f41ad1cc85865ceb1aa7485ceead70ff54 (commit)
via bcff555f9786f24ded842f1cf45e162f1a744c32 (commit)
via 7f67cf41cb8f834debddc5c2a26abdd72e6278d4 (commit)
via 3369c8fa24b8cb40c9f9da74a1744130e0aea83e (commit)
via 9cb30aa6a84d5b3c7a3ae0d4fc398d64cbd6c306 (commit)
via cb05caebb2978eb19a93e9156aafba71e9aaa82a (commit)
via 2456d3322ba8397401d5033e6509cf0ffc59f98e (commit)
via 6f70a514652050bde05301a4715be8769f213ac6 (commit)
via 975b1912434cdd158abcf2d8b882d90c57c4299e (commit)
from 060faf29bb6c267ad9489ed64afcc04ddc93e974 (commit)
Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.
commit a1fc48d0bdba5062da9d8ea57e2cda805421aab8
Merge: 060faf2 10543be
Author: radhika <radhika at curoverse.com>
Date: Mon Jul 7 13:46:12 2014 -0400
Merge branch 'master' into 2380-ssh-doc
-----------------------------------------------------------------------
hooks/post-receive
--
More information about the arvados-commits
mailing list