bh20-seq-resource/bh20sequploader, branch upload-download-status Tool to upload SARS-CoV-2 sequences to BH20 Arvados instance and orchestrate analysis http://git.systemreboot.net/bh20-seq-resource/atom?h=upload-download-status 2020-07-08T21:10:10+00:00 Give uploader an option to trust local validation (for batch imports) 2020-07-08T21:10:10+00:00 Peter Amstutz 2020-07-08T21:10:10+00:00 urn:sha1:e821857e7a9403739f321feb7418d33d6bd8b2c7 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Uploader checks for duplicates 2020-07-08T20:52:48+00:00 Peter Amstutz 2020-07-08T20:51:14+00:00 urn:sha1:bfcebbd349687ebe2d1d47185db9fda38803b674 Avoid redundant loading of schema 2020-07-08T20:18:51+00:00 Peter Amstutz 2020-07-08T20:17:09+00:00 urn:sha1:ae8991618927f81343038f235c3e3f76932f80ea Hack in a valid-uri check 2020-07-08T19:48:44+00:00 Peter Amstutz 2020-07-08T19:48:44+00:00 urn:sha1:46e28c1d5da1c242fe49e5e5d6fdcae7dc544070 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> minimap2 returns nothing when there is no alignment. 2020-07-07T20:41:11+00:00 Peter Amstutz 2020-07-07T20:41:11+00:00 urn:sha1:54e0ce85ef3abafb8870ef5a9244a03f16b5e3f5 Use minimap2 instead of clustalw for fasta QC 2020-07-07T19:55:06+00:00 Peter Amstutz 2020-07-07T19:52:46+00:00 urn:sha1:7cf561c1b92a44d488d36dd3d883750b261c6550 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Add bh20-seq-analyzer --print-status 2020-07-05T21:33:26+00:00 Peter Amstutz 2020-07-05T21:33:26+00:00 urn:sha1:4f30e506055acb788a1ff1bbcb6359c4413a4eab Get status from new property "status: validated/rejected" Also store QC fail error message. Add --skip-qc for faster batch import 2020-07-03T21:15:48+00:00 Peter Amstutz 2020-07-03T21:15:48+00:00 urn:sha1:38340e0cedb465cd592ac40b11c9d22c75973fed Adding --skip-qc 2020-07-03T21:08:25+00:00 Peter Amstutz 2020-07-03T21:08:25+00:00 urn:sha1:04df498f5cd85015afce79e1e87a3979e596dcc6 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Fix qc_fasta bug closing stream. 2020-07-03T20:55:16+00:00 Peter Amstutz 2020-07-03T20:55:16+00:00 urn:sha1:c50e611f7be281a3b7955254be097c01e6461c20