bh20-seq-resource/workflows/pangenome-generate, branch analysis-refactor Tool to upload SARS-CoV-2 sequences to BH20 Arvados instance and orchestrate analysis http://git.systemreboot.net/bh20-seq-resource/atom?h=analysis-refactor 2020-06-18T16:08:27+00:00 removed double sorting 2020-06-18T16:08:27+00:00 Andrea Guarracino 2020-06-18T16:08:27+00:00 urn:sha1:bbc563d1d6d45bcaa15d054f872bb3a448c94734 The -s argument in odgi build do the same thing that odgi sort -p s does. Can have list of sequence labels to exclude from combined fasta 2020-05-26T22:12:23+00:00 Peter Amstutz 2020-05-26T21:30:30+00:00 urn:sha1:7a96d0b1b15ab28fe3a618db35364891ab5d0328 refs #68 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Workflow fixes 2020-05-14T20:47:08+00:00 Peter Amstutz 2020-05-14T20:47:08+00:00 urn:sha1:a259ff7f26458c0810741508df39a4b391ff18d4 Merge pull request #49 from mr-c/add_pangenome_browser_prep 2020-05-11T14:38:15+00:00 Peter Amstutz 2020-05-11T14:38:15+00:00 urn:sha1:55bab826fda6c6bc3190476f8e2c61e51ef092d6 add pangenome browser prep preserve the directory layout of segmentation.py 2020-05-05T16:24:56+00:00 Michael R. Crusoe 2020-05-05T16:24:56+00:00 urn:sha1:ca7df27a6349e7b7009e1d1d5fec372106a072b1 move some tools into the shared repo 2020-05-05T11:11:02+00:00 Michael R. Crusoe 2020-05-05T11:11:02+00:00 urn:sha1:6599feb6a6f8b488bd2d12fcf532c3b8a917a17f bump jerven/spodgi image to 0.0.6 2020-05-04T17:39:45+00:00 Peter Amstutz 2020-05-04T17:39:45+00:00 urn:sha1:84744602734d84972c9220c08afbde1675de6866 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> add pangenome browser prep 2020-05-04T16:37:52+00:00 Michael R. Crusoe 2020-05-04T16:37:52+00:00 urn:sha1:4618a271193fa5cd5cb1e10d6f8acee9c6e8132a Increase RAM for minimap2 2020-05-04T15:45:44+00:00 Peter Amstutz 2020-05-04T13:09:46+00:00 urn:sha1:7ae370273020132e7d8bfe7e07591264d6a47960 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Set a RAM requirement on odgi_to_rdf to influence it to run on c5 2020-05-03T18:57:35+00:00 Peter Amstutz 2020-05-03T18:57:35+00:00 urn:sha1:dc6bdac06d06020fa0cb1cc5021e2136c3950a09 (because on a t3 it takes forever) Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>