Move /scripts/genomes from single_cell_portal to scp-ingest-pipeline (SCP-2470) #102
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…e into ew-move-genomes
eweitz
requested review from
bistline,
devonbush,
jlchang and
knapii-developments
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@@ Coverage Diff @@
## master #102 +/- ##
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- Coverage 75.27% 50.56% -24.71%
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Files 13 20 +7
Lines 1662 2474 +812
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Hits 1251 1251
- Misses 411 1223 +812
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bistline
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Just a question about the HSTlib dependencies - will you add something about that to the README?
| """ | ||
| # Example: | ||
| # $ sort -k1,1 -k4,4n gencode.vM17.annotation.gtf > gencode.vM17.annotation.possorted.gtf | ||
| # $ bgzip gencode.vM17.annotation.possorted.gtf |
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I have the same comment here that I had in https://github.com/broadinstitute/single_cell_portal/pull/99/files#r434173376. You mentioned a README update in this repo to address it?
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This was referenced Jun 8, 2020
jlchang
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devonbush
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This copies code from
single_cell_portalto Ingest Pipeline. Code for generating species and genome reference data has been moved from/scripts/genomesthere to a new directory here,/ingest/genomes. Andmake_toy_data.pyhas been copied to/ingesthere.The genome pipeline in
/ingest/genomeshere will need to be updated to fix an igv.js issue. That pipeline isn't intended for technical end-users, so it doesn't fit insingle_cell_portal, and having that andmake_toy_data.pyhere simplifies dependency management formake_toy_data.py. More background is available in broadinstitute/single_cell_portal#99.To complete the move, I've also opened two PRs (broadinstitute/single_cell_portal_core#621 and broadinstitute/single_cell_portal#101) to remove the slightly different(!) copies of this code in those places. That will resolve the biggest tech debt in the genome pipeline and satisfy SCP-2470. Other pre-existing tech debt is documented and scoped in SCP-2491.
This PR and the two noted above satisfy SCP-2470.