Our docker containers for the coarse and the fine grain challenge had problems interpreting the `hugo.expr.file` for DS473 and DS344. It seems the first row of the HUGO table for DS473, where we expected to find the sample names, may only contain comma-separated `NA`s. The same may hold for DS344, but my log ran into the 50 KB limit before it got there. @andrewelamb can you confirm that the files listed under `hugo.expr.file` for DS473 and DS344 in the `input.csv` meet the specifications of the [wiki](https://www.synapse.org/#!Synapse:syn15589870/wiki/592699)?
Other than that, everything went perfectly.
Cheers,
Dominik
Created by Dominik Otto djo Hi @andrewelamb,
Thank you for investigating. The problem was that our bash script could not deal with spaces in the `normalization` column what led to unexpected effects. Yet another step towards robust software :)
Regards,
Dominik Hi @djo,
The files where the docker image is being processed seem to have correctly formatted headers:
ubuntu@ip-172-31-2-145:~/leaderboard2_dir$ head -n1 DS473-hugo-gene-expr.csv
Gene,S1,S2,S3,S4,S5,S6,S7,S8,S9,S10,S11,S12,S13,S14,S15,S16,S17,S18,S19,S20,S21,S22,S23,S24,S25,S26,S27,S28
ubuntu@ip-172-31-2-145:~/leaderboard2_dir$ head -n1 DS344-hugo-gene-expr.csv
Gene,S1,S2,S3,S4,S5,S6,S7,S8,S9,S10,S11,S12,S13,S14,S15,S16,S17,S18,S19,S20,S21,S22,S23,S24,S25,S26,S27,S28,S29,S30,S31,S32,S33,S34,S35,S36,S37,S38,S39,S40,S41,S42,S43,S44,S45,S46
Drop files to upload
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