JSON version files duplicated

[julie-sullivan]

Pretty sure this is because I did something wrong but I have this:

/tmp:$ find . -name gnomadVersion.json
./gnomadVersion.json
./homo_sapiens_grch37/gnomadVersion.json

I think there should only be one?

[julie-sullivan]

Also my code repo looks like this:

Jenkinsfile                     cellbase-core                       disgenetReadme.txt
LICENSE                         cellbase-lib                        disgenetReadme.txt.log
README.md                       cellbase-server                     download_summary.log
all_gene_disease_associations.tsv.gz            cellbase-test                       gnomad.v2.1.1.lof_metrics.by_transcript.txt.bgz
all_gene_disease_associations.tsv.gz.log        cellbase-web                        gnomad.v2.1.1.lof_metrics.by_transcript.txt.bgz.log
build                           cellbase.iml                        pom.xml
cellbase-app                        checkstyle.xml                      target

I guess in one of my download commands, I had the wrong config? But then why didn't everything download to my current location?

[imedina]

Just tried branch issue-386 and all looks good:

[julie-sullivan]

Nacho, can you post which command you used? Maybe that's my problem?

This is what I am doing to get the errant JSON files:

rm -rf /tmp/homo_sapiens_grch37/; build/bin/cellbase.sh download --assembly GRCh37 
--common /tmp/ --data gene,genome --output /tmp/ --species hsapiens

[julie-sullivan]

I also get stray download files?

~/git/cellbase (next) $ git status
On branch next
Your branch is ahead of 'upstream/next' by 4 commits.
  (use "git push" to publish your local commits)

Untracked files:
  (use "git add <file>..." to include in what will be committed)

    all_gene_disease_associations.tsv.gz
    disgenetReadme.txt
    gnomad.v2.1.1.lof_metrics.by_transcript.txt.bgz

My config is wrong somewhere!

[imedina]

I'm running this CLI:

http://bioinfo.hpc.cam.ac.uk/downloads/cellbase/