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galaxyproject
Dependency package needed for TwoBit Data Manager
Currently listed as requiring 'ucsc_tools', needs to have TS installable package that provides the 'faToTwoBit' executable.
@blankenberg what is your preferred way to do this?
- [ ] downloading latest version from UCSC mirror (I do this in deepTools)
- [ ] mirroring and versioning the UCSC binaries by ourself (we did that once in my github repository)
- [x] build the entire ucsc src tree with https://github.com/natefoo/docker-build (we have some initial work on this)
+1 for the last option. In IRC @natefoo mentioned possibility of getting output files from docker build into depot
xref https://botbot.me/freenode/galaxyproject/2015-04-01/?msg=35585301&page=2
- apr. 2015 10.29 a.m. skrev "Björn Grüning" [email protected]:
@blankenberg https://github.com/blankenberg what is your preferred way to do this?
- downloading latest version from UCSC mirror (I do this in deepTools)
- mirroring and versioning the UCSC binaries by ourself (we did that once in my github repository)
- build the entire ucsc src tree with https://github.com/natefoo/docker-build (we have some initial work on this)
— Reply to this email directly or view it on GitHub https://github.com/galaxyproject/tools-devteam/issues/94#issuecomment-90105959 .
I think the preferred order of preference would be the reverse order of the check list. With importance on keeping versioned copies, instead of just the latest.
@blankenberg I think the only missing piece is to convince @natefoo to put the compiled binaries into the Galaxy depot :)
Do we want to have one package_ucsc_2015_1 package with all binaries or do we want to have X packages for every needed binary? I think the entire UCSC source tree is released every 3 month.
@bgruening UCSC are versioned, they just don't keep old versions. https://github.com/natefoo/docker-build/blob/master/ucsc/build.sh#L4 We'll need to update that on a regular basis whenever builds start failing.
Yes I know, imho we just need to pick on version sync it to the depot build from this location and we are good.