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biod / sambamba

Tools for working with SAM/BAM data
http://thebird.nl/blog/D_Dragon.html
GNU General Public License v2.0
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Makefile.docker requires ldmd2 to be installed locally #373

Closed fwip closed 4 years ago

fwip commented 5 years ago

Hi,

I tried to compile sambamba using Docker on my Mac, and found that it still requires ldmd2 to be installed locally on the system. I believe the offending line is here: https://github.com/biod/sambamba/blob/v0.6.8/Makefile.docker#L42 - the $(shell which ldmd2) fails if there is no local version of ldmd2 available.

I am not sure what the appropriate fix here is, but it seems like the right thing to do might be to take the version information from the docker container's version of ldmd2 instead.

Sambamba version: v0.6.8 (96d1b7). Script: make -f Makefile.docker

pjotrp commented 5 years ago

@fwip I had almost forgotten about this makefile! Does the bioconda or brew version of sambamba not work for you?

fwip commented 5 years ago

Oh, sorry, those versions work fine. I wanted to have a go at compiling it myself, to see if I could hack on it a little bit (mostly for fun).

pjotrp commented 5 years ago

That would be really cool! If you check the .travis.yml file in the source tree you can see we build for macos on Travis which works out of the box: https://travis-ci.org/biod/sambamba/jobs/442531351 If you check that output you can see how you can install ldc on macos and compile everything. I suggest to try that. Use ldc 1.11 and not 1.12 - the latter is giving us problems.