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Fix for GNU Make 4.3 #3

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Fix for GNU Make 4.3 #3

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e-t-k
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@e-t-k e-t-k commented May 8, 2023

Fixes the docker: invalid reference format: repository name must be lowercase. error when run on make 4.3 (current version is working ok on make 3.82).

Replaces $$UID with $(shell id -u) in the Makefile.

$ make run-treehouse COHORT=v11_polya
Running ucsctreehouse/care:0.17.1.0 vs compendium v11_polya
mkdir -p outputs
docker run \
        --rm \
        --user $UID \
        -v `pwd`:/work/rollup:ro \
        -v `pwd`/manifest.tsv:/work/manifest.tsv:ro \
        -v `pwd`/outputs:/work/outputs \
        -v /private/groups/treehouse/archive:/treehouse:ro \
        ucsctreehouse/care:0.17.1.0 pass-args \
                --inputs /treehouse/downstream \
                --cohort /treehouse/compendium/v11_polya \
                --references /treehouse/references
docker: invalid reference format: repository name must be lowercase.
See 'docker run --help'.
make: *** [Makefile:23: run-treehouse] Error 125

$ make --version
GNU Make 4.3
Built for x86_64-pc-linux-gnu

Fixes the `docker: invalid reference format: repository name must be lowercase.` error when run on make 4.3 (current version is working ok on  make 3.82).

```
$ make run-treehouse COHORT=v11_polya
Running ucsctreehouse/care:0.17.1.0 vs compendium v11_polya
mkdir -p outputs
docker run \
        --rm \
        --user $UID \
        -v `pwd`:/work/rollup:ro \
        -v `pwd`/manifest.tsv:/work/manifest.tsv:ro \
        -v `pwd`/outputs:/work/outputs \
        -v /private/groups/treehouse/archive:/treehouse:ro \
        ucsctreehouse/care:0.17.1.0 pass-args \
                --inputs /treehouse/downstream \
                --cohort /treehouse/compendium/v11_polya \
                --references /treehouse/references
docker: invalid reference format: repository name must be lowercase.
See 'docker run --help'.
make: *** [Makefile:23: run-treehouse] Error 125

$ make --version
GNU Make 4.3
Built for x86_64-pc-linux-gnu

```
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