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Use quilt_rs #203

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@fiskus fiskus commented May 22, 2024

On top of #202

You need fresh version of https://github.com/quiltdata/quilt-rs/pull/187: there are slightly different methods names, because Quilt now is Java_nextflow_quilt_jep_Quilt

  1. Go to quilt_rs repo, git pull latest change of the jni branch. Then cargo build. It will build libquilt_rs.so in target/debug
  2. Back to this repo
  3. cd plugins/nf-quilt/src/main/nextflow/quilt/jep
  4. Change path in System.load in Quilt.java to the correct location of the libquilt_rs.so
  5. javac Quilt.java. It will compile Quilt.class
  6. Then you can run tests: cd - && make check

Tests are failing because they rely on one directories' structure, but quilt_rs uses different directories. I couldn't manage to fix them.

@fiskus fiskus marked this pull request as draft May 22, 2024 15:41
@drernie drernie deleted the branch 168-rewrite-on-top-of-quilt-rs June 13, 2024 22:51
@drernie drernie closed this Jun 13, 2024
@drernie drernie deleted the quilt-rs-library branch June 18, 2024 21:02
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