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| author | pjotrp | 2026-04-05 09:57:58 +0200 |
|---|---|---|
| committer | pjotrp | 2026-04-05 09:57:58 +0200 |
| commit | ff9cdbc3510c3223ec3e9e9ec213082b21caa0eb (patch) | |
| tree | 69bac2e1676dfa20225fe5dcf77a609ba1b74c6a | |
| parent | ca5ced4129c10c8fef988915868c9e368b3691a0 (diff) | |
| download | guix-bioinformatics-ff9cdbc3510c3223ec3e9e9ec213082b21caa0eb.tar.gz | |
Add test (impg) integration test
| -rw-r--r-- | gn/packages/pangenome-rust.scm | 28 |
1 files changed, 26 insertions, 2 deletions
diff --git a/gn/packages/pangenome-rust.scm b/gn/packages/pangenome-rust.scm index 124539e..913f7f3 100644 --- a/gn/packages/pangenome-rust.scm +++ b/gn/packages/pangenome-rust.scm @@ -3752,8 +3752,32 @@ sequences to accelerate the alignment process.") (let ((src (string-append fastga-bin "/" name))) (when (file-exists? src) (symlink src (string-append bin "/" name))))) - '("FastGA" "ALNtoPAF" "FAtoGDB" "GIXmake")))))))) - (native-inputs (list pkg-config cmake-minimal clang)) + '("FastGA" "ALNtoPAF" "FAtoGDB" "GIXmake"))))) + (add-after 'symlink-fastga-binaries 'integration-test + (lambda* (#:key outputs #:allow-other-keys) + (setenv "PATH" (string-append + (assoc-ref outputs "out") "/bin:" + (getenv "PATH"))) + (invoke "sh" "-ec" + (string-append + "D=$(mktemp -d); cd $D; " + "zcat ../source/tests/test_data/yeast.chrV.fa.gz > y.fa; " + "samtools faidx y.fa; " + "minimap2 -x asm20 --eqx -c -X y.fa y.fa 2>/dev/null | bgzip > y.paf.gz; " + "T=$(zcat y.paf.gz | head -1 | cut -f6); " + "echo test1-query-bedpe; " + "impg query -a y.paf.gz -r $T:0-10000 -o bedpe >/dev/null; " + "echo test2-query-gfa; " + "impg query -a y.paf.gz -r $T:100000-105000 -o gfa " + "--sequence-files y.fa -O g -t 2 -v 0; " + "test -s g.gfa; " + "echo test3-fasta; " + "impg query -a y.paf.gz -r $T:100000-102000 -o fasta " + "--sequence-files y.fa -O r -t 2 -v 0; " + "test -s r.fa; " + "echo INTEGRATION_TESTS_PASSED"))))))) + (native-inputs (list minimap2 samtools htslib gzip + pkg-config cmake-minimal clang)) (propagated-inputs (list fastga-rs)) (inputs (cons* htslib spoa |