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Merge pull request #19 from refresh-bio/actions
GitHub Actions, basic tests
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| name: GitHub Actions CI | ||
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| on: | ||
| push: | ||
| paths-ignore: | ||
| - '**.md' | ||
| jobs: | ||
| linux-remote: | ||
| name: Linux test (remote) | ||
| runs-on: ubuntu-latest | ||
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| env: | ||
| EXE: ../agc | ||
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| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: make agc | ||
| run: make agc | ||
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| #CREATE | ||
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| - name: toy example create | ||
| run: | | ||
| cd toy_ex | ||
| $EXE create -o toy.agc ref.fa a.fa b.fa c.fa | ||
| - name: toy example listset | ||
| run: | | ||
| cd toy_ex | ||
| printf "a\nb\nc\nref\n" > list | ||
| $EXE listset toy.agc > list_dec | ||
| cmp list list_dec | ||
| - name: toy example listctg | ||
| run: | | ||
| cd toy_ex | ||
| printf "a\n chr1a\n chr3a\n" > list | ||
| $EXE listctg toy.agc a > list_dec | ||
| cmp list list_dec | ||
| - name: toy example getset | ||
| run: | | ||
| cd toy_ex | ||
| $EXE getset toy.agc a > a_dec.fa | ||
| $EXE getset toy.agc b > b_dec.fa | ||
| $EXE getset toy.agc c > c_dec.fa | ||
| $EXE getset toy.agc ref > ref_dec.fa | ||
| cmp a.fa a_dec.fa | ||
| cmp b.fa b_dec.fa | ||
| cmp c.fa c_dec.fa | ||
| cmp ref.fa ref_dec.fa | ||
| - name: toy example getcol | ||
| run: | | ||
| cd toy_ex | ||
| mkdir getcol | ||
| $EXE getcol -o getcol toy.agc | ||
| cmp a.fa getcol/a.fa | ||
| cmp b.fa getcol/b.fa | ||
| cmp c.fa getcol/c.fa | ||
| cmp ref.fa getcol/ref.fa | ||
| - name: toy example getctg | ||
| run: | | ||
| cd toy_ex | ||
| head -n 2 a.fa > chr1a.fa | ||
| $EXE getctg toy.agc chr1a > chr1a_dec.fa | ||
| cmp chr1a.fa chr1a_dec.fa | ||
| tail -n 2 b.fa > t.fa | ||
| $EXE getctg toy.agc t > t_dec.fa | ||
| cmp t.fa t_dec.fa | ||
| head -n 2 ref.fa > ref-chr1.fa | ||
| $EXE getctg toy.agc chr1@ref > ref-chr1_dec.fa | ||
| cmp ref-chr1.fa ref-chr1_dec.fa | ||
| echo ">chr1:3-10" > ctg.fa | ||
| echo "TAGCTAGC" >> ctg.fa | ||
| $EXE getctg toy.agc chr1@ref:3-10 > ctg_dec.fa | ||
| cmp ctg.fa ctg_dec.fa | ||
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| echo ">chr3a:1-3" > ctg.fa | ||
| echo "GTT" >> ctg.fa | ||
| $EXE getctg toy.agc chr3a:1-3 > ctg_dec.fa | ||
| cmp ctg.fa ctg_dec.fa | ||
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| #APPEND | ||
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| - name: toy example create-append-getset | ||
| run: | | ||
| cd toy_ex | ||
| $EXE create -o tmp0.agc ref.fa | ||
| $EXE append tmp0.agc a.fa > tmp1.agc | ||
| $EXE append tmp1.agc b.fa > tmp2.agc | ||
| $EXE append tmp2.agc c.fa > toy_app.agc | ||
| $EXE getset toy_app.agc a > a_dec.fa | ||
| $EXE getset toy_app.agc b > b_dec.fa | ||
| $EXE getset toy_app.agc c > c_dec.fa | ||
| $EXE getset toy_app.agc ref > ref_dec.fa | ||
| cmp a.fa a_dec.fa | ||
| cmp b.fa b_dec.fa | ||
| cmp c.fa c_dec.fa | ||
| cmp ref.fa ref_dec.fa | ||
| - name: toy example append listset | ||
| run: | | ||
| cd toy_ex | ||
| printf "a\nb\nc\nref\n" > list | ||
| $EXE listset toy_app.agc > list_dec | ||
| cmp list list_dec | ||
| - name: toy example append listctg | ||
| run: | | ||
| cd toy_ex | ||
| printf "a\n chr1a\n chr3a\n" > list | ||
| $EXE listctg toy_app.agc a > list_dec | ||
| cmp list list_dec | ||
| - name: toy example append getcol | ||
| run: | | ||
| cd toy_ex | ||
| mkdir getcola | ||
| $EXE getcol -o getcola toy_app.agc | ||
| cmp a.fa getcola/a.fa | ||
| cmp b.fa getcola/b.fa | ||
| cmp c.fa getcola/c.fa | ||
| cmp ref.fa getcola/ref.fa | ||
| - name: toy example append getctg | ||
| run: | | ||
| cd toy_ex | ||
| head -n 2 a.fa > chr1a.fa | ||
| $EXE getctg toy_app.agc chr1a > chr1a_dec.fa | ||
| cmp chr1a.fa chr1a_dec.fa | ||
| tail -n 2 b.fa > t.fa | ||
| $EXE getctg toy_app.agc t > t_dec.fa | ||
| cmp t.fa t_dec.fa | ||
| head -n 2 ref.fa > ref-chr1.fa | ||
| $EXE getctg toy_app.agc chr1@ref > ref-chr1_dec.fa | ||
| cmp ref-chr1.fa ref-chr1_dec.fa | ||
| echo ">chr1:3-10" > ctg.fa | ||
| echo "TAGCTAGC" >> ctg.fa | ||
| $EXE getctg toy_app.agc chr1@ref:3-10 > ctg_dec.fa | ||
| cmp ctg.fa ctg_dec.fa | ||
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| echo ">chr3a:1-3" > ctg.fa | ||
| echo "GTT" >> ctg.fa | ||
| $EXE getctg toy_app.agc chr3a:1-3 > ctg_dec.fa | ||
| cmp ctg.fa ctg_dec.fa | ||
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| #ADAPTIVE APPEND | ||
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| - name: toy example create-append adaptive-getset | ||
| run: | | ||
| cd toy_ex | ||
| $EXE create -a -o tmp0.agc ref.fa | ||
| $EXE append -a tmp0.agc a.fa > tmp1.agc | ||
| $EXE append -a tmp1.agc b.fa > tmp2.agc | ||
| $EXE append -a tmp2.agc c.fa > toy_app.agc | ||
| $EXE getset toy_app.agc a > a_dec.fa | ||
| $EXE getset toy_app.agc b > b_dec.fa | ||
| $EXE getset toy_app.agc c > c_dec.fa | ||
| $EXE getset toy_app.agc ref > ref_dec.fa | ||
| cmp a.fa a_dec.fa | ||
| cmp b.fa b_dec.fa | ||
| cmp c.fa c_dec.fa | ||
| cmp ref.fa ref_dec.fa | ||
| - name: toy example append adaptive listset | ||
| run: | | ||
| cd toy_ex | ||
| printf "a\nb\nc\nref\n" > list | ||
| $EXE listset toy_app.agc > list_dec | ||
| cmp list list_dec | ||
| - name: toy example append adaptive listctg | ||
| run: | | ||
| cd toy_ex | ||
| printf "a\n chr1a\n chr3a\n" > list | ||
| $EXE listctg toy_app.agc a > list_dec | ||
| cmp list list_dec | ||
| - name: toy example append adaptive getcol | ||
| run: | | ||
| cd toy_ex | ||
| mkdir getcolaa | ||
| $EXE getcol -o getcolaa toy_app.agc | ||
| cmp a.fa getcolaa/a.fa | ||
| cmp b.fa getcolaa/b.fa | ||
| cmp c.fa getcolaa/c.fa | ||
| cmp ref.fa getcolaa/ref.fa | ||
| - name: toy example append adaptive getctg | ||
| run: | | ||
| cd toy_ex | ||
| head -n 2 a.fa > chr1a.fa | ||
| $EXE getctg toy_app.agc chr1a > chr1a_dec.fa | ||
| cmp chr1a.fa chr1a_dec.fa | ||
| tail -n 2 b.fa > t.fa | ||
| $EXE getctg toy_app.agc t > t_dec.fa | ||
| cmp t.fa t_dec.fa | ||
| head -n 2 ref.fa > ref-chr1.fa | ||
| $EXE getctg toy_app.agc chr1@ref > ref-chr1_dec.fa | ||
| cmp ref-chr1.fa ref-chr1_dec.fa | ||
| echo ">chr1:3-10" > ctg.fa | ||
| echo "TAGCTAGC" >> ctg.fa | ||
| $EXE getctg toy_app.agc chr1@ref:3-10 > ctg_dec.fa | ||
| cmp ctg.fa ctg_dec.fa | ||
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| echo ">chr3a:1-3" > ctg.fa | ||
| echo "GTT" >> ctg.fa | ||
| $EXE getctg toy_app.agc chr3a:1-3 > ctg_dec.fa | ||
| cmp ctg.fa ctg_dec.fa | ||
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| macos-remote: | ||
| name: macOS build (remote) | ||
| runs-on: macOS-12 | ||
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| env: | ||
| EXE: ../agc | ||
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| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: make | ||
| run: make | ||
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| - name: toy example | ||
| run: | | ||
| cd toy_ex | ||
| $EXE create -o toy.agc ref.fa a.fa b.fa c.fa | ||
| $EXE getset toy.agc a > a_dec.fa | ||
| cmp a.fa a_dec.fa | ||