GitHub Actions CI toy example #5
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| name: GitHub Actions CI toy example | |
| on: | |
| #push: | |
| # paths-ignore: | |
| # - '**.md' | |
| workflow_dispatch: | |
| jobs: | |
| toy-example: | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, ubuntu-22.04] | |
| name: Toy Test GH linux | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| EXE_AGC: ../agc | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: make CXX=g++-11 agc | |
| run: make CXX=g++-11 agc | |
| #CREATE | |
| - name: toy example create | |
| run: | | |
| cd toy_ex | |
| $EXE_AGC create -o toy.agc ref.fa a.fa b.fa c.fa | |
| - name: toy example create (+gz) | |
| run: | | |
| cd toy_ex | |
| gzip -k a.fa | |
| gzip -k b.fa | |
| gzip -k c.fa | |
| gzip -k ref.fa | |
| $EXE_AGC create -d -o t1.agc a.fa.gz a.fa | |
| $EXE_AGC create -o t2.agc b.fa.gz b.fa | |
| $EXE_AGC create -t 3 -d -o toygz.agc ref.fa.gz a.fa.gz b.fa.gz c.fa.gz | |
| - name: toy example listref | |
| run: | | |
| cd toy_ex | |
| echo -n "ref" > rr | |
| $EXE_AGC listref toy_ex.agc > r | |
| cmp r rr | |
| - name: toy example listset | |
| run: | | |
| cd toy_ex | |
| printf "a\nb\nc\nref\n" > list | |
| $EXE_AGC 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_AGC listctg toy.agc a > list_dec | |
| cmp list list_dec | |
| - name: toy example getset | |
| run: | | |
| cd toy_ex | |
| $EXE_AGC getset toy.agc a > a_dec.fa | |
| $EXE_AGC getset toy.agc b > b_dec.fa | |
| $EXE_AGC getset toy.agc c > c_dec.fa | |
| $EXE_AGC 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 getset -g (+gz) | |
| run: | | |
| cd toy_ex | |
| $EXE_AGC getset -g 9 toygz.agc a > a_dec.fa.gz | |
| gzip -df a_dec.fa.gz | |
| $EXE_AGC getset -g 6 toy.agc b > b_dec.fa.gz | |
| gzip -df b_dec.fa.gz | |
| $EXE_AGC getset toygz.agc c > c_dec.fa | |
| $EXE_AGC getset -g 2 toy.agc ref > ref_dec.fa.gz | |
| gzip -df ref_dec.fa.gz | |
| 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_AGC 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_AGC getctg toy.agc chr1a > chr1a_dec.fa | |
| cmp chr1a.fa chr1a_dec.fa | |
| tail -n 2 b.fa > t.fa | |
| $EXE_AGC getctg toy.agc t > t_dec.fa | |
| cmp t.fa t_dec.fa | |
| head -n 2 ref.fa > ref-chr1.fa | |
| $EXE_AGC 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_AGC getctg toy.agc chr1@ref:3-10 > ctg_dec.fa | |
| cmp ctg.fa ctg_dec.fa | |
| echo ">chr3a:1-3" > ctg.fa | |
| echo "GTT" >> ctg.fa | |
| $EXE_AGC getctg toy.agc chr3a:1-3 > ctg_dec.fa | |
| cmp ctg.fa ctg_dec.fa | |
| echo ">g h i 21:3-4" > ctg.fa | |
| echo "AG" >> ctg.fa | |
| $EXE_AGC getctg toy.agc g:3-4 > ctg_dec.fa | |
| cmp ctg.fa ctg_dec.fa | |
| #CREATE-C | |
| - name: toy example create -c AND -a -c | |
| run: | | |
| cd toy_ex | |
| $EXE_AGC create -c -o toy.agc ref2.fa c.fa | |
| $EXE_AGC create -a -c ref2.fa b.fa > toy2.agc | |
| - name: toy example listset -c | |
| run: | | |
| cd toy_ex | |
| printf "1\n2\n3\nchr1\n" > list | |
| $EXE_AGC listset toy.agc > list_dec | |
| cmp list list_dec | |
| printf "c\nchr1\ng\nt\n" > list | |
| $EXE_AGC listset toy2.agc > list_dec | |
| cmp list list_dec | |
| - name: toy example getset -c | |
| run: | | |
| cd toy_ex | |
| $EXE_AGC getset toy.agc chr1 > chr1_dec.fa | |
| $EXE_AGC getset toy.agc 1 > 1_dec.fa | |
| $EXE_AGC getset toy.agc 2 > 2_dec.fa | |
| $EXE_AGC getset toy.agc 3 > 3_dec.fa | |
| head -n 2 c.fa > 1.fa | |
| head -n 4 c.fa | tail -n 2 > 2.fa | |
| tail -n 2 c.fa > 3.fa | |
| cmp 1.fa 1_dec.fa | |
| cmp 2.fa 2_dec.fa | |
| cmp 3.fa 3_dec.fa | |
| cmp ref2.fa chr1_dec.fa | |
| $EXE_AGC getset toy2.agc chr1 > chr1_dec.fa | |
| cmp ref2.fa chr1_dec.fa | |
| $EXE_AGC getset toy2.agc c > c_dec.fa | |
| $EXE_AGC getset toy2.agc g > g_dec.fa | |
| $EXE_AGC getset toy2.agc t > t_dec.fa | |
| sed -n '3p;4p' < b.fa > g.fa | |
| sed -n '5p;6p' < b.fa > c.fa | |
| sed -n '7p;8p' < b.fa > t.fa | |
| cmp g.fa g_dec.fa | |
| cmp c.fa c_dec.fa | |
| cmp t.fa t_dec.fa | |
| - name: toy example getcol -c | |
| run: | | |
| cd toy_ex | |
| rm -rf getcol | |
| mkdir getcol | |
| $EXE_AGC getcol -o getcol toy.agc | |
| cmp 1.fa getcol/1.fa | |
| cmp 2.fa getcol/2.fa | |
| cmp 3.fa getcol/3.fa | |
| cmp ref2.fa getcol/chr1.fa | |
| rm -rf getcol | |
| mkdir getcol | |
| $EXE_AGC getcol -o getcol toy2.agc | |
| cmp c.fa getcol/c.fa | |
| cmp t.fa getcol/t.fa | |
| cmp g.fa getcol/g.fa | |
| cmp ref2.fa getcol/chr1.fa | |
| - name: toy example getctg -c | |
| run: | | |
| cd toy_ex | |
| $EXE_AGC getctg toy.agc chr1 > chr1_dec.fa | |
| cmp ref2.fa chr1_dec.fa | |
| echo ">chr1:3-7" > ctg.fa | |
| echo "TAGCT" >> ctg.fa | |
| $EXE_AGC getctg toy.agc chr1:3-7 > ctg_dec.fa | |
| cmp ctg.fa ctg_dec.fa | |
| echo ">3:3-10" > ctg.fa | |
| echo "TCCCGGGA" >> ctg.fa | |
| $EXE_AGC getctg toy.agc 3:3-10 > ctg_dec.fa | |
| cmp ctg.fa ctg_dec.fa | |
| echo ">g h i 21:3-4" > ctg.fa | |
| echo "AG" >> ctg.fa | |
| $EXE_AGC getctg toy2.agc g:3-4 > ctg_dec.fa | |
| cmp ctg.fa ctg_dec.fa | |
| #APPEND | |
| - name: toy example create-append-getset | |
| run: | | |
| cd toy_ex | |
| $EXE_AGC create -o tmp0.agc ref.fa | |
| $EXE_AGC append tmp0.agc a.fa > tmp1.agc | |
| $EXE_AGC append tmp1.agc b.fa > tmp2.agc | |
| $EXE_AGC append tmp2.agc c.fa > toy_app.agc | |
| $EXE_AGC getset toy_app.agc a > a_dec.fa | |
| $EXE_AGC getset toy_app.agc b > b_dec.fa | |
| $EXE_AGC getset toy_app.agc c > c_dec.fa | |
| $EXE_AGC 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_AGC 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_AGC listctg toy_app.agc a > list_dec | |
| cmp list list_dec | |
| - name: toy example append getcol | |
| run: | | |
| cd toy_ex | |
| mkdir getcola | |
| $EXE_AGC 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_AGC getctg toy_app.agc chr1a > chr1a_dec.fa | |
| cmp chr1a.fa chr1a_dec.fa | |
| tail -n 2 b.fa > t.fa | |
| $EXE_AGC getctg toy_app.agc t > t_dec.fa | |
| cmp t.fa t_dec.fa | |
| head -n 2 ref.fa > ref-chr1.fa | |
| $EXE_AGC 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_AGC getctg toy_app.agc chr1@ref:3-10 > ctg_dec.fa | |
| cmp ctg.fa ctg_dec.fa | |
| echo ">chr3a:1-3" > ctg.fa | |
| echo "GTT" >> ctg.fa | |
| $EXE_AGC getctg toy_app.agc chr3a:1-3 > ctg_dec.fa | |
| cmp ctg.fa ctg_dec.fa | |
| #ADAPTIVE APPEND | |
| - name: toy example create-append adaptive-getset | |
| run: | | |
| cd toy_ex | |
| $EXE_AGC create -a -o tmp0.agc ref.fa | |
| $EXE_AGC append -a tmp0.agc a.fa > tmp1.agc | |
| $EXE_AGC append -a tmp1.agc b.fa > tmp2.agc | |
| $EXE_AGC append -a tmp2.agc c.fa > toy_app.agc | |
| $EXE_AGC getset toy_app.agc a > a_dec.fa | |
| $EXE_AGC getset toy_app.agc b > b_dec.fa | |
| $EXE_AGC getset toy_app.agc c > c_dec.fa | |
| $EXE_AGC 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_AGC 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_AGC listctg toy_app.agc a > list_dec | |
| cmp list list_dec | |
| - name: toy example append adaptive getcol | |
| run: | | |
| cd toy_ex | |
| mkdir getcolaa | |
| $EXE_AGC 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_AGC getctg toy_app.agc chr1a > chr1a_dec.fa | |
| cmp chr1a.fa chr1a_dec.fa | |
| tail -n 2 b.fa > t.fa | |
| $EXE_AGC getctg toy_app.agc t > t_dec.fa | |
| cmp t.fa t_dec.fa | |
| head -n 2 ref.fa > ref-chr1.fa | |
| $EXE_AGC 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_AGC getctg toy_app.agc chr1@ref:3-10 > ctg_dec.fa | |
| cmp ctg.fa ctg_dec.fa | |
| echo ">chr3a:1-3" > ctg.fa | |
| echo "GTT" >> ctg.fa | |
| $EXE_AGC getctg toy_app.agc chr3a:1-3 > ctg_dec.fa | |
| cmp ctg.fa ctg_dec.fa | |
| toy-example-macos: | |
| strategy: | |
| matrix: | |
| os: [macos-latest, macos-14, macos-13, macos-12] | |
| name: Make Test GitHub macos | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| EXE_AGC: ../agc | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - uses: maxim-lobanov/setup-xcode@v1 | |
| with: | |
| xcode-version: latest-stable | |
| # xcode-version: '14.1' | |
| - name: make CXX=g++-11 agc | |
| run: | | |
| make clean | |
| make CXX=g++-11 agc | |
| - name: toy example | |
| run: | | |
| cd toy_ex | |
| $EXE_AGC | |
| $EXE_AGC create | |
| $EXE_AGC create -o toy.agc ref.fa a.fa b.fa c.fa | |
| $EXE_AGC getset toy.agc a > a_dec.fa | |
| cmp a.fa a_dec.fa | |