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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 | ||