add .github/workflow

from @danielecook requires changes to functional tests due to zcat differences on osx
brentp · May 11, 2020 · 48eae5f · 48eae5f · danielecook · May 12, 2020
1 parent ada9402
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -0,0 +1,96 @@
+# copied from Daniel Cook's Seq collection
+name: Build
+
+on: 
+  - push
+  - pull_request
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-18.04, macos-10.15]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    # Caching
+    - name: Cache choosenim
+      id: cache-choosenim
+      uses: actions/cache@v1
+      with:
+        path: ~/.choosenim
+        key: ${{ runner.os }}-choosenim-stable
+
+    - name: Cache nimble
+      id: cache-nimble
+      uses: actions/cache@v1
+      with:
+        path: ~/.nimble
+        key: ${{ runner.os }}-nimble-stable
+
+    - name: Cache htslib
+      id: cache-htslib
+      uses: actions/cache@v1
+      with:
+        path: $HOME/htslib
+        key: ${{ runner.os }}-htslib-1.10
+
+    # Setup nim
+    - uses: jiro4989/[email protected]
+      with:
+          nim-version: 1.0.6
+
+    # Install Dependencies
+    - name: Install dependencies (Linux)
+      if: runner.os == 'Linux'
+      run: |
+        sudo apt-get update
+        sudo apt-get -qy install bwa make build-essential cmake libncurses-dev ncurses-dev libbz2-dev lzma-dev liblzma-dev \
+             curl libssl-dev libtool autoconf automake libcurl4-openssl-dev
+
+    # Setup htslib
+    - name: Install htslib (linux)
+      if: runner.os == 'Linux'
+      run: |
+        cd
+        git clone --recursive https://github.com/samtools/htslib.git
+        cd htslib && git checkout 1.10 && autoheader && autoconf && ./configure --enable-libcurl
+        cd
+        make -j 4 -C htslib
+        echo "::set-env name=LD_LIBRARY_PATH::${LD_LIBRARY_PATH}:${HOME}/htslib"
+        ls -lh $HOME/htslib/*.so
+
+    - name: Install hstlib (macos)
+      if: runner.os == 'macOS'
+      run: |
+        brew install htslib
+
+    # Build and Test
+    - name: Build test executable
+      run: nimble build -Y mosdepth.nimble
+
+    - name: "Copy binary"
+      run: chmod +x mosdepth && mkdir bin && cp mosdepth bin/mosdepth_debug_${{ matrix.os }}
+
+    - name: "Build and Copy release binary"
+      run: nim c -d:danger -d:release -o:bin/mosdepth_${{ matrix.os }} mosdepth
+
+    - name: Functional Tests
+      env:
+        TERM: "xterm"
+      run: |
+        bash ./functional-tests.sh
+
+    - name: Unit Tests
+      run: |
+        nim c -r tests/all.nim
+
+    - name: Upload Artifact
+      if: success()
+      uses: actions/[email protected]
+      with:
+        name: mosdepth_${{ matrix.os }}_executable
+        path: bin/
diff --git a/README.md b/README.md
@@ -4,6 +4,7 @@ fast BAM/CRAM depth calculation for **WGS**, **exome**, or **targeted sequencing
 
 ![logo](https://user-images.githubusercontent.com/1739/29678184-da1f384c-88ba-11e7-9d98-df4fe3a59924.png "logo")
 
+[![Build](https://github.com/brentp/mosdepth/workflows/Build/badge.svg?branch=master)](https://github.com/brentp/mosdepth/actions?query=workflow%3ABuild)
 [![Build Status](https://travis-ci.com/brentp/mosdepth.svg?branch=master)](https://travis-ci.com/brentp/mosdepth)
 
 [![citation](https://img.shields.io/badge/cite-open%20access-orange.svg)](https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btx699/4583630?guestAccessKey=35b55064-4566-4ab3-a769-32916fa1c6e6)

diff --git a/functional-tests.sh b/functional-tests.sh
@@ -47,7 +47,7 @@ assert_exit_code 1
 
 run unordered_bed $exe --by tests/unordered.bed t tests/ovl.bam
 assert_exit_code 0
-assert_equal $(zcat t.regions.bed.gz | wc -l) 2
+assert_equal $(zcat < t.regions.bed.gz | wc -l) 2
 
 # theres data left in the bam but the region tree is empty...
 run missing_bed_chrom $exe --by tests/missing.bed t tests/ovl.bam
@@ -74,13 +74,13 @@ assert_exit_code 0
 
 rm -f t.thresholds.bed.gz*
 run threshold_test $exe --by 100 -T 0,1,2,3,4,5 -c MT t tests/ovl.bam
-assert_equal "$(zcat t.thresholds.bed.gz | tail -n +2 | head -1)" "MT	0	100	unknown	100	80	0	0	0	0"
-assert_equal "0" "$(zcat t.thresholds.bed.gz | tail -n+2 | cut -f 7 | uniq)"
+assert_equal "$(zcat < t.thresholds.bed.gz | tail -n +2 | head -1)" "MT	0	100	unknown	100	80	0	0	0	0"
+assert_equal "0" "$(zcat < t.thresholds.bed.gz | tail -n+2 | cut -f 7 | uniq)"
 assert_exit_code 0
 
 rm -f t.thresholds.bed.gz*
 run threshold_test_by $exe --by tests/track.bed -T 0,1,2 -c MT t tests/ovl.bam
-assert_equal "$(zcat t.thresholds.bed.gz | tail -n +2)" "MT	2	80	aregion	78	78	0"
+assert_equal "$(zcat < t.thresholds.bed.gz | tail -n +2)" "MT	2	80	aregion	78	78	0"
 assert_exit_code 0
 
 export MOSDEPTH_Q0=AAA
@@ -97,7 +97,7 @@ assert_equal "$(tail -n 1 t.mosdepth.summary.txt)" "total	16569	80	0.0048283	0	1
 
 run track_header $exe --by tests/track.bed t tests/ovl.bam
 assert_exit_code 0
-assert_equal "$(zcat t.regions.bed.gz)" "MT	2	80	aregion	1.00"
+assert_equal "$(zcat < t.regions.bed.gz)" "MT	2	80	aregion	1.00"
 
 run track_header_by $exe --by tests/bad.bed t tests/ovl.bam
 assert_exit_code 1
@@ -136,7 +136,7 @@ assert_equal $(diff -u t_regions.mosdepth.region.dist.txt t_regions.mosdepth.glo
 rm -f t_regions.*
 
 run overlappingPairs $exe t tests/overlapping-pairs.bam
-assert_equal "$(zcat t.per-base.bed.gz)" "1	0	565173	0
+assert_equal "$(zcat < t.per-base.bed.gz)" "1	0	565173	0
 1	565173	565253	1
 1	565253	249250621	0"
 assert_exit_code 0