diff --git a/.github/workflows/dnmtools_release_linux.yml b/.github/workflows/dnmtools_release_linux.yml index 42502cf3..55ec3b16 100644 --- a/.github/workflows/dnmtools_release_linux.yml +++ b/.github/workflows/dnmtools_release_linux.yml @@ -23,8 +23,9 @@ jobs: env: SCRIPT: | export DEBIAN_FRONTEND=noninteractive && \ - apt-get update && apt-get install --no-install-recommends -y automake && \ + apt-get update && apt-get install --no-install-recommends -y automake libgsl-dev && \ find /usr -name libz.so -exec rm {} \; && \ + find /usr -name libgsl\*.so -exec rm {} \; && \ git clone --recursive https://github.com/samtools/htslib.git && \ cd htslib && \ autoreconf -i && \ @@ -35,7 +36,7 @@ jobs: --disable-lzma \ --disable-ref-cache \ LDADD="-L/usr/local/lib" && \ - make CFLAGS="-Wall -O2 -fvisibility=hidden" libhts.a && \ + make -j4 CFLAGS="-Wall -O2 -fvisibility=hidden" libhts.a && \ cp libhts.a /usr/local/lib/ && \ cp -r ../htslib /usr/local/include/ && \ cd /workspace && \ @@ -48,7 +49,7 @@ jobs: - name: Get version number id: get-vn run: | - awk '/AC_INIT/ {print "vn="$2}' configure.ac | sed -e "s/\[//; s/\]//; s/,//" >> "$GITHUB_OUTPUT" + awk '/AC_INIT/ {print "vn="$2}' configure.ac | sed "s/\[//; s/\]//; s/,//" >> "$GITHUB_OUTPUT" env: GH_TOKEN: ${{ github.token }} - name: Upload the binary diff --git a/.github/workflows/dnmtools_release_macos.yml b/.github/workflows/dnmtools_release_macos.yml index 1000cf1a..481ee31d 100644 --- a/.github/workflows/dnmtools_release_macos.yml +++ b/.github/workflows/dnmtools_release_macos.yml @@ -36,7 +36,7 @@ jobs: --disable-ref-cache \ --without-libdeflate \ LDADD="-L/usr/local/lib" - make CFLAGS="-Wall -O2 -fvisibility=hidden" libhts.a + make -j4 CFLAGS="-Wall -O2 -fvisibility=hidden" libhts.a sudo cp libhts.a /opt/dnmtools/lib - name: Build dnmtools run: | diff --git a/src/abismal b/src/abismal index 022c31e0..38d8087c 160000 --- a/src/abismal +++ b/src/abismal @@ -1 +1 @@ -Subproject commit 022c31e0faa2229b0aad65d781b0dca26cdbc3a0 +Subproject commit 38d8087c07e14f8c84cdc7d6ce12dcca43d024b8