From 0ff5fdbfa3ac3cd7aafc2287abd416ceb28ac94b Mon Sep 17 00:00:00 2001 From: Erik Garrison Date: Tue, 2 Jul 2024 11:25:27 +0200 Subject: [PATCH 1/5] wfmash v0.16.0 --- Dockerfile | 2 +- pggb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 8834531..725c1e2 100644 --- a/Dockerfile +++ b/Dockerfile @@ -50,7 +50,7 @@ RUN wget https://github.com/samtools/bcftools/releases/download/1.19/bcftools-1. RUN git clone --recursive https://github.com/waveygang/wfmash \ && cd wfmash \ && git pull \ - && git checkout 251f4e1d7770723d3495e9d7b443f941798d4174 \ + && git checkout 2243583d2f4272ce5254be9ffc508d492dd8b6f8 \ && git submodule update --init --recursive \ && sed -i 's/-march=native/-march=sandybridge/g' src/common/wflign/deps/WFA2-lib/Makefile \ && cmake -H. -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-march=sandybridge -Ofast' -Bbuild && cmake --build build -- -j $(nproc) \ diff --git a/pggb b/pggb index 290621e..672824c 100755 --- a/pggb +++ b/pggb @@ -590,7 +590,7 @@ if [[ "$input_paf" == false ]]; then "$input_fasta" \ --lower-triangular \ --hg-filter-ani-diff $hg_filter_ani_diff \ - -i "$prefix_mappings_paf".mappings.$mapper.paf --invert-filtering \ + -i "$prefix_mappings_paf".mappings.$mapper.paf \ > "$prefix_paf".alignments.$mapper.paf) 2> >(tee -a "$log_file") fi fi From 8951c0af7e29a5ae437e6c6108b3da7c9fc3cfaa Mon Sep 17 00:00:00 2001 From: Erik Garrison Date: Tue, 2 Jul 2024 12:11:34 +0200 Subject: [PATCH 2/5] fix wfmash build --- Dockerfile | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/Dockerfile b/Dockerfile index 725c1e2..362b375 100644 --- a/Dockerfile +++ b/Dockerfile @@ -52,14 +52,11 @@ RUN git clone --recursive https://github.com/waveygang/wfmash \ && git pull \ && git checkout 2243583d2f4272ce5254be9ffc508d492dd8b6f8 \ && git submodule update --init --recursive \ - && sed -i 's/-march=native/-march=sandybridge/g' src/common/wflign/deps/WFA2-lib/Makefile \ - && cmake -H. -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-march=sandybridge -Ofast' -Bbuild && cmake --build build -- -j $(nproc) \ + && cmake -H. -Bbuild -DBUILD_STATIC=ON -DBUILD_RETARGETABLE=ON && cmake --build build -- -j $(nproc) \ && cp build/bin/wfmash /usr/local/bin/wfmash \ # Libraries aren't getting installed - && cp build/lib/libwfa2cpp.so.0 /usr/local/lib/ \ - && cp build/lib/libwfa2cpp.so /usr/local/lib/ \ - && cp build/lib/libwfa2.so.0 /usr/local/lib/ \ - && cp build/lib/libwfa2.so /usr/local/lib/ \ + && cp build/lib/libwfa2cpp.a /usr/local/lib/ \ + && cp build/lib/libwfa2.a /usr/local/lib/ \ && cd ../ \ && rm -rf wfmash From 34ce440e9fc5ed6b5a70dadecbb67836c48ca869 Mon Sep 17 00:00:00 2001 From: Erik Garrison Date: Tue, 2 Jul 2024 16:52:54 +0200 Subject: [PATCH 3/5] lto buggy in gcc-10 used in docker --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index 362b375..5b70538 100644 --- a/Dockerfile +++ b/Dockerfile @@ -52,6 +52,7 @@ RUN git clone --recursive https://github.com/waveygang/wfmash \ && git pull \ && git checkout 2243583d2f4272ce5254be9ffc508d492dd8b6f8 \ && git submodule update --init --recursive \ + && sed -i 's/ -flto//g' \ && cmake -H. -Bbuild -DBUILD_STATIC=ON -DBUILD_RETARGETABLE=ON && cmake --build build -- -j $(nproc) \ && cp build/bin/wfmash /usr/local/bin/wfmash \ # Libraries aren't getting installed From 09114b388f49cb601cdd9c79f8f18589d47266dd Mon Sep 17 00:00:00 2001 From: Erik Garrison Date: Wed, 3 Jul 2024 11:17:18 +0200 Subject: [PATCH 4/5] oops --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 5b70538..2b45c1c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -52,7 +52,7 @@ RUN git clone --recursive https://github.com/waveygang/wfmash \ && git pull \ && git checkout 2243583d2f4272ce5254be9ffc508d492dd8b6f8 \ && git submodule update --init --recursive \ - && sed -i 's/ -flto//g' \ + && sed -i 's/ -flto//g' CMakeLists.txt \ && cmake -H. -Bbuild -DBUILD_STATIC=ON -DBUILD_RETARGETABLE=ON && cmake --build build -- -j $(nproc) \ && cp build/bin/wfmash /usr/local/bin/wfmash \ # Libraries aren't getting installed From 3961c02e445428fce5391adb5287923266744133 Mon Sep 17 00:00:00 2001 From: AndreaGuarracino Date: Sun, 7 Jul 2024 15:42:55 +0200 Subject: [PATCH 5/5] test --- Dockerfile | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/Dockerfile b/Dockerfile index 2b45c1c..053f3aa 100644 --- a/Dockerfile +++ b/Dockerfile @@ -52,12 +52,11 @@ RUN git clone --recursive https://github.com/waveygang/wfmash \ && git pull \ && git checkout 2243583d2f4272ce5254be9ffc508d492dd8b6f8 \ && git submodule update --init --recursive \ - && sed -i 's/ -flto//g' CMakeLists.txt \ - && cmake -H. -Bbuild -DBUILD_STATIC=ON -DBUILD_RETARGETABLE=ON && cmake --build build -- -j $(nproc) \ + && sed -i 's/-march=native/-march=sandybridge/g' src/common/wflign/deps/WFA2-lib/Makefile \ + && cmake -H. -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-march=sandybridge -Ofast' -Bbuild && cmake --build build -- -j $(nproc) \ && cp build/bin/wfmash /usr/local/bin/wfmash \ # Libraries aren't getting installed - && cp build/lib/libwfa2cpp.a /usr/local/lib/ \ - && cp build/lib/libwfa2.a /usr/local/lib/ \ + && cp build/lib/* /usr/local/lib/ \ && cd ../ \ && rm -rf wfmash