diff --git a/HPC/lumpy/0.3.1/24.03-lts-sp2/Dockerfile b/HPC/lumpy/0.3.1/24.03-lts-sp2/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..e0ddb0dbe33b37b6552397598321d98475afc95f --- /dev/null +++ b/HPC/lumpy/0.3.1/24.03-lts-sp2/Dockerfile @@ -0,0 +1,26 @@ +ARG BASE=openeuler/openeuler:24.03-lts-sp2 +FROM ${BASE} + +ARG VERSION=0.3.1 + +RUN yum install -y git make gcc g++ clang automake zlib-devel libcurl-devel openssl-devel wget && \ + yum clean all + +WORKDIR /opt/ +# install required autoconf version +RUN rpm -e --nodeps autoconf && \ + wget https://mirrors.aliyun.com/gnu/autoconf/autoconf-2.69.tar.gz && \ + tar -xzf autoconf-2.69.tar.gz && rm -rf autoconf-2.69.tar.gz && \ + cd autoconf-2.69 && \ + ./configure && \ + make && make install + +COPY lumpy.patch /opt/ +RUN git clone --recursive -b v${VERSION} https://github.com/arq5x/lumpy-sv.git && \ + cd /opt/lumpy-sv/lib/htslib/ && \ + autoreconf -i && ./configure --disable-bz2 --disable-lzma --enable-libcurl && \ + make && make install && \ + cd /opt/lumpy-sv && \ + mv /opt/lumpy.patch ./ && \ + git apply lumpy.patch && \ + make && cp bin/* /usr/local/bin/ diff --git a/HPC/lumpy/0.3.1/24.03-lts-sp2/lumpy.patch b/HPC/lumpy/0.3.1/24.03-lts-sp2/lumpy.patch new file mode 100644 index 0000000000000000000000000000000000000000..e9ca498fe6a1bafcf9a6563fd246a16fcb5771e5 --- /dev/null +++ b/HPC/lumpy/0.3.1/24.03-lts-sp2/lumpy.patch @@ -0,0 +1,63 @@ +diff --git a/Makefile b/Makefile +index 9b206fc..8b94c94 100644 +--- a/Makefile ++++ b/Makefile +@@ -64,17 +64,17 @@ lumpy: + echo ""; \ + done + +-lumpy_filter: htslib ++lumpy_filter: + [ -d $(BIN_DIR) ] || mkdir -p $(BIN_DIR) + $(MAKE) --no-print-directory -C src/filter/ + cp src/filter/lumpy_filter $(BIN_DIR) + + +-htslib: +- $(shell cd lib/htslib && autoreconf) +- cd lib/htslib && \ +- ./configure --disable-bz2 --disable-lzma --enable-libcurl +- CFLAGS="$(CFLAGS) -DBGZF" $(MAKE) -C lib/htslib --no-print-directory CFLAGS="-DBGZF_MT" ++#htslib: ++# cd lib/htslib && autoreconf ++# cd lib/htslib && \ ++# ./configure --disable-bz2 --disable-lzma --enable-libcurl ++# CFLAGS="$(CFLAGS) -DBGZF" $(MAKE) -C lib/htslib --no-print-directory CFLAGS="-DBGZF_MT" + + lumpyexpress: + [ -d $(BIN_DIR) ] || mkdir -p $(BIN_DIR) +diff --git a/src/utils/BamTools/src/api/algorithms/Sort.h b/src/utils/BamTools/src/api/algorithms/Sort.h +index 32902e1..754df63 100644 +--- a/src/utils/BamTools/src/api/algorithms/Sort.h ++++ b/src/utils/BamTools/src/api/algorithms/Sort.h +@@ -76,7 +76,7 @@ struct API_EXPORT Sort { + { } + + // comparison function +- bool operator()(const BamTools::BamAlignment& lhs, const BamTools::BamAlignment& rhs) { ++ bool operator()(const BamTools::BamAlignment& lhs, const BamTools::BamAlignment& rhs) const { + return sort_helper(m_order, lhs.Name, rhs.Name); + } + +@@ -112,7 +112,7 @@ struct API_EXPORT Sort { + { } + + // comparison function +- bool operator()(const BamTools::BamAlignment& lhs, const BamTools::BamAlignment& rhs) { ++ bool operator()(const BamTools::BamAlignment& lhs, const BamTools::BamAlignment& rhs) const { + + // force unmapped aligmnents to end + if ( lhs.RefID == -1 ) return false; +diff --git a/src/utils/BamTools/src/api/internal/bam/BamMultiMerger_p.h b/src/utils/BamTools/src/api/internal/bam/BamMultiMerger_p.h +index 3000097..ceac8ed 100644 +--- a/src/utils/BamTools/src/api/internal/bam/BamMultiMerger_p.h ++++ b/src/utils/BamTools/src/api/internal/bam/BamMultiMerger_p.h +@@ -61,7 +61,7 @@ struct MergeItemSorter : public std::binary_function + : m_comp(comp) + { } + +- bool operator()(const MergeItem& lhs, const MergeItem& rhs) { ++ bool operator()(const MergeItem& lhs, const MergeItem& rhs) const { + const BamAlignment& l = *lhs.Alignment; + const BamAlignment& r = *rhs.Alignment; + return m_comp(l,r); diff --git a/HPC/lumpy/README.md b/HPC/lumpy/README.md index 2087cff14ce4fe62656371944eed039c864056fa..a3a9f0bc1113f4386cc6c0a8d5d8d4ac94c3b786 100644 --- a/HPC/lumpy/README.md +++ b/HPC/lumpy/README.md @@ -18,6 +18,7 @@ The tag of each lumpy-sv container image is consist of the version of lumpy-sv a | Tags | Currently | Architectures| |------|-----------|---------------| +|[0.3.1-oe2403sp2](https://gitee.com/openeuler/openeuler-docker-images/blob/master/HPC/lumpy/0.3.1/24.03-lts-sp2/Dockerfile) | lumpy 0.3.1 on openEuler 24.03-LTS-SP2 | amd64, arm64 | |[0.3.1-oe2403sp1](https://gitee.com/openeuler/openeuler-docker-images/blob/master/HPC/lumpy-sv/0.3.1/24.03-lts-sp1/Dockerfile)| lumpy-sv 0.3.1 on openEuler 24.03-LTS-SP1 | amd64, arm64 | diff --git a/HPC/lumpy/doc/image-info.yml b/HPC/lumpy/doc/image-info.yml index a563fb051b6396354caf4faa438b973e36c6a817..8703cbaa44442ab72ad8f6d5c09a7ce3ea4d5c4a 100644 --- a/HPC/lumpy/doc/image-info.yml +++ b/HPC/lumpy/doc/image-info.yml @@ -11,6 +11,7 @@ tags: | | Tags | Currently | Architectures| |------|-----------|---------------| + |[0.3.1-oe2403sp2](https://gitee.com/openeuler/openeuler-docker-images/blob/master/HPC/lumpy/0.3.1/24.03-lts-sp2/Dockerfile) | lumpy 0.3.1 on openEuler 24.03-LTS-SP2 | amd64, arm64 | |[0.3.1-oe2403sp1](https://gitee.com/openeuler/openeuler-docker-images/blob/master/HPC/lumpy-sv/0.3.1/24.03-lts-sp1/Dockerfile)| lumpy-sv 0.3.1 on openEuler 24.03-LTS-SP1 | amd64, arm64 | download: | 拉取镜像到本地 diff --git a/HPC/lumpy/meta.yml b/HPC/lumpy/meta.yml index 683bf0c4f2fa077cf5f925801754bbdf631131e6..c902eced189d8a577ab8c8d339e7fff80404cda1 100644 --- a/HPC/lumpy/meta.yml +++ b/HPC/lumpy/meta.yml @@ -1,2 +1,4 @@ 0.3.1-oe2403sp1: - path: 0.3.1/24.03-lts-sp1/Dockerfile \ No newline at end of file + path: 0.3.1/24.03-lts-sp1/Dockerfile +0.3.1-oe2403sp2: + path: 0.3.1/24.03-lts-sp2/Dockerfile \ No newline at end of file