diff --git a/package/cern_root/6.18.04/install.sh b/package/cern_root/6.18.04/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..c8ab9ae778a288a33785e59d2a99fdcfb0482bc3 --- /dev/null +++ b/package/cern_root/6.18.04/install.sh @@ -0,0 +1,26 @@ +#!/bin/bash +set -x +set -e +root_version=6.18.04 +. ${DOWNLOAD_TOOL} -u https://root.cern/download/root_v${root_version}.source.tar.gz -f root_v${root_version}.tar.gz +. ${DOWNLOAD_TOOL} -u ${JARVIS_PROXY}/cern-fts/davix/archive/refs/tags/R_0_6_7.tar.gz -f davix-embedded-0.6.7.tar.gz + +yum install -y python3-devel libX11-devel libXpm-devel libXft-devel libXext-devel +cd ${JARVIS_TMP} +rm -rf root_v${root_version} +tar -zxvf ${JARVIS_DOWNLOAD}/root_v${root_version}.tar.gz -C . +cd root-${root_version}/ +rm -rf root_build +mkdir root_build +cd root_build/ +CC=mpicc CXX=mpicxx cmake .. -DCMAKE_INSTALL_PREFIX=$1 -DCMAKE_C_FLAGS="-fPIC" -DCMAKE_CXX_FLAGS="-fPIC" + +cp -ar ${JARVIS_DOWNLOAD}/davix-embedded-0.6.7.tar.gz builtins/davix/DAVIX-prefix/src/ +sed -i 's/1694152a20a5c5e692c4bc545b2efbacec5274fb799e60725412ebae40cced3d/da1f65a86a4ebc3fb825b70a2b1147b72757003ca0ddfce4169d7fff4863de6f/' ../builtins/davix/CMakeLists.txt +sed -i 's/CMAKE_BUILD_TYPE:STRING=RelWithDebInfo/CMAKE_BUILD_TYPE:STRING=Release/' CMakeCache.txt +sed -i 's/clad:BOOL=ON/clad:BOOL=OFF/' CMakeCache.txt + +make -j8 +make install + +exit 0 diff --git a/templates/CNVnator/0.4.1/cnvnator.arm.kgcc.hmpi.config b/templates/CNVnator/0.4.1/cnvnator.arm.kgcc.hmpi.config new file mode 100755 index 0000000000000000000000000000000000000000..b86031c3b0229381caaedf64e48697ae1ce6a983 --- /dev/null +++ b/templates/CNVnator/0.4.1/cnvnator.arm.kgcc.hmpi.config @@ -0,0 +1,56 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +CNVnator/0.4.1 ${JARVIS_PROXY}/abyzovlab/CNVnator/releases/download/v0.4.1/CNVnator_v0.4.1.zip + +[DEPENDENCY] +set -e +yum install -y readline-devel libcurl-devel bzip2-devel +module purge +module use ./software/modulefiles +./jarvis -install kgcc/10.3.1 com +module load kgcc/10.3.1 +./jarvis -install hmpi/2.4.2 gcc +module load hmpi/2.4.2 +./jarvis -install samtools/1.10 gcc+mpi +module load samtools/1.10 +./jarvis -install cern_root/6.18.04 gcc+mpi +module load cern_root/6.18.04 + +mkdir -p ${JARVIS_ROOT}/software/app/cnvnator/bin +unzip ${JARVIS_DOWNLOAD}/CNVnator_v0.4.1.zip -d ${JARVIS_TMP_DOWNLOAD} + +[ENV] +module purge +module use ./software/modulefiles +module load kgcc/10.3.1 +module load hmpi/2.4.2 +module load cern_root/6.18.04 + +[APP] +app_name = cnvnator +build_dir = ${JARVIS_TMP_DOWNLOAD}/CNVnator_v0.4.1/src +binary_dir = +case_dir = ${JARVIS_TMP_DOWNLOAD}/CNVnator_v0.4.1/ExampleData + +[BUILD] +ln -s ${JARVIS_LIBS}/kgcc10.3.1/hmpi2.4.2/cern_root/6.18.04 cern_root +ln -s ${JARVIS_LIBS}/kgcc10.3.1/hmpi2.4.2/samtools/1.10 samtools +sed -i '3a ROOTSYS = cern_root' Makefile +sed -i 's|-I\$(SAMDIR)|-I\$(SAMDIR)/include/bam|' Makefile +sed -i 's|^SAMLIB =.*|SAMLIB = \$(SAMDIR)/lib/libbam.a -lz -llzma -lbz2 -lreadline -lcurl|' Makefile +sed -i 's|^HTSDIR =.*|HTSDIR = \$(wildcard \$(SAMDIR)/include)|' Makefile +sed -i 's|\$(HTSDIR)/libhts\.a|\$(SAMDIR)/lib/libhts\.a|' Makefile +sed -i 's/g++/mpicxx/' Makefile +make LIBS="-lcrypto" OMP=yes -j + +cp -ar cnvnator cnvnator2VCF.pl ${JARVIS_ROOT}/software/app/cnvnator/bin/ + +[CLEAN] +make clean + +[RUN] +run = cp -ar ${JARVIS_ROOT}/templates/CNVnator/0.4.1/cnvnator_test.sh . && bash cnvnator_test.sh +binary = +nodes = 1 \ No newline at end of file diff --git a/templates/CNVnator/0.4.1/cnvnator_test.sh b/templates/CNVnator/0.4.1/cnvnator_test.sh new file mode 100755 index 0000000000000000000000000000000000000000..545f621881415bc805be4ef043e8152aa740152d --- /dev/null +++ b/templates/CNVnator/0.4.1/cnvnator_test.sh @@ -0,0 +1,22 @@ +#!/bin/bash + +set -e + +cd ${JARVIS_TMP_DOWNLOAD}/CNVnator_v0.4.1/ExampleData/ +#该测试BAM文件仅作为cnvnator命令使用参考的小demo。若需包含拷贝数变异CNV测试请自行以实际为准 +wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/chr20.fa.gz +wget https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/NA12878/alignment/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam + +gunzip chr20.fa.gz +mv NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam NA12878_ali.bam +../src/samtools/bin/samtools index NA12878_ali.bam +../src/samtools/bin/samtools faidx chr20.fa + +../src/cnvnator -root NA12878_ali.root -tree NA12878_ali.bam -chrom 20 +../src/cnvnator -root NA12878_ali.root -his 1000 -chrom 20 +../src/cnvnator -root NA12878_ali.root -stat 1000 +../src/cnvnator -root NA12878_ali.root -partition 1000 +../src/cnvnator -root NA12878_ali.root -call 1000 > cnv_calls.txt +../src/cnvnator2VCF.pl -prefix sample -reference hg19 chr20.fa cnv_calls.txt > NA12878_ali.cnv.vcf +#检查VCF头部信息 +grep "^#" NA12878_ali.cnv.vcf