diff --git a/templates/augustus/3.3.3/data.augustus.arm.cpu.config b/templates/augustus/3.3.3/data.augustus.arm.cpu.config index c8cab357cab79d108c8d0c9a9166142baf1fcbc8..9d0063a379befa53ac7d84062d7c31467cb1a4ba 100644 --- a/templates/augustus/3.3.3/data.augustus.arm.cpu.config +++ b/templates/augustus/3.3.3/data.augustus.arm.cpu.config @@ -7,7 +7,7 @@ augustus/3.3.3 $JARVIS_PROXY/Gaius-Augustus/Augustus/archive/refs/tags/v3.3.3.ta [DEPENDENCY] set -x set -e -yum install gsl* mysql-devel sqlite* suitesparse* -y +yum install gsl* mysql-devel sqlite* suitesparse* libcurl-devel bzip2-devel -y pip3 install parallel_augustus -i https://mirrors.aliyun.com/pypi/simple --trusted-host mirrors.aliyun.com . ${DOWNLOAD_TOOL} -u https://rpmfind.net/linux/mageia/distrib/9/aarch64/media/core/release/lpsolve-5.5.2.5-5.mga9.aarch64.rpm . ${DOWNLOAD_TOOL} -u https://www.rpmfind.net/linux/mageia/distrib/9/aarch64/media/core/release/lpsolve-devel-5.5.2.5-5.mga9.aarch64.rpm @@ -42,7 +42,7 @@ module load bamtools/2.5.0 [APP] app_name = Augustus build_dir = ${JARVIS_ROOT} -binary_dir = ${JARVIS_ROOT}/Augustus-3.3.3/install-3.3.3/bin +binary_dir = case_dir = ${JARVIS_ROOT}/Augustus-3.3.3/run [BUILD] @@ -55,6 +55,8 @@ sed -i "s|\/opt\/augustus|$AUGUSTUS_PATH|g" Makefile sed -i -e "18s|.*|SAMTOOLS=${SAMTOOLS_PATH}/lib|" \ -e "19s|.*|HTSLIB=${HTSLIB_PATH}/lib|" \ ./auxprogs/bam2wig/Makefile +sed -i "s/g++/clang++/g" ./auxprogs/joingenes/Makefile ./auxprogs/utrrnaseq/Debug/makefile ./auxprogs/utrrnaseq/Debug/src/subdir.mk ./auxprogs/bam2hints/Makefile ./auxprogs/homGeneMapping/src/Makefile ./src/Makefile ./src/unittests/Makefile +sed -i "s?\/usr\/include\/boost?${BOOST_CLANG_PATH}\/include?g" ./auxprogs/utrrnaseq/Debug/src/subdir.mk make -j VERBOSE=1 CC=clang CXX=clang++ \ CFLAGS="-g -lstdc++ -I${SAMTOOLS_PATH}/include -I${BAMTOOLS_PATH}/include/bamtools -I${BOOST_CLANG_PATH}/include -I${HTSLIB_PATH}/include -I${HTSLIB_PATH}/include/htslib -I${MYSQL_PATH}/include/mysql++ -L${BAMTOOLS_PATH}/lib64 -L${BOOST_CLANG_PATH}/lib -L${HTSLIB_PATH}/lib -L${MYSQL_PATH}/lib -L/usr/lib64/mysql" \