From a44a2e417187c5f857955b8d86a3925842f1ac6b Mon Sep 17 00:00:00 2001 From: limingyang Date: Tue, 15 Jul 2025 14:31:13 +0800 Subject: [PATCH] Add jellyfish, Update htslib and diamond. --- package/htslib/1.11/install.sh | 4 ++ .../diamond/2.0.4/data.diamond.arm.cpu.config | 50 +++++++++++++ .../2.0.4/diamond.arm.cpu.bisheng.hmpi.config | 70 ------------------- .../2.2.10/data.jellyfish.arm.cpu.config | 47 +++++++++++++ 4 files changed, 101 insertions(+), 70 deletions(-) create mode 100644 templates/diamond/2.0.4/data.diamond.arm.cpu.config delete mode 100644 templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config create mode 100644 templates/jellyfish/2.2.10/data.jellyfish.arm.cpu.config diff --git a/package/htslib/1.11/install.sh b/package/htslib/1.11/install.sh index 5c081db..343a483 100755 --- a/package/htslib/1.11/install.sh +++ b/package/htslib/1.11/install.sh @@ -1,10 +1,14 @@ #!/bin/bash set -x set -e + . ${DOWNLOAD_TOOL} -u $JARVIS_PROXY/samtools/htslib/releases/download/1.11/htslib-1.11.tar.bz2 cd ${JARVIS_TMP} tar -xvf ${JARVIS_DOWNLOAD}/htslib-1.11.tar.bz2 cd htslib-1.11 + +yum install bzip2-devel -y + autoreconf -i ./configure --prefix=$1 --host=aarch64-unknown-linux-gnu make -j diff --git a/templates/diamond/2.0.4/data.diamond.arm.cpu.config b/templates/diamond/2.0.4/data.diamond.arm.cpu.config new file mode 100644 index 0000000..b02a6da --- /dev/null +++ b/templates/diamond/2.0.4/data.diamond.arm.cpu.config @@ -0,0 +1,50 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +diamond/2.0.4 $JARVIS_PROXY/bbuchfink/diamond/archive/v2.0.4.tar.gz diamond-2.0.4.tar.gz +swissprot http://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/swissprot.gz swissprot.gz +human_g1k_v37 http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz human_g1k_v37.fasta.gz + +[DEPENDENCY] +set -e +set -x + +module purge +./jarvis -install bisheng/4.1.0 com + +[ENV] +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 + +[APP] +app_name = diamond +build_dir = ${JARVIS_ROOT} +binary_dir = ${JARVIS_ROOT}/diamond-2.0.4/install/bin/ +case_dir = ${JARVIS_ROOT}/diamond-2.0.4/examples + +[BUILD] +rm -rf diamond-2.0.4 +tar -xvzf ${JARVIS_DOWNLOAD}/diamond-2.0.4.tar.gz +cd diamond-2.0.4 +mkdir build install examples +cd build +cmake -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/diamond-2.0.4/install \ + -DCMAKE_CXX_FLAGS="-O3 -g -mcpu=hip09" \ + ../ +make -j +make install + +cd ../examples +gzip -dkcv ${JARVIS_DOWNLOAD}/human_g1k_v37.fasta.gz > human_g1k_v37.fasta +gzip -dkcv ${JARVIS_DOWNLOAD}/swissprot.gz > swissprot + +[CLEAN] +cd build +make clean + +[RUN] +run = time -p numactl -C 0-113 +binary = diamond blastp -p 114 -q human_g1k_v37.fasta -d swissprot -o out.tsv --very-sensitive +nodes = 1 diff --git a/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config b/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config deleted file mode 100644 index 33619c3..0000000 --- a/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config +++ /dev/null @@ -1,70 +0,0 @@ -[SERVER] -11.11.11.11 - -[DOWNLOAD] -diamond/2.0.4 https://github.com/bbuchfink/diamond/archive/v2.0.4.tar.gz diamond-2.0.4.tar.gz -swissprot http://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/swissprot.gz swissprot.gz -human_g1k_v37 http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz human_g1k_v37.fasta.gz - -[DEPENDENCY] -set -e -set -x - -yum install -y vim tar git wget make cmake -module purge -./jarvis -install bisheng/4.1.0 com -module use ./software/modulefiles -module load bisheng/4.1.0 -export CC=`which clang` -export CXX=`which clang++` -export FC=`which flang` -./jarvis -install hmpi/2.4.2 clang -module use ./software/moduledeps/bisheng4.1.0 -module load hmpi/2.4.2 -tar -vzxf ${JARVIS_DOWNLOAD}/diamond-2.0.4.tar.gz -mkdir -p DIAMOND -mkdir -p TESTCASE -cp -r ${JARVIS_DOWNLOAD}/swissprot.gz ./TESTCASE -cp -r ${JARVIS_DOWNLOAD}/human_g1k_v37.fasta.gz ./TESTCASE -cd ./TESTCASE -gzip -dk swissprot.gz -gzip -dk human_g1k_v37.fasta.gz || true -split -l 1000000 human_g1k_v37.fasta human_g1k_part_ -cd .. - -[ENV] -module purge -module use ./software/modulefiles -module load bisheng/4.1.0 -export CC=`which clang` -export CXX=`which clang++` -export FC=`which flang` -module use ./software/moduledeps/bisheng4.1.0 -module load hmpi/2.4.2 - -[APP] -app_name = diamond -build_dir = ${JARVIS_ROOT}/diamond-2.0.4/ -binary_dir = ${JARVIS_ROOT}/DIAMOND/bin/ -case_dir = ${JARVIS_ROOT}/TESTCASE/ - -[BUILD] -mkdir build -cd build -cmake -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/DIAMOND ../ -make -j 16 -make install - -[CLEAN] -cd build -make clean - -[RUN] -run = -binary = diamond blastp -p 16 -q human_g1k_part_aa -d swissprot -o out_part_aa.tsv --very-sensitive -nodes = 1 - -[PERF] -perf= -nsys= -ncu=--target-processes all diff --git a/templates/jellyfish/2.2.10/data.jellyfish.arm.cpu.config b/templates/jellyfish/2.2.10/data.jellyfish.arm.cpu.config new file mode 100644 index 0000000..ac013d0 --- /dev/null +++ b/templates/jellyfish/2.2.10/data.jellyfish.arm.cpu.config @@ -0,0 +1,47 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +jellyfish/2.2.10 $JARVIS_PROXY/gmarcais/Jellyfish/releases/download/v2.2.10/jellyfish-2.2.10.tar.gz + +[DEPENDENCY] +. ${DOWNLOAD_TOOL} -u http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz +yum install liblink-devel -y +set -x +set -e +module purge +module use ./software/modulefiles +./jarvis -install bisheng/4.1.0 com +module load bisheng/4.1.0 +export CC=clang CXX=clang++ FC=flang + +[ENV] +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 + +[APP] +app_name = jellyfish +build_dir = ${JARVIS_ROOT} +binary_dir = ${JARVIS_ROOT}/jellyfish-2.2.10/install/bin/ +case_dir = ${JARVIS_ROOT}/jellyfish-2.2.10/examples + +[BUILD] +rm -rf jellyfish-2.2.10 +tar -zxvf ${JARVIS_DOWNLOAD}/jellyfish-2.2.10.tar.gz +cd jellyfish-2.2.10 +mkdir install examples +./configure --prefix=$(realpath ./install) CXXFLAGS='-O3 -std=c++11 -march=armv8.2-a -mtune=tsv110 -flto' CFLAGS='-O3 -march=armv8.2-a -mtune=tsv110 -flto' +make -j 32 +make install + +cd examples +gzip -dkcv ${JARVIS_DOWNLOAD}/human_g1k_v37.fasta.gz > human_g1k_v37.fasta + +[CLEAN] +make clean + +[RUN] +run = time -p numactl -C 0-111 +binary = jellyfish count -m 21 -s 100M -t 112 -o mer_counts -c 7 human_g1k_v37.fasta +nodes = 1 -- Gitee