ARM软件编译

-mtune=tsv110 -march=armv8-a

$ ./configure 
checking for gawk... gawk
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in '/share/home/software/package/samtools/samtools-1.22.1':
configure: error: C compiler cannot create executables
See 'config.log' for more details

# 解决
yum install glibc-static libxcrypt-static libstdc++-static

$ ldd samtools_static
    not a dynamic executable

$ ldd samtools_dynamic
./samtools_d2: /lib64/libm.so.6: version 'GLIBC_2.23' not found (required by ./samtools_d2)
    linux-vdso.so.1 =>  (0x00007fff33b8a000)
    /usr/local/bin/snoopy/lib/libsnoopy.so (0x00007fe3ca389000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fe3ca16d000)
    libz.so.1 => /lib64/libz.so.1 (0x00007fe3c9f57000)
    libm.so.6 => /lib64/libm.so.6 (0x00007fe3c9c55000)
    libbz2.so.1 => /lib64/libbz2.so.1 (0x00007fe3c9a45000)
    liblzma.so.5 => /lib64/liblzma.so.5 (0x00007fe3c981f000)
  ...
    libcrypto.so.10 => /lib64/libcrypto.so.10 (0x00007fe3c66ca000)
    librt.so.1 => /lib64/librt.so.1 (0x00007fe3c64c2000)
    libkrb5support.so.0 => /lib64/libkrb5support.so.0 (0x00007fe3c62b2000)
    libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x00007fe3c60ae000)
    libresolv.so.2 => /lib64/libresolv.so.2 (0x00007fe3c5e95000)
    libsasl2.so.3 => /lib64/libsasl2.so.3 (0x00007fe3c5c78000)
    libselinux.so.1 => /lib64/libselinux.so.1 (0x00007fe3c5a51000)
    libcrypt.so.1 => /lib64/libcrypt.so.1 (0x00007fe3c581a000)
    libpcre.so.1 => /lib64/libpcre.so.1 (0x00007fe3c55b8000)
    libfreebl3.so => /lib64/libfreebl3.so (0x00007fe3c53b5000)

$ ll -h
-rwxr-xr-x 1 software software  14M Sep 21 00:49 samtools_static
-rwxr-xr-x 1 software software 9.2M Sep 21 00:13 samtools_dynamic

$ ./samtools_dynamic
./samtools_d2: /lib64/libm.so.6: version 'GLIBC_2.23' not found (required by ./samtools_d2)

$ ./samtools_static --version
samtools 1.22.1
Using htslib 1.22.1
Copyright (C) 2025 Genome Research Ltd.

Samtools compilation details:
    Features:       build=configure curses=no
    CC:             gcc
    CPPFLAGS:
    CFLAGS:         -Wall -g -O2
    LDFLAGS:        -static
    HTSDIR:         htslib-1.22.1
    LIBS:
    CURSES_LIB:

HTSlib compilation details:
    Features:       build=configure libcurl=no S3=no GCS=no libdeflate=no lzma=yes bzip2=no plugins=no htscodecs=1.6.4
    CC:             gcc
    CPPFLAGS:
    CFLAGS:         -Wall -g -O2 -fvisibility=hidden
    LDFLAGS:        -fvisibility=hidden

HTSlib URL scheme handlers present:
    built-in:    file, data, preload
    crypt4gh-needed:     crypt4gh
    mem:     mem

export CC="gcc -static"
export CPPFLAGS="-I/opt/static/include"
export LDFLAGS="-L/opt/static/lib -static"
export LIBS="-lssl -lcrypto -lz -ldl -pthread"
./configure --disable-shared --enable-static
make

iperf3_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
    $(LIBTOOLFLAGS) --mode=link $(CCLD) -all-static $(iperf3_CFLAGS) $(CFLAGS) \
    $(iperf3_LDFLAGS) $(LDFLAGS) -o $@

LTCOMPILE = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \
    $(LIBTOOLFLAGS) --mode=compile $(CC) -static $(DEFS) \
    $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) \
    $(AM_CFLAGS) $(CFLAGS)

libtool looks at the parameters of gcc, so you should have something like below

$ cat Makefile
all: libone libtwo
        rm *.o
        @libtool --mode=link gcc -all-static -o libcombo.a libone.a libtwo.a

libone: one.c
        @libtool --mode=compile gcc -c one.c -o one.lo
        @libtool --mode=link gcc -static -o libone.a one.lo

libtwo: two.c
        @libtool --mode=compile gcc -c two.c -o two.lo
        @libtool --mode=link gcc -static -o libtwo.a two.lo

cmake -B build -G Ninja \
  -DCMAKE_BUILD_TYPE=Release \
  -DBUILD_SHARED_LIBS=OFF \
  -DCMAKE_EXE_LINKER_FLAGS="-static" \
  -DCMAKE_C_FLAGS="-fPIC" \
  -DCMAKE_CXX_FLAGS="-fPIC" \
  -DZLIB_USE_STATIC_LIBS=ON \
  -DCMAKE_INSTALL_PREFIX=/opt/static
cmake --build build

git clone https://github.com/baoxingsong/anchorwave.git
cd anchorwave
mv CMakeLists_arm.txt CMakeLists.txt
cmake ./
make

module load gcc/compiler/gccmodule gcc/hmpi/hmpi 
tar xf Amber24.tar.bz2
tar xf AmberTools24.tar.bz2
pip install --prefix=/path/to/amber/ numpy scipy matplotlib
cd amber24_src
$ ./update_amber --update
cd build

  cmake $AMBER_PREFIX/amber24_src \
    -DCMAKE_INSTALL_PREFIX=/share/software/app/arm/amber/24/ \
    -DCOMPILER=GNU  \
    -DMPI=TRUE -DCUDA=FALSE -DINSTALL_TESTS=TRUE \
    -DDOWNLOAD_MINICONDA=FALSE \
    2>&1 | tee  cmake.log

$ tar xf apbs-3.4.1.tar.gz
$ cd apbs-3.4.1
$ mkdir build && cd build
$ export APBS_BUILD_DIR=${PWD}
$ export SuiteSparse_DIR="/path/to/suitesparse/"
$ export CMAKE_PREFIX_PATH="/path/to/suitesparse/:$CMAKE_PREFIX_PATH"
$ cmake .. -DUMFPACK_INCLUDES=/path/to/suitesparse/include/suitesparse/umfpack.h -DUMFPACK_LIBRARIES=/path/to/suitesparse/lib64/libumfpack.a -DAMD_INCLUDE_DIR=/path/to/suitesparse/include/suitesparse/ -DAMD_STATIC=/path/to/suitesparse/lib64/libamd.a -DPython3_EXECUTABLE=/usr/bin/python3 -DCMAKE_C_COMPILER=`which gcc` -DCMAKE_CXX_COMPILER=`which g++` -DCMAKE_C_FLAGS="-fopenmp" -DCMAKE_CXX_FLAGS="-fopenmp"
$ make -j
$ make install

$ wget http://bioinf.uni-greifswald.de/augustus/binaries/augustus.current.tar.gz
$ tar -xzf augustus.current.tar.gz
$ cd augustus

$ module load arm/bamtools/2.5.2    arm/htslib/1.21
$ tar -xzf augustus.current.tar.gz
$ cd augustus
$ make

$ mkdir build && cd build
$ ../configure --prefix=/path/to/atlas/ -Si archdef 0 -b 64 -D c -DATL_ARM_HARDFP=1   --cripple-atlas-performance 
# make -j 20 会报错
$ make && make install
# 查看安装的库
$ $ ls -1 /path/to/atlas/
libatlas.a
libcblas.a
libf77blas.a
liblapack.a
libptcblas.a
libptf77blas.a

$ git clone https://github.com/GuoliangLi-HZAU/BatMeth2.git

$ cp  ~/package/sse2neon.h src/mealign/
$ sed -i.bak 's/<emmintrin.h>/"sse2neon.h"/g' ./src/mealign/ksw.c 
$ sed -i.bak 's/-m64/ /g' ./src/Makefile 

$ ./configure --prefix=/path/to/batmeth2/
$ make -j20 && make install

$ wget https://codeload.github.com/djhshih/blat/tar.gz/v35.1
$ mv v35.1 blat_35.1.tar.gz
$ tar xf blat_35.1.tar.gz
$ cd blat-35.1/
$ make
# 或编译静态库版本
$ CFLAGS="-static -static-libgcc -D_STATIC" make

$ wget https://github.com/berkeleydb/libdb/releases/download/v5.3.28/db-5.3.28.tar.gz
$ tar xf db-5.3.28.tar.gz
$ cd db-5.3.28/build_unix
$ ../dist/configure --build=aarch64-unknown-linux-gnu --prefix=/path/to/berkeley-db/
$ make -j20 && make install

$ wget https://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/bmtagger.sh
$ wget https://anaconda.org/bioconda/bmfilter/3.101/download/linux-aarch64/bmfilter-3.101-h78569d1_5.tar.bz2
$ wget https://anaconda.org/bioconda/srprism/2.4.24/download/linux-aarch64/srprism-2.4.24-h76f4f2e_5.tar.bz2
$ wget https://conda.anaconda.org/bioconda/linux-aarch64/extract_fullseq-3.101-h78569d1_5.tar.bz2

$ tar xf *bz2
$ ls -1 bin/
bmfilter
extract_fullseq
srprism

$ module load arm/blast/2.16.0

#!/bin/sh

echo "bmtagger.sh: You may want to edit bmtagger.conf" >&2
SRPRISM=./bin/srprism 
BMFILTER="./bin/bmfilter"
EXTRACT_FA="./bin/extract_fullseq"
#bmfiles="hs/quick_mask/indexes/washu_mask18" 
#blastdb="hs/quick_mask/indexes/HUMAN_SCREENING"
#srindex="hs/quick_mask/indexes/HUMAN_SCREENING.srprism"
#TMPDIR="/tmp"

$ wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.16.0+-aarch64-linux.tar.gz

# 下载二进制版本
wget https://anaconda.org/bioconda/bwa-mem2/2.2.1/download/linux-aarch64/bwa-mem2-2.2.1-h0010869_6.tar.bz2

git clone https://github.com/ComparativeGenomicsToolkit/cactus.git --recursive
cd cactus

make -j20
pip install --prefix=/path/to/cactus/  submodules/sonLib
pip install --prefix=/path/to/cactus/  .
pip install --prefix=/path/to/cactus/ -r toil-requirement.txt

$ mkdir build
$ cd build
$ cmake -DCMAKE_INSTALL_PREFIX=/path/to/cereal/ -DBoost_INCLUDE_DIR=/path/to/boost/include/   ..
$ make -j12
$ make install

$ wget https://circos.ca/distribution/circos-0.69-10.tgz

$ tar xf circos-0.69-10.tgz

$ cd circos-0.69-10

$ module load arm/perl/5.34.0

# 查看确实的 perl 模块
$ bin/circos -modules|grep missing
missing            Font::TTF::Font
missing            GD
missing            GD::Polyline
missing            Math::Bezier
missing            Math::Round
missing            Math::VecStat
missing            Params::Validate
missing            Regexp::Common
missing            Set::IntSpan
missing            Statistics::Basic
missing            Text::Format

# 安装缺失的 perl 模块
$ cpanm -l  /share/software/app/arm/perl/5.34.0/ Text::Format Statistics::Basic Set::IntSpan Regexp::Common Params::Validate Math::VecStat Math::Round Math::Bezier Font::TTF::Font


# 加载 libgd 用于安装 GD 模块，注意 libgd 版本需要低于 2.3，否则 GD 模块安装会报错
# 报错是高版本的 libgd 中没有 gdlib-config 导致的
$ module load arm/libgd/2.2.5
$ cpanm -l  /share/software/app/arm/perl/5.34.0/ GD GD::Polyline

# 测试
$ bin/circos -conf /share/software/app/arm/circos/0.69-10/example/etc/circos.conf

wget http://www.clustal.org/download/current/clustalw-2.1.tar.gz
tar xf clustalw-2.1.tar.gz
cd clustalw-2.1/
./configure --build=arm  --prefix=/path/to/clustalw/
make -j20 && make install

$ tar xf cppunit-1.13.2.tar.gz 
$ cd cppunit-1.13.2
$ ./configure --prefix=/path/to/cppunit/ --build=aarch64-unknown-linux-gnu
$ make -j20 && make install

mamba create -n EDTA2.2 -c conda-forge -c bioconda annosine2 biopython cd-hit coreutils genericrepeatfinder genometools-genometools glob2 tir-learner ltr_finder_parallel ltr_retriever mdust multiprocess muscle openjdk perl perl-text-soundex r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr tesorter samtools bedtools LTR_HARVEST_parallel HelitronScanner

glob2 
https://github.com/lutianyu2001/TIR-Learner

$ git clone https://github.com/haplotype/ELAI
$ cd src

cd ../example
$ ../src/elai -g hap.ceu.chr22.inp -p 10 -g hap.yri.chr22.inp -p 11 -g admix-1cm.inp -p 1 -pos hgdp.chr22.pos -o test -s 20 --exclude-nopos --exclude-maf 0.01 --exclude-miss1 -mg 20

$ wget https://anaconda.org/bioconda/emboss/6.6.0/download/linux-aarch64/emboss-6.6.0-h70f19aa_11.tar.bz2

# 2.1.13
pip install --prefix=/path/to/eggnog-mapper eggnog-mapper

# eggnog-mapper 安装包自带了这几个软件的预编译版，但都是 x86 的，使用时需要载入 arm 版
# eggnog-mapper 会优先使用 $PATH 中有的软件，然后再使用自己安装的
$ module load arm/diamond/2.1.10 arm/prodigal/2.6.3 arm/mmseqs2/16-747c6 arm/hmmer/3.4 
$ emapper.py -h

# 2759 是真核数据库，一路 Y 就可以了
$ download_eggnog_data.py -F -f -P -M -H -d 2759

$ tar xf EVidenceModeler-v2.1.0.tar.gz
$ cd EVidenceModeler-v2.1.0

$ make

$ wget https://anaconda.org/bioconda/exonerate/2.4.0/download/linux-aarch64/exonerate-2.4.0-he4d9ad3_8.tar.bz2

$ wget https://anaconda.org/bioconda/fastqc/0.12.1/download/noarch/fastqc-0.12.1-hdfd78af_0.tar.bz2

# 设置静态库地址
$ export LIBRARY_PATH=/path/to/isa-l/lib/:/path/to/libdeflate/lib/:/path/to/gcc/lib64/
$ git clone https://github.com/OpenGene/fastp.git
$ cd fastp
$ make -j12 static

git clone https://github.com/jashapiro/fastStructure.git
cd fastStructure
git checkout py3

$ module load arm/gsl/2.4
$ pip install --prefix=/path/to/faststructure/ numpy scipy cython
$ cd var
$ PYTHONPATH=/path/to/faststructure/1.0/lib64/python3.9/site-packages/:/path/to/faststructure/1.0/lib/python3.9/site-packages/ python setup.py build_ext -f --inplace
$ cd ..
$ PYTHONPATH=/path/to/faststructure/1.0/lib64/python3.9/site-packages/:/path/to/faststructure/1.0/lib/python3.9/site-packages/ python setup.py build_ext -f --inplace

# 测试，将 ./var/ 加入 PYTHONPATH，否则出现 allelefreq 相关报错
$ PYTHONPATH=/path/to/faststructure/1.0/lib64/python3.9/site-packages/:/path/to/faststructure/1.0/lib/python3.9/site-packages/:$PWD python structure.py -h

Traceback (most recent call last):
  File "//path/to/faststructure/fastStructure/structure.py", line 176, in <module>
    Q, P, other = fastStructure.infer_variational_parameters(G, params['K'], \
  File "fastStructure.pyx", line 99, in fastStructure.infer_variational_parameters
    psi.update(G, pi)
TypeError: Cannot convert allelefreq.AlleleFreq to allelefreq.AlleleFreq

$ module load arm/python/2.7.18
$ git clone https://github.com/rajanil/fastStructure/
$ cd fastStructure

$ pip install --prefix=/path/to/fastStructure/ numpy
# 设置编译参数 -fallow-argument-mismatch，否则 scipy 编译过程中出现报错 Error: Rank mismatch between actual argument at (1) and actual argument at (2) (scalar and rank-1)
$ export FCFLAGS="-fallow-argument-mismatch"
$ export FFLAGS="-fallow-argument-mismatch"
$ PYTHONPATH=/path/to/lib/python2.7/site-packages/ pip install --prefix=/path/to/fastStructure/ scipy  Cython matplotlib

$ cd vars
$ PYTHONPATH=/path/to/lib/python2.7/site-packages/ python setup.py build_ext -f --inplace
$ cd ..
$ PYTHONPATH=/path/to/lib/python2.7/site-packages/ python setup.py build_ext -f --inplace
# 测试
$ PYTHONPATH=/path/to/lib/python2.7/site-packages/:$PWD/vars/ python structure.py -h

$ wget http://meta.microbesonline.org/fasttree/FastTree.c
$ gcc -DOPENMP -DUSE_DOUBLE -fopenmp -O3 -march=armv8.2-a -mtune=tsv110 -finline-functions -funroll-loops -Wall -o FastTreePar-2.1.11 FastTree.c -lm
$ export OMP_NUM_THREADS=128

$ module load arm/openmpi/5.0.5
$ wget wget https://fftw.org/pub/fftw/fftw-3.3.8.tar.gz
$ tar xf fftw-3.3.8.tar.gz
$ cd fftw-3.3.8/
$ ./configure --prefix=/path/to/fftw/ --enable-single --enable-float --enable-neon --enable-shared --enable-threads --enable-openmp --enable-mpi CFLAGS="-O3 -fomit-frame-pointer -fstrict-aliasing"
$ make -j20
$ make install

wget wget https://anaconda.org/bioconda/flye/2.9.5/download/linux-aarch64/flye-2.9.5-py39h989d1c4_2.tar.bz2
tar xf flye-2.9.5-py39h989d1c4_2.tar.bz2

# 下载这个 arm64 分支
git clone -b devel https://github.com/syalavarthi/GKL.git
cd GKL

git clone https://github.com/IntelLabs/GKL.git

git submodule update --init
git clone https://github.com/jianyangqt/gcta.git
cd gcta
mdir build; cd build
module load arm/gcc/12.2.0
export EIGEN3_INCLUDE_DIR=/path/to/eigen/3.4.0/include/eigen3
export SPECTRA_LIB=/path/to/spectra/1.1.0/include/
export BOOST_LIB=/path/to/boost/1.72.0/include/
export OPENBLAS=/path/to/openblas/0.3.13/
cmake ..
make -j20

$ cd build
$ cmake -DCMAKE_CXX_FLAGS="-static" 
$ make -j VERBOSE=1
$ ldd gcta64
    not a dynamic executable

$ wget https://ftp.gnu.org/gnu/gcc/gcc-10.3.0/gcc-10.3.0.tar.xz
$ tar xf gcc-10.3.0.tar.xz
$ cd gcc-10.3.0
$ contrib/download_prerequisites 
$ mkdir build
$ cd build
../configure \
    --prefix=/path/to/gcc \
    --enable-languages=all \
    --enable-threads=posix \
    --enable-shared \
    --enable-static \
    --disable-multilib \
    --enable-libatomic \
    --enable-libgomp \
    --enable-libstdcxx \
$ make -j20 && make install

# 使用静态链接库编译，设置环境变量
$ export LIBRARY_PATH=/path/to/gsl/lib/:/path/to/openblas/lib/:/path/to/gcc/lib64/

$ wget https://github.com/genetics-statistics/GEMMA/archive/refs/tags/v0.98.5.tar.gz
$ mv v0.98.5.tar.gz gemma-0.98.5.tar.gz
$ tar xf gemma-0.98.5.tar.gz
$ cd GEMMA-0.98.5/
$ make -j12 static

$ module load arm/r/4.4.1 
$ wget https://cran.r-project.org/src/contrib/Archive/GenABEL.data/GenABEL.data_1.0.0.tar.gz
$ wget https://cran.r-project.org/src/contrib/Archive/GenABEL/GenABEL_1.8-0.tar.gz
$ tar xf GenABEL_1.8-0.tar.gz
$ R CMD INSTALL GenABEL.data_1.0.0.tar.gz

$ git clone https://github.com/gpertea/gffread
$ cd gffread/
$ make release

$ git clone https://github.com/gflow/GFlow.git
$ cd GFlow
# 加载 petsc
$ module load arm/petsc/3.22.2-openmpi
# 下载测试算例
$ wget https://github.com/gflow/GFlow/releases/download/v0.1.7-alpha/inputs.tar.gz

#define MAX(a, b) ((a) > (b) ? (a) : (b))

$ tar xf inputs.tar.gz
$ cp input/* .
# 修改 execute_example.sh 中 PETSC_DIR 的位置为 petsc 的安装目录
$ sh execute_example.sh

git clone https://github.com/dnanexus-rnd/GLnexus
cd GLnexus

https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2
https://github.com/facebook/rocksdb/archive/v6.29.3.tar.gz
https://github.com/jbeder/yaml-cpp/archive/yaml-cpp-0.6.3.zip
https://github.com/vit-vit/CTPL/archive/v.0.0.2.zip
https://github.com/giacomodrago/fcmm/archive/v1.0.1.zip
https://github.com/gabime/spdlog/archive/v1.8.2.tar.gz
https://capnproto.org/capnproto-c++-0.7.0.tar.gz
https://github.com/philsquared/Catch/archive/v1.12.2.zip

$ ls -1 external/src/{*gz,*zip,*bz2}
external/src/capnproto-c++-0.7.0.tar.gz
external/src/htslib-1.9.tar.bz2
external/src/v.0.0.2.zip
external/src/v1.0.1.zip
external/src/v1.8.2.tar.gz
external/src/v6.29.3.tar.gz
external/src/yaml-cpp-0.6.3.zip

//#ifndef __x86_64__
//if (uint64_t(data.data) % sizeof(::capnp::word)) {
 //    return Status::Failure("BCFBucketReader: input buffer isn't word-aligned");
//}
//#endif

/usr/bin/ld: cannot find -lsnappy
/usr/bin/ld: cannot find -lzstd
/usr/bin/ld: cannot find -lstdc++

[ 76%] Linking CXX executable glnexus_cli
[ 77%] Built target glnexus_cli
[ 78%] Creating directories for 'catch'
[ 79%] Performing download step (download, verify and extract) for 'catch'

$ ./glnexus_cli -h
[2871613] [2025-03-09 19:12:19.710] [GLnexus] [info] glnexus_cli release v1.4.5-0-gfae491b-dirty Mar  9 2025
[2871613] [2025-03-09 19:12:19.710] [GLnexus] [warning] jemalloc absent, which will impede performance with high thread counts. See https://github.com/dnanexus-rnd/GLnexus/wiki/Performance
Usage: ./glnexus_cli [options] /vcf/file/1 .. /vcf/file/N
Merge and joint-call input gVCF files, emitting multi-sample BCF on standard output.

Options:
  --dir DIR, -d DIR              scratch directory path (mustn't already exist; default: ./GLnexus.DB)
  --config X, -c X               configuration preset name or .yml filename (default: gatk)
  --bed FILE, -b FILE            three-column BED file with ranges to analyze (if neither --range nor --bed: use full length of all contigs)
  --list, -l                     expect given files to contain lists of gVCF filenames, one per line

  --more-PL, -P                  include PL from reference bands and other cases omitted by default
  --squeeze, -S                  reduce pVCF size by suppressing detail in cells derived from reference bands
  --trim-uncalled-alleles, -a    remove alleles with no output GT calls in postprocessing

  --mem-gbytes X, -m X           memory budget, in gbytes (default: most of system memory)
  --threads X, -t X              thread budget (default: all hardware threads)

  --help, -h                     print this help message

Configuration presets:
            Name          CRC32C    Description
            gatk      1926883223    Joint-call GATK-style gVCFs
 gatk_unfiltered      4039280095    Merge GATK-style gVCFs with no QC filters or genotype revision
          xAtlas      1991666133    Joint-call xAtlas gVCFs
xAtlas_unfiltered       221875257   Merge xAtlas gVCFs with no QC filters or genotype revision
          weCall      2898360729    Joint-call weCall gVCFs
weCall_unfiltered      4254257210   Merge weCall gVCFs with no filtering or genotype revision
     DeepVariant      2932316105    Joint call DeepVariant whole genome sequencing gVCFs
  DeepVariantWGS      2932316105    Joint call DeepVariant whole genome sequencing gVCFs
  DeepVariantWES      1063427682    Joint call DeepVariant whole exome sequencing gVCFs
DeepVariantWES_MED_DP      2412618877   Joint call DeepVariant whole exome sequencing gVCFs, populating 0/0 DP from MED_DP instead of MIN_DP
DeepVariant_unfiltered      3285998180  Merge DeepVariant gVCFs with no QC filters or genotype revision
        Strelka2       395868656    [EXPERIMENTAL] Merge Strelka2 gVCFs with no QC filters or genotype revision
             GxS      3929547104    [EXPERIMENTAL] merging for GxS

$ wget http://research-pub.gene.com/gmap/src/gmap-gsnap-2023-12-01.tar.gz
$ tar xf gmap-gsnap-2023-12-01.tar.gz
$ cd gmap-2023-12-01/
$ ./configure --prefix=/path/to/gmap/ --with-simd-level=arm

$ wget http://nchc.dl.sourceforge.net/project/gnuplot/gnuplot/5.4.9/gnuplot-5.4.9.tar.gz
$ tar xf gnuplot-5.4.9.tar.gz
$ cd gnuplot-5.4.9
$ module load arm/lua/5.4.7
$ ./configure --prefix=/path/gnuplot/ --with-qt=no
$ make -j20 && make install

$ module load arm/openmpi/5.0.5 arm/openblas/0.3.28
$ wget http://ftp.gromacs.org/pub/gromacs/gromacs-2019.5.tar.gz
$ tar xf gromacs-2019.5.tar.gz
$ cd gromacs-2019.5/
$ mkdir build && cd build/
$ cmake .. -DCMAKE_INSTALL_PREFIX=/path/to/gromacs/ -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_OPENMP=on -DGMX_MPI=on -DGMX_X11=off -DGMX_GPU=off -DFFTWF_LIBRARY=/path/to/lib//libfftw3f.so -DFFTWF_INCLUDE_DIR=/path/to/include
$ make -j20
$ make install

$ cmake .. -DGMX_GPU=CUDA -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=/path/to/gromacs/
$ make -j20
$ make install

$ cmake .. -DGMX_GPU=CUDA -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_C_COMPILER=`which gcc` -DCMAKE_INSTALL_PREFIX=/path/to/GROMACS/ -DGMX_BUILD_OWN_FFTW_URL=/path/to/fftw-3.3.8.tar.gz -DGMX_BUILD_OWN_FFTW_MD5=8aac833c943d8e90d51b697b27d4384d
$ make -j20 && make install

$ module load arm/plumed/2.9.2-bisheng arm/hyper-mpi/24.6.30_bisheng
$ wget http://ftp.gromacs.org/pub/gromacs/gromacs-2021.7.tar.gz
$ tar xf gromacs-2021.7.tar.gz
$ cd gromacs-2021.7/
# 为 plumed 打 patch
$ plumed-patch -p -e gromacs-2021.7
$ mkdir build && cd build/
$ cmake .. -DCMAKE_INSTALL_PREFIX=/path/to/2021.7-plumed -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_THREAD_MPI=OFF -DGMX_OPENMP=on -DGMX_MPI=on -DGMX_X11=off -DGMX_GPU=off -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMXAPI=OFF -DCMAKE_C_COMPILER=`which mpicc` -DCMAKE_CXX_COMPILER=`which mpic++` -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_PREFIX_PATH=/path/to/fftw3/
$ make -j96 && make install

git clone https://github.com/glennhickey/hal2vg.git --recursive
cd hal2vg

sed -i '1,$s/std=c++11/std=c++17/` deps/libbdsg-easy/deps/DYNAMIC/CMakeLists.txt 
# 需要运行 3 次 make
make -j
make -j
make -j

./hal2vg 

$ module load arm/python/2.7.18

$ pip install --prefix=/path/to/hicplotter/ bx-python==1.16.6

# 设置这2个环境变量，否则 scipy 安装编译报错，Error: Rank mismatch between actual argument at (1) and actual argument at (2) (scalar and rank-1)
$ export FCFLAGS="-fallow-argument-mismatch"
$ export FFLAGS="-fallow-argument-mismatch"
$ pip install --prefix=/path/to/hicplotter/ scipy==1.2.3

$ pip install --prefix=/path/to/hicplotter/ matplotlib==1.4.3
# 在 mpl_toolkits 目录下添加 __init__.py，否则会出现报错 ImportError: No module named mpl_toolkits.axes_grid1
$ touch /path/to/hicplotter/lib/python2.7/site-packages/mpl_toolkits/__init__.py

$ tar xf HiCPlotter-0.6.6.tar.gz
$ cd HiCPlotter-0.6.6/
# 编辑 HiCPlotter.py，在首行添加 #!/bin/env python
$ chmod +x HiCPlotter.py
$ cp HiCPlotter.py /path/to/hicplotter/bin/
$ /path/to/hicplotter/bin/HiCPlotter.py -h

module load arm/python/2.7.18 arm/lzo/2.10
pip install --prefix=/path/to/hic-pro/ bx-python==0.8.1 numpy==1.8.2  pysam==0.8.3

# 设置这2个环境变量，否则 scipy 安装编译报错，Error: Rank mismatch between actual argument at (1) and actual argument at (2) (scalar and rank-1)
export FCFLAGS="-fallow-argument-mismatch"
export FFLAGS="-fallow-argument-mismatch"
pip install --prefix=/path/to/hic-pro/ scipy==1.2.3

tar xf HiC-Pro-2.11.4.tar.gz
cd HiC-Pro-2.11.4/

# 载入相关依赖软件，需要安装这3个R包，ggplot2 (>2.2.1) RColorBrewer grid
module load arm/r/4.4.1 arm/bowtie2/2.5.4 arm/samtools/1.21
# 编辑 config-install.txt，PREFIX = /path/to/hic-pro/
make configure
make CONFIG_SYS=config-install.txt

wget https://files.pythonhosted.org/packages/e2/3f/c2747248931fc997d2fe303c4e18827cc0c94114fba3e2c709e530db7226/iced-0.5.13.tar.gz
pip install --prefix=/path/to/hic-pro/ numpy==1.19.5 scipy==1.9.3 pysam==0.17.0 bx-python==0.9.0 cython
tar xf iced-0.5.13.tar.gz
cd iced-0.5.13
cython iced/normalization/_normalization_.pyx
python setup.py install --prefix=/path/to/hic-pro/

tar xf hic-pro-3.1.0.tar.gz
HiC-Pro-3.1.0

# 载入相关依赖软件，需要安装这3个R包，ggplot2 (>2.2.1) RColorBrewer grid
module load arm/r/4.4.1 arm/bowtie2/2.5.4 arm/samtools/1.21
# 编辑 config-install.txt，PREFIX = /path/to/hic-pro/
make configure
make CONFIG_SYS=config-install.txt

$ git clone https://github.com/DaehwanKimLab/hisat2.git
cd hisat2
$ wget https://raw.githubusercontent.com/lh3/ksw2/refs/heads/master/ksw2.h
$ wget https://raw.githubusercontent.com/DLTcollab/sse2neon/refs/heads/master/sse2neon.h

char mask2iupac[16] = { 
        char(-1),
        'A', // 0001
        'C', // 0010
        'M', // 0011
        'G', // 0100
        'R', // 0101
        'S', // 0110
        'V', // 0111
        'T', // 1000
        'W', // 1001
        'Y', // 1010
        'H', // 1011
        'K', // 1100
        'D', // 1101
        'B', // 1110
        'N', // 1111
};

BITS_FLAG =

ifeq (32,$(BITS))
    BITS_FLAG = -m32
endif

ifeq (64,$(BITS))
    BITS_FLAG = -m64
endif
SSE_FLAG=-msse2

BITS_FLAG =

BITS=64
ifeq (32,$(BITS))
        BITS_FLAG = -m32
endif

ifeq (64,$(BITS))
         ifeq (0, $(AARCH64))
        BITS_FLAG = -m64
  endif
endif
SSE_FLAG =
ifeq (0, $(AARCH64))
  SSE_FLAG=-msse2
        BITS_FLAG = -m64
endif
#SSE_FLAG=-msse2

$ git https://github.com/chhylp123/hifiasm.git
$ cd hifiasm
$ wget https://raw.githubusercontent.com/DLTcollab/sse2neon/refs/heads/master/sse2neon.h

#include "emmintrin.h"
#include "nmmintrin.h"
#include "smmintrin.h"
#include <immintrin.h>

//#include "emmintrin.h"
//#include "nmmintrin.h"
//#include "smmintrin.h"
//#include <immintrin.h>
#include "sse2neon.h"

module load arm/python/3.11.10
pip install --prefix=/path/to/ibspy/ numpy pandas cython biopython pyfaidx pandas psutil matplotlib pyranges multiprocess pysam scikit-learn
wget https://github.com/Uauy-Lab/IBSpy/archive/refs/tags/0.4.6.tar.gz
tar 0.4.6.tar.gz
cd IBSpy-0.4.6
pip install --prefix=/path/to/ibspy/
# /path/to/ibspy/lib/python3.11/site-packages/IBSpy/window_affinity_propagation.py 中 `from numpy import NaN, ndarray` 改为 `from numpy import nan, ndarray`

# KMC api 安装
cd ..
wget https://github.com/refresh-bio/KMC/archive/refs/tags/v3.1.1.tar.gz
tar xf v3.1.1.tar.gz
cd KMC-3.1.1
# 将 makefile 中的 -I $(PY_KMC_API_DIR)/libs/pybind11/include 替换为 -I /share/software/app/arm/python/3.11.10/lib/python3.11/site-packages/pybind11/include/ 
make py_kmc_api
cp  bin/*so /path/to/ibspy/lib/python3.11/site-packages/

# 测试
IBSpy -h
sh  tests/integration_python.sh 

$ wget https://anaconda.org/bioconda/k8/1.2/download/linux-aarch64/k8-1.2-h7f4e536_0.tar.bz2
$ tar xf k8-1.2-h7f4e536_0.tar.bz2
$ module load arm/gcc/12.2.0
$ ./bin/k8
Usage: k8 [options] <script.js> [arguments]
Options:
  -e STR      execute STR
  -E STR      execute STR and print results
  -m INT      v8 max size of the old space (in Mbytes) [16384]
  -v          print version number
  --help      show v8 command-line options

# 注意 samtools 的版本不高于 0.1.19，samtools的include目录结构为 include/bam/xxxx.h
# boost 版本不高于 1.70.0
$ module load arm/samtools/0.1.19  arm/boost/1.60.0
$ tar xf shendurelab-LACHESIS-2e27abb.tar.gz
$ cd shendurelab-LACHESIS-2e27abb
$ ./configure --with-samtools=/path/to/samtools/0.1.19/  --prefix=/path/to/lachesis/  --with-boost=/path/to/boost/1.60.0
$ make -j 20
$ make install

$ module load  arm/openmpi/5.0.5
$ wget https://download.lammps.org/tars/lammps.tar.gz
$ #tar xf lammps.tar.gz 
$ cd lammps-29Aug2024
$ cd src
$ mkdir build
# 添加所需的包
$ make yes-manybody yes-meam yes-extra-fix yes-mc
$ make -j80 g++_openmpi

$ wget http://www.netlib.org/lapack/lapack.tgz
$ tar lapack
$ cd lapack-3.10.1
$ cp make.inc.example make.inc
$ make blaslib
$ make cblaslib
$ make lapacklib
$ make lapackelib

$ wget http://www.netlib.org/lapack/lapack.tgz
$ tar lapack
$ cd lapack-3.10.1
$ mkdir build && cd build
$ cmake .. -DCMAKE_BUILD_TYPE=RELEASE -DBUILD_SHARED_LIBS=ON  -DCBLAS=ON -DLAPACKE=ON
$ make -j

$ ls -1 lib/
libblas.so -> libblas.so.3
libblas.so.3 -> libblas.so.3.10.0
libblas.so.3.10.0
libcblas.so -> libcblas.so.3
libcblas.so.3 -> libcblas.so.3.10.0
libcblas.so.3.10.0
liblapacke.so -> liblapacke.so.3
liblapacke.so.3 -> liblapacke.so.3.10.0
liblapacke.so.3.10.0
liblapack.so -> liblapack.so.3
liblapack.so.3 -> liblapack.so.3.10.0
liblapack.so.3.10.0

option(BUILD_SHARED_LIBS "Build shared libraries" OFF)
option(BUILD_INDEX64 "Build Index-64 API libraries" OFF)
option(BUILD_TESTING "Build tests" ${_is_coverage_build})
option(BUILD_DEPRECATED "Build deprecated routines" OFF)
option(BUILD_SINGLE "Build single precision real" ON)
option(BUILD_DOUBLE "Build double precision real" ON)
option(BUILD_COMPLEX "Build single precision complex" ON)
option(BUILD_COMPLEX16 "Build double precision complex" ON)
option(USE_OPTIMIZED_BLAS "Whether or not to use an optimized BLAS library instead of included netlib BLAS" OFF)
option(CBLAS "Build CBLAS" OFF)
option(USE_XBLAS "Build extended precision (needs XBLAS)" OFF)
option(USE_OPTIMIZED_LAPACK "Whether or not to use an optimized LAPACK library instead of included netlib LAPACK" OFF)
option(LAPACKE "Build LAPACKE" OFF)
option(LAPACKE_WITH_TMG "Build LAPACKE with tmglib routines" OFF)
option(BLAS++ "Build BLAS++" OFF)
option(LAPACK++ "Build LAPACK++" OFF)
option(BUILD_HTML_DOCUMENTATION "Create and install the HTML based API
option(BUILD_MAN_DOCUMENTATION "Create and install the MAN based documentation (requires Doxygen) - command: make man" OFF)

$ git clone https://github.com/berkeleydb/libdb.git
$ cd libdb/build_unix
$ ../dist/configure --prefix=/path/to/libdb/ --build=arm-linux-gnueabi
$ make -j20
$ make install

git clone https://github.com/agshumate/Liftoff
cd Liftoff
pip install --prefix=/path/to/liftoff/ numpy pysam
PYTHONPATH=//path/to/liftoff/lib/python3.9/site-packages/://path/to/liftoff/lib64/python3.9/site-packages/ python setup.py install --prefix=/path/to/liftoff/

git clone https://github.com/llvm/llvm-project.git
cd llvm-project
cmake -S llvm -B build -DCMAKE_INSTALL_PREFIX=/path/to/llvm/ -DCMAKE_BUILD_TYPE=Release -DLLVM_ENABLE_PROJECTS="clang;lld"
cmake --build build -j 80

$ module load capnproto/1.1.0 gsl/2.8 gcc/10.3.0 
$ tar xf Mash-2.3.tar.gz
$ cd Mash-2.3
$ sed -i  '8,10s/^/#/' Makefile.in
$ autoreconf -i
$ ./configure --prefix=/path/to/mash/ --with-capnp=/path/to/capnproto/ --with-gsl=/path/to/gsl/ --enable-static-gsl
$ make -j
$ make install 
$ /path/to/mash/bin/mash -h

Mash version 2.3

Type 'mash --license' for license and copyright information.

Usage:

  mash <command> [options] [arguments ...]

Commands:

  bounds     Print a table of Mash error bounds.

  dist       Estimate the distance of query sequences to references.

  info       Display information about sketch files.

  paste      Create a single sketch file from multiple sketch files.

  screen     Determine whether query sequences are within a larger mixture of
             sequences.

  sketch     Create sketches (reduced representations for fast operations).

  taxscreen  Create Kraken-style taxonomic report based on mash screen.

  triangle   Estimate a lower-triangular distance matrix.

tar xf lapack-3.10.0.tgz
cd lapack-3.10.0
mkdir build && cd build
cmake .. -DCMAKE_INSTALL_PREFIX=/path/to/mash/ -DCMAKE_BUILD_TYPE=RELEASE -DCBLAS=ON
make -j
make install

$ wget https://anaconda.org/bioconda/mash/2.3/download/linux-aarch64/mash-2.3-heca2785_9.tar.bz2
$ tar xf mash-2.3-heca2785_9.tar.bz2
$ module load arm/gsl/2.7   arm/gcc/14.2.0
$ cp -r bin/ /path/to/mash/
$ export LD_LIBRARY_PATH=/path/to/mash/lib64/:$LD_LIBRARY_PATH
$ /path/to/mash/bin/mash -h

Mash version 2.3

Type 'mash --license' for license and copyright information.

Usage:

  mash <command> [options] [arguments ...]

Commands:

  bounds     Print a table of Mash error bounds.

  dist       Estimate the distance of query sequences to references.

  info       Display information about sketch files.

  paste      Create a single sketch file from multiple sketch files.

  screen     Determine whether query sequences are within a larger mixture of
             sequences.

  sketch     Create sketches (reduced representations for fast operations).

  taxscreen  Create Kraken-style taxonomic report based on mash screen.

  triangle   Estimate a lower-triangular distance matrix.

cd ~/megacc

# 准备编译环境
# wget https://downloads.freepascal.org/fpc/beta/3.2.4-rc1/aarch64-linux/fpc-3.2.4-rc1.aarch64-linux.tar
wget https://sourceforge.net/projects/lazarus-ccr/files/FPSpreadsheet/fpspreadsheet-1.16.zip

wget https://download.lazarus-ide.org/Lazarus%20Linux%20arm64%20DEB/Lazarus%204.2/lazarus-project_4.2.0-0_arm64.deb
wget https://download.lazarus-ide.org/Lazarus%20Linux%20arm64%20DEB/Lazarus%204.2/fpc-laz_3.2.3-240813_arm64.deb

$ mkdir lazarus-project
$ mv lazarus-project_4.2.0-0_arm64.deb lazarus-project
$ ar -vx lazarus-project_4.2.0-0_arm64.deb
$ tar xf data.tar.xz
$ mkdir fpc-laz
$ mv fpc-laz_3.2.3-240813_arm64.deb fpc-laz
$ cd fpc-laz
$ ar -vx fpc-laz_3.2.3-240813_arm64.deb
$ tar xf data.tar.xz
$ cd usr/bin
$ mkdir aarch64-linux
$ mv * aarch64-linux
$ cd aarch64-linux
$ ln -s ../../lib/fpc/3.2.3/ppca64 ppca64
$ cd ~/megacc/lazarus-project
$ mv ../fpc-laz/usr  usr/share/lazarus/4.2.0/fpc
export PATH=$HOME/megacc/lazarus-project/usr/bin/:$HOME/megacc/lazarus-project/usr/share/lazarus/4.2.0/fpc/bin/aarch64-linux:$PATH
$ which lazbuild fpc fpcres 
~/megacc/lazarus-project/usr/bin/lazbuild
~/megacc/lazarus-project/usr/share/lazarus/4.2.0/fpc/bin/aarch64-linux/fpc
~/megacc/lazarus-project/usr/share/lazarus/4.2.0/fpc/bin/aarch64-linux/fpcres

$ mkdir ~/megacc/fpspreadsheet
$ cd ~/megacc/fpspreadsheet
$ cp  ../fpspreadsheet-1.16.zip .
$ unzip fpspreadsheet-1.16.zip

# 编译生成 laz_fpspreadsheet.pas
$ lazbuild  --lazarusdir="$HOME/megacc/lazarus-project/usr/share/lazarus/4.2.0"   --pcp="$HOME/.lazarus" laz_fpspreadsheet.lpk

# 下载mega源码并编译megacc
$ cd ~/megacc
$ git clone https://github.com/KumarMEGALab/MEGA-source-code/
$ cd MEGA-source-code/MEGA12-source/MEGA-CC
$ cp resources_windows.lrs resources_unix.lrs

将 megaccxplatform.lpi 中的以下三行删除
<ExecuteAfter>
  <Command Value="test_cc_dependencies.sh"/>
</ExecuteAfter>

$ lazbuild  --lazarusdir="$HOME/megacc/lazarus-project/usr/share/lazarus/4.2.0" megaccxplatform.lpi --build-mode=release-Linux --cpu=aarch64  > megacc-build.log 2>&1

# 确认编译成功
$ ../megacc -v

Molecular Evolutionary Genetics Analysis
Molecular Evolutionary Genetics Analysis - Computational Core
Version: 12.0.4
Build: 12241219-arm64
Authors: Koichiro Tamura, Glen Stecher, Sudhir Kumar
Copyright 2011-2025
Web: http://www.megasoftware.net

#if PHMAP_HAVE_SSE2
    //#include <emmintrin.h>
    #include "../sse2neon.h"
#endif

#if PHMAP_HAVE_SSSE3
    //#include <tmmintrin.h>
    #include "../sse2neon.h"
#endif

#if defined(__GNUC__)
#  if defined(__AVX2__)
//#    include <immintrin.h>
#include "../sse2neon.h"
#  elif defined(__SSE2__)
//#    include <emmintrin.h>
#include "../sse2neon.h"

 } else if (strcmp(argv[1], "checkcpu") == 0) {
//    pprintf("{}\n", HasPopcnt() && HasBmi2());
  } else if (strcmp(argv[1], "checkpopcnt") == 0) {
 //   pprintf("{}\n", HasPopcnt());
  } else if (strcmp(argv[1], "checkbmi2") == 0) {
  //  pprintf("{}\n", HasBmi2());
  } else if (strcmp(argv[1], "dumpversion") == 0) {

// #include <x86intrin.h>

set_target_properties(megahit_core PROPERTIES COMPILE_FLAGS "-mbmi2 -DUSE_BMI2 -mpopcnt")
set_target_properties(megahit_core_popcnt PROPERTIES COMPILE_FLAGS "-mpopcnt")

$ mkdir build
$ cd build
$ cmake ../ .. -DCMAKE_BUILD_TYPE=Release
$ make -j12
$ make install

$ module load arm/libdeflate/1.8 arm/boost/1.85.0  arm/gcc/12.2.0 
$ wget https://anaconda.org/bioconda/metabat2/2.17/download/linux-aarch64/metabat2-2.17-hb490ba1_0.tar.bz2
$ tar xf metabat2-2.17-hb490ba1_0.tar.bz2
$ ./bin/metabat1

$ git clone https://bitbucket.org/berkeleylab/metabat.git
$ cd metabat
$ mkdir build && cd build
$ cmake -DCMAKE_INSTALL_PREFIX=/path/to/metabat ..
# make 时会从 github 下载依赖，需保持 github 网络通畅
$ make -j20
$ make install

$ tar xf MCScanX-1.0.0.tar.gz 
$ cd MCScanX-1.0.0/
$ make
# 测试
$ ./MCScanX -h

# 使用下游分析脚本
$ cd downstream_analyses/
$ java bar_plotter -h
Usage: java bar_plotter -g gff_file -s collinearity_file -c control_file -o output_PNG_file

$ git clone https://github.com/lh3/minigraph
$ cd minigraph
# 去掉 -msse4 编译选项
$ sed -i 's/-msse4//g' Makefile
$ make

$ git clone https://github.com/lh3/minimap2
$ cd minimap2
$ make arm_neon=1 aarch64=1

$ git clone https://github.com/lh3/miniprot
$ cd miniprot && make

$ module load arm/ldc2/1.41.0
$ cd /path/to/ldc2/1.41.0/bin/
$ ln -s ldmd2 dmd
$ tar xf msmc2-2.1.4.tar.gz
$ cd msmc2-2.1.4
# 将 Makefile 中的 GSLDIR=/usr/local/lib 替换为 GSLDIR=/path/to/gsl/2.4/lib/
$ make -j
$ build/release/msmc2

muscle-5.3.tar.gz
tar xf muscle-5.3.tar.gz
cd muscle-5.3/src/

$ wget https://anaconda.org/bioconda/muscle/5.3/download/linux-aarch64/muscle-5.3-h78569d1_0.tar.bz2
$ tar xf muscle-5.3-h78569d1_0.tar.bz2
$ ls bin/muscle

# 注意固定 numpy 和 xgboost 的版本，否则可能会安装或运行出错
$ pip install --prefix=/path/to/nanom6a/ joblib numpy==1.21 pysam scikit-learn scipy tqdm xgboost==0.80 h5py statsmodels

$ wget https://anaconda.org/HCC/jvarkit-sam2tsv/1.0/download/linux-64/jvarkit-sam2tsv-1.0-0.tar.bz2
tar xf jvarkit-sam2tsv-1.0-0.tar.bz2
mkdir /path/to/nanom6a/jar/
cp dist/sam2tsv.jar /path/to/nanom6a/jar/
cp lib/com/beust/jcommander/1.64/jcommander-1.64.jar /path/to/nanom6a/jar/
cp lib/com/github/samtools/htsjdk/2.9.1/htsjdk-2.9.1.jar /path/to/nanom6a/jar/

# 创建sam2tsv脚本
$ cat /path/to/nanom6a/bin/sam2tsv
#!/bin/bash

java -Djvarkit.log.name=sam2tsv -Dfile.encoding=UTF8 -Xmx500m     -cp "/path/to/nanom6a/jar/htsjdk-2.9.1.jar:/path/to/nanom6a/jar/jcommander-1.64.jar:/path/to/nanom6a/jar/sam2tsv.jar" com.github.lindenb.jvarkit.tools.sam2tsv.Sam2Tsv $*

cd nanom6A_2022_12_22
$ export PYTHONPATH=/path/to/nanom6a/lib/python3.9/site-packages/:/path/to/nanom6a/lib64/python3.9/site-packages/
$ export PATH="/path/to/nanom6a/bin/:$PATH"
$ module load arm/samtools/1.21 arm/minimap2/2.28 arm/bedtools/2.31.1 
$ sh run_source_code.sh

$ wget https://ftp.gnu.org/pub/gnu/ncurses/ncurses-6.5.tar.gz
$ tar xf ncurses-6.5.tar.gz
$ cd ncurses-6.5
$ ./configure --prefix=/path/to/ncurses/ \
    --with-shared \
    --enable-overwrite \
    --without-ada \
    --enable-symlinks \
    --with-versioned-syms \
    --enable-pc-files \
    --enable-ext-colors \
    --enable-widec \
$ make
$ make install
$ mkdir /path/to/ncurses/lib/pkconfig
$ cp misc/*pc /path/to/ncurses/lib/pkconfig
# 作用说明
--with-shared   生成动态链接库，允许程序运行时动态加载
--enable-overwrite  允许安装时覆盖现有文件，避免冲突
--without-ada   禁用 Ada 语言支持，减少编译时间和依赖
--enable-symlinks   创建符号链接，提供版本兼容性
--with-versioned-syms   使用版本化符号，支持多版本共存
--enable-pc-files   生成 pkg-config 文件，方便其他软件查找依赖
--enable-widec  重要：启用宽字符支持，支持 Unicode 和 UTF-8
--enable-ext-colors 启用扩展颜色支持，提供更多颜色选项

$ wget https://github.com/OpenMathLib/OpenBLAS/releases/download/v0.3.28/OpenBLAS-0.3.28.tar.gz
$ tar xf OpenBLAS-0.3.28.tar.gz
$ cd OpenBLAS
$ make -j20
$ make install PREFIX=/path/to/openblas/

export OPENBLAS_NUM_THREADS=4
export GOTO_NUM_THREADS=4
export OMP_NUM_THREADS=4

$ git clone --recursive https://github.com/pangenome/odgi.git
$ cd odgi

# 去掉 -msse4.2 编译选项
$ sed -i 's/-msse4.2//g' ./CMakeLists.txt
$ sed -i 's/-msse4.2//g' ./deps/sdsl-lite/CMakeLists.txt
$ sed -i 's/-msse4.2//g' ./deps/mmmulti/deps/sdsl-lite/CMakeLists.txt

$ sed -i 's/arch=x86-64/arch=armv8-a/g' src/main.cpp

$ module load arm/jemalloc/5.2.1
# 使用自己编译好的 gcc，否则会出现报错 /usr/bin/ld: cannot find -latomic 
$ module load arm/gcc/10.3.0 
$ cmake -H. -Bbuild
$ cmake --build build -- -j 20
$ bin/odgi -h

$ cd /path/to/orca/
$ tar xf orca_6_0_1_linux_arm64_shared_openmpi418.tar.xz
$ mv orca_6_0_1_linux_arm64_shared_openmpi418 orca
$ git clone https://github.com/matrix1001/glibc-all-in-one
$ cd glibc-all-in-one

# 下载适合版本的 libc6，此处的 glibc 版本为 2.41
$ wget https://ftp.debian.org/debian/pool/main/g/glibc/libc6_2.41-6_arm64.deb
$ mkdir glibc

# 解压 deb 
$ ./extract libc6_2.41-6_arm64.deb glibc
$ mv glibc ../orca

# 使用 patchelf 更改可执行文件的 interpreter
module load arm/patchelf/0.18.0
$ ls -1 /path/to/orca/orca/orca* |xargs -i patchelf --set-interpreter /path/to/orca/orca/glibc/ld-linux-aarch64.so.1 --add-rpath /path/to/orca/orca/glibc/ {}
$ ls -1 /path/to/orca/orca/autoci_* |xargs -i patchelf --set-interpreter /path/to/orca/orca/glibc/ld-linux-aarch64.so.1 --add-rpath /path/to/orca/orca/glibc/ {}

# 更改 orca 动态库的 rpath
$ patchelf --add-rpath /path/to/orca/orca/glibc/ /path/to/orca/orca/lib/liborca_tools_6_0_1.so.6
$ patchelf --add-rpath /path/to/orca/orca/glibc/ /path/to/orca/orca/lib/liborca_tools_6_0_1_mpi.so.6

# 加载 gcc 和 openmpi 依赖
$ module load arm/gcc/14.2.0 arm/openmpi/5.0.5

# 测试
$ orca
This program requires the name of a parameterfile as argument
For example ORCA TEST.INP 

# 可用
$ #singularity build --sandbox orca_openmpi2 docker://dockerpull.org/fenicsproject/test-env:current-openmpi
# 不可用
$ #singularity build --sandbox orca_openmpi3 docker://dockerpull.org/mfisherman/openmpi:4.1.6

$ wget https://github.com/davidemms/OrthoFinder/archive/refs/tags/3.0.1b1.tar.gz
$ tar xf 3.0.1b1.tar.gz
$ cd OrthoFinder-3.0.1b1
$ pip install numpy scipy --prefix=/path/to/orthofinder/
$ pip install . --prefix=/path/dir/orthofinder/
# 载入依赖
$ module load arm/diamond/2.1.10 arm/mcl/22-282 arm/fastme/2.1.6.4 arm/mafft/7.525 arm/fasttree/2.1.11
# 测试
$ orthofinder -f ExampleData/

$ module load arm/curl/8.10.1 arm/openssl/3.3.2
$ git clone git@github.com:Nextomics/NextDenovo.git
$ cd NextDenovo && make arm_neon=1 aarch64=1

$ module load arm/libdeflate/1.8 arm/htslib/1.21 
$ git clone https://github.com/HuiyangYu/PanDepth.git
$ cd PanDepth
$ mkdir include2
$ cp include/{comm.h,DataClass.h,gzstream.*} include2/
$ g++  --std=c++11 -g -O3 src/PanDepth.cpp -lhts -ldeflate -lz -pthread -Iinclude2 -o  bin/pandepth
$ cd bin
$ ./pandepth -h

$ git clone https://github.com/HuiyangYu/PanDepth.git
$ cd PanDepth
$ rm -rf lib/*a
$ cp /path/to/zlib/lib/libz.a /path/to/libdeflate/lib/libdeflate.a /path/to/htslib/lib/libhts.a lib
$ make
# 编译出的是动态文件
$ ldd bin/pandepth
$ linux-vdso.so.1 (0x0000400038237000)
    libstdc++.so.6 => /share/software/app/arm/gcc/10.3.0//lib64/libstdc++.so.6 (0x0000400038254000)
    libm.so.6 => /usr/lib64/libm.so.6 (0x000040003843a000)
    libgcc_s.so.1 => /share/software/app/arm/gcc/10.3.0//lib64/libgcc_s.so.1 (0x00004000384db000)
    libc.so.6 => /usr/lib64/libc.so.6 (0x000040003850c000)
    /lib/ld-linux-aarch64.so.1 (0x0000400038212000)

# 编译静态文件
# 在 Makefile 文件中给gcc 添加静态编译选项 -static
$ module load gcc/10.3.0 
$ make
$ ldd  bin/pandepth
    not a dynamic executable

$ export PKG_CONFIG_PATH=/path/to/jellyfish/lib/pkgconfig

$ git clone https://github.com/USCiLab/cereal
$ export CPATH=/path/to/cereal/include/

$ git clone https://github.com/eblerjana/pangenie.git  
$ cd pangenie

$ mkdir build
$ cd build
$ cmake ..
$ make -j12
$ ls src/
libPanGenieLib.so
PanGenie-index
PanGenie

cd ~
wget http://downloads.sourceforge.net/project/boost/boost/1.65.0/boost_1_65_0.tar.bz2
tar xf boost_1_65_0.tar.bz2
cd boost_1_65_0
./bootstrap.sh
./b2 --prefix=/path/to/boost/ link=static install

tar xf paragraph-2.4a.tar.gz
cd paragraph-2.4a

# 注释x86编译选项 -msse4.1
sed -i.bak 's/set_source_files_properties/#set_source_files_properties/g'  ./external/CMakeLists.txt

# 将 x86的 sse2 替换为 arm 的相关指令
cp  ~/package/sse2neon.h  ./external/gssw/ 
cp  ~/package/sse2neon.h  ./external/klib/
sed -i.bak 's/<emmintrin.h>/"sse2neon.h"/g' ./external/gssw/gssw.c
sed -i.bak 's/<smmintrin.h>/"sse2neon.h"/g' ./external/gssw/gssw.h
sed -i.bak 's/<emmintrin.h>/"sse2neon.h"/g' ./external/klib/ksw.c 

# 编译 warning 报错
sed -i.bak 's/-Werror/ /g' src/cmake/cxx.cmake

mkdir build && cd build
BOOST_ROOT=/path/to/boost/ ../configure --prefix=//path/to/paragrpah

[ 97%] Linking CXX executable ../../../bin/test_blackbox
/usr/bin/ld: CMakeFiles/test_blackbox.dir/test_paragraph.cpp.o:/share/home/software/package/paragrpah/tmp/paragraph-2.4a/src/c++/test-blackbox/test_paragraph.cpp:47: multiple definition of `compare_values'; CMakeFiles/test_blackbox.dir/test_multithreading.cpp.o:/share/home/software/package/paragrpah/tmp/paragraph-2.4a/src/c++/test-blackbox/test_multithreading.cpp:39: first defined here
collect2: error: ld returned 1 exit status
make[2]: *** [src/c++/test-blackbox/CMakeFiles/test_blackbox.dir/build.make:174: bin/test_blackbox] Error 1
make[1]: *** [CMakeFiles/Makefile2:784: src/c++/test-blackbox/CMakeFiles/test_blackbox.dir/all] Error 2
make: *** [Makefile:136: all] Error 2

$ ls -1 bin/
addVariants.py
compare-alignments.py
findgrm.py
graph-to-fasta
grmpy
grmpy-vcf-merge.py
idxdepth
__init__.py
kmerstats
msa2vcf.py
multigrmpy.py
multiparagraph.py
pam
paragraph
paragraph2dot.py
test_grm
vcf2paragraph.py

$ ./bin/paragraph -h

pip install --prefix=/path/to/paragrpah/ -r requirements.txt 

$ cpanm --reinstall --configure-args='INC="-I/path/to/berkeley-db/5.3.21/include" LIBS="-L/path//berkeley-db/5.3.21/lib -ldb"' -l /path/to/perl/5.34.0/ DB_File

$ wget https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-3.22.2.tar.gz
$ tar xf petsc-3.22.2.tar.gz
$ cd petsc-3.22.2
$ module load arm/openmpi/5.0.5 arm/openblas/0.3.28
$ ./configure --prefix=//path/to/petsc/  --with-hypre=1  --download-hypre=yes
$ make all check
$ make install

tar xf plink-ng-2.0.0-a.6.5.tar.gz
cd plink-ng-2.0.0-a.6.5/1.9
module load arm/zlib/1.3

$ git clone https://github.com/schneebergerlab/plotsr.git
$ pip install --prefix=/path/to/plotsr/ numpy==1.21.2 pandas==1.2.4 matplotlib setuptools
$ PYTHONPATH=/path/to/plotsr/lib/python3.9/site-packages/:/path/to/plotsr/lib64/python3.9/site-packages/ python setup.py install --prefix=/path/to/plotsr/
$ cd dist/
$ unzip plotsr-0.0.0-py3.9.egg
$ cp -r plotsr /path/to/plotsr/lib64/python3.9/
$ export PYTHONPATH=/path/to/plotsr/lib/python3.9/site-packages/:/path/to/plotsr/lib64/python3.9/site-packages/
$ export PATH="/path/to/plotsr/bin/:$PATH"
$ plotsr -h

# 使用hmpi编译
# 使用 FFTW_ROOT 设置使用 fftw3，否则默认可能使用fftw，导致后面编译gromacs使用fftw3时报错
$ module load arm/hyper-mpi/24.6.30_bisheng arm/jq/1.7.1
$ FFTW_ROOT=/path/to/fftw3/ ./configure --prefix=/path/to/plumed2 --enable-fftw --enable-zlib --enable-mpi  CXX=`which mpicxx` CC=`which mpicc`
$ make -j96 && install

$ tar xf Python-3.9.19.tgz
$ cd Python-3.9.19
$ ./configure --enable-optimizations --prefix=/python/to/path/ --with-openssl=/libpath/to/lib/  CPPFLAGS="I/libpath/to/include"  LDFLAGS="I/libpath/to/lib" LIBS="-Wl,-Bstatic -lncursesw -lpanelw -lz -lbz2 -lreadline -lffi -Wl,-Bdynamic"

$ make -j
....
# make 结束后查看是否有预期未编译的模块
Python build finished successfully!
The necessary bits to build these optional modules were not found:
_dbm                  _gdbm                 _tkinter           
_uuid                 nis                                      
To find the necessary bits, look in setup.py in detect_modules() for the module's name.


The following modules found by detect_modules() in setup.py, have been
built by the Makefile instead, as configured by the Setup files:
_abc                  atexit                pwd                
time                       

# 查看这些模块是否链接额外的动态库
$ ldd  ./build/lib.linux-x86_64-3.9/{zlib.cpython-39-x86_64-linux-gnu.so,readline.cpython-39-x86_64-linux-gnu.so,_bz2.cpython-39-x86_64-linux-gnu.so,readline.cpython-39-x86_64-linux-gnu.so,_ctypes.cpython-39-x86_64-linux-gnu.so,_sqlite3.cpython-39-x86_64-linux-gnu.so,_curses.cpython-39-x86_64-linux-gnu.so}
./build/lib.linux-x86_64-3.9/zlib.cpython-39-x86_64-linux-gnu.so:
    linux-vdso.so.1 (0x00007fff3a9fc000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x00001486580e9000)
    libc.so.6 => /lib64/libc.so.6 (0x0000148657d13000)
    /lib64/ld-linux-x86-64.so.2 (0x0000148658524000)
./build/lib.linux-x86_64-3.9/readline.cpython-39-x86_64-linux-gnu.so:
    linux-vdso.so.1 (0x00007ffd46f94000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x0000152f99393000)
    libc.so.6 => /lib64/libc.so.6 (0x0000152f98fbd000)
    /lib64/ld-linux-x86-64.so.2 (0x0000152f9982f000)
./build/lib.linux-x86_64-3.9/_bz2.cpython-39-x86_64-linux-gnu.so:
    linux-vdso.so.1 (0x00007ffc9b4bf000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x000015043136b000)
    libc.so.6 => /lib64/libc.so.6 (0x0000150430f95000)
    /lib64/ld-linux-x86-64.so.2 (0x00001504317a1000)
./build/lib.linux-x86_64-3.9/readline.cpython-39-x86_64-linux-gnu.so:
    linux-vdso.so.1 (0x00007ffda3bb5000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x000014700bde9000)
    libc.so.6 => /lib64/libc.so.6 (0x000014700ba13000)
    /lib64/ld-linux-x86-64.so.2 (0x000014700c285000)
./build/lib.linux-x86_64-3.9/_ctypes.cpython-39-x86_64-linux-gnu.so:
    linux-vdso.so.1 (0x00007ffcdd2f3000)
    libdl.so.2 => /lib64/libdl.so.2 (0x00001466222fc000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x00001466220dc000)
    libc.so.6 => /lib64/libc.so.6 (0x0000146621d06000)
    /lib64/ld-linux-x86-64.so.2 (0x000014662272a000)
./build/lib.linux-x86_64-3.9/_sqlite3.cpython-39-x86_64-linux-gnu.so:
    linux-vdso.so.1 (0x000014dfe9518000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x000014dfe8d76000)
    libc.so.6 => /lib64/libc.so.6 (0x000014dfe89a0000)
    /lib64/ld-linux-x86-64.so.2 (0x000014dfe92eb000)
./build/lib.linux-x86_64-3.9/_curses.cpython-39-x86_64-linux-gnu.so:
    linux-vdso.so.1 (0x00007ffcaf4f1000)
    libpthread.so.0 => /lib64/libpthread.so.0 (0x00001531e9136000)
    libc.so.6 => /lib64/libc.so.6 (0x00001531e8d60000)
    /lib64/ld-linux-x86-64.so.2 (0x00001531e95c6000)

# 测试使用
$ ./python -c "
import sys, zlib, bz2, readline
print('zlib 版本:', zlib.ZLIB_VERSION)
print('bz2 库版本:', bz2.__doc__)
print('readline 动态库路径:', readline.__file__)
"

# 安装
$ make install     
$                                

install=/path/to/r/

export LDFLAGS="-L${install}/lib"
export CFLAGS="-I${install}/include"
export LD_LIBRARY_PATH="${install}/lib/"

# 编译安装 readline
$ wget https://ftp.gnu.org/gnu/readline/readline-8.2.tar.gz
$ tar xf readline-8.2.tar.gz 
$ cd readline-8.2/
$ ./configure --prefix=$install
$ make -j20 && make install

# 编译安装 libpsl
$ wget https://github.com/rockdaboot/libpsl/releases/download/0.21.5/libpsl-0.21.5.tar.gz
$ tar xf libpsl-0.21.5.tar.gz 
$ cd libpsl-0.21.5/
$ ./configure --prefix=$install
$ make -j20 && make install

# 编译安装 curl
$ wget https://curl.se/download/curl-8.13.0.tar.gz
$ tar xf curl-8.13.0.tar.gz 
$ cd curl-8.13.0/
$ ./configure --prefix=$install --with-ssl
$ make -j20 && make install

# 编译 R
$ wget https://cran.r-project.org/src/base/R-4/R-4.5.0.tar.xz
$ tar xf R-4.5.0.tar.xz
$ cd R-4.5.0/
# 如果系统没有安装图形界面，添加选项 --with-x=no 
$ ./configure --enable-R-shlib --with-x=no --with-pcre1 --prefix=$install CPPFLAGS="-I$install/include" LDFLAGS="-L$install/lib"
$ make -j20 && make install

export CFLAGS="-O2 -fPIC"
export FFLAGS="-O2 -fPIC"
export FCFLAGS="-O2 -fPIC"

tar xf R-4.4.1.tar.gz
cd R-4.4.1

export PATH="/libpath/to/bin/:$PATH"
$ ./configure --prefix=/path/to/R/ --enable-R-static-lib --enable-static --with-x=no --with-cairo --with-readline=no LDFLAGS="-L/libpath/to/libs -static" CPPFLAGS="-I/libpath/to/include/" LIBS="-lreadline -lncursesw -lcurl -lssl -lcrypto -lpsl -llzma -lbz2 -lz -lrt -lzstd -lm -ldl -lpthread"

$ wget wget https://github.com/CostaLab/reg-gen/archive/refs/tags/RGT-1.0.2.tar.gz
$ tar xf RGT-1.0.2.tar.gz
$ cd RGT-1.0.2
# 将 hint THOR 依赖的 hmmlearn==0.2.2 改为 hmmlearn==0.2.7，添加 numpy<1.24
# 将 ./rgt/THOR/neg_bin_rep_hmm.py 中的 from hmmlearn.hmm import _BaseHMM 改为 from hmmlearn.base import _BaseHMM
$ pip install --prefix=/path/to/rgt/ .

$ tar xf rmats_turbo_v4_3_0.tar.gz
$ cd rmats_turbo_v4_3_0/
$ export FC=gfortran
$ sed -i 's/-msse2//g' rMATS_C/lbfgs_scipy/Makefile
$ sed -i 's/-msse2//g' rMATS_C/Makefile
$ pip install --prefix=/path/to/rmats-turbo/ cython
$ module load arm/r/4.4.1
$ ./build_rmats

# 使用
run_rmats --b1 Y_Adipose_file.txt --b2 E_Adipose_file.txt  --gtf Mus_musculus.GRCm39.114.gtf --od rmats/rMATs_Y_E/ --tmp rmats/tmp_WT_CRC/ -t paired --readLength 150 --variable-read-length --cstat 0.0001 --nthread 20

#!/bin/bash

set -xe

mkdir $PREFIX/rMATS

GSL_LDFLAGS="$(gsl-config --libs)"
GSL_CFLAGS="$(gsl-config --cflags)"
export GSL_LDFLAGS
export GSL_CFLAGS
export LD_LIBRARY_PATH=${PREFIX}/lib

case $(uname -m) in
    aarch64)
        sed -i.bak -e "s/-msse2//" rMATS_C/Makefile
        ;;
    *)
        ;;
esac

make -j ${CPU_COUNT}

cp rmats.py $PREFIX/rMATS
cp cp_with_prefix.py $PREFIX/rMATS
mkdir $PREFIX/rMATS/rMATS_C
cp rMATS_C/rMATSexe $PREFIX/rMATS/rMATS_C
cp -R rMATS_P $PREFIX/rMATS
cp -R rMATS_R $PREFIX/rMATS
cp *.so $PREFIX/rMATS

chmod +x $PREFIX/rMATS/rmats.py
ln -s $PREFIX/rMATS/rmats.py $PREFIX/bin/rmats.py
ln -s $PREFIX/rMATS/rMATS_P/FDR.py $PREFIX/bin/FDR.py
ln -s $PREFIX/rMATS/rMATS_P/inclusion_level.py $PREFIX/bin/inclusion_level.py
ln -s $PREFIX/rMATS/rMATS_P/joinFiles.py $PREFIX/bin/joinFiles.py
ln -s $PREFIX/rMATS/rMATS_P/paste.py $PREFIX/bin/paste.py

# for backwards compatibility with the previous recipe, create a symlink named
# for the previously-used executable
ln -s $PREFIX/rMATS/rmats.py $PREFIX/bin/RNASeq-MATS.py