diff --git a/LifeSciences/Lumpy-0.3.1/build.sh b/LifeSciences/Lumpy-0.3.1/build.sh index 4547526a38e7532cf06a4a5ac5ef6407fe271430..e43ce7a002b7d580c792d1f4058e83be1d9fbcb9 100644 --- a/LifeSciences/Lumpy-0.3.1/build.sh +++ b/LifeSciences/Lumpy-0.3.1/build.sh @@ -65,7 +65,7 @@ cat>"pkg/lumpy-0.3.1-hpc/run.sh"< /dev/null current_dir="\$(cd "\$(dirname "\${BASH_SOURCE[0]}")" && pwd -P)" for f in "\${current_dir}"/*; do diff --git a/LifeSciences/Lumpy-0.3.1/dependency/ldc2-1.15.0.sh b/LifeSciences/Lumpy-0.3.1/dependency/ldc2-1.15.0.sh index 94960cb73d92ec7def740742c4b4aad364623f3b..b1c40e141e69523f86532429a07ad41a1e075017 100644 --- a/LifeSciences/Lumpy-0.3.1/dependency/ldc2-1.15.0.sh +++ b/LifeSciences/Lumpy-0.3.1/dependency/ldc2-1.15.0.sh @@ -20,7 +20,15 @@ installpath=$2 set -e yum install -y wget tar environment-modules -wget -t 10 -c -P $buildpath https://github.com/ldc-developers/ldc/releases/download/v1.15.0-beta2/ldc2-1.15.0-beta2-linux-aarch64.tar.xz +if `wget -t 40 -c -P $buildpath https://ghproxy.com/https://github.com/ldc-developers/ldc/releases/download/v1.15.0-beta2/ldc2-1.15.0-beta2-linux-aarch64.tar.xz` +then + echo "ldc2-1.15.0-beta2-linux-aarch64.tar.xz下载成功!(国内github加速下载)" +elif `wget -t 40 -c -P $buildpath https://github.com/ldc-developers/ldc/releases/download/v1.15.0-beta2/ldc2-1.15.0-beta2-linux-aarch64.tar.xz` +then + echo "ldc2-1.15.0-beta2-linux-aarch64.tar.xz下载成功!" +else + echo "ldc2-1.15.0-beta2-linux-aarch64.tar.xz下载失败!" +fi tar xf $buildpath/ldc2-1.15.0-beta2-linux-aarch64.tar.xz -C $buildpath && rm -rf $buildpath/ldc2-1.15.0-beta2-linux-aarch64.tar.xz mkdir -p $installpath/ldc2-1.15.0 && cp -r $buildpath/ldc2-1.15.0-beta2-linux-aarch64/* $installpath/ldc2-1.15.0 diff --git a/LifeSciences/Lumpy-0.3.1/dependency/pysam-0.19.0.sh b/LifeSciences/Lumpy-0.3.1/dependency/pysam-0.19.0.sh index 1736612980bec24dcfcbe40367f9293d65a494b8..bc0f9a2de9ccea0a5dd92ac82ba01183744318e3 100644 --- a/LifeSciences/Lumpy-0.3.1/dependency/pysam-0.19.0.sh +++ b/LifeSciences/Lumpy-0.3.1/dependency/pysam-0.19.0.sh @@ -19,7 +19,15 @@ set -e yum install -y wget tar environment-modules \ zlib-devel bzip2-devel Cython -wget -t 10 -c -P $buildpath https://github.com/pysam-developers/pysam/archive/refs/tags/v0.19.0.tar.gz +if `wget -t 40 -c -P $buildpath https://ghproxy.com/https://github.com/pysam-developers/pysam/archive/refs/tags/v0.19.0.tar.gz` +then + echo "v0.19.0.tar.gz下载成功!(国内github加速下载)" +elif `wget -t 40 -c -P $buildpath https://github.com/pysam-developers/pysam/archive/refs/tags/v0.19.0.tar.gz` +then + echo "v0.19.0.tar.gz下载成功!" +else + echo "v0.19.0.tar.gz下载失败!" +fi tar -zxvf $buildpath/v0.19.0.tar.gz -C $buildpath && rm -rf $buildpath/v0.19.0.tar.gz cd $buildpath/pysam-0.19.0 python setup.py install diff --git a/LifeSciences/Lumpy-0.3.1/dependency/sambamba-0.8.2.sh b/LifeSciences/Lumpy-0.3.1/dependency/sambamba-0.8.2.sh index 424d4eeb43603e7e1cfec553ea0d7001363d230e..8129797aba5af412d6cfdf7b5ea30854f708ba80 100644 --- a/LifeSciences/Lumpy-0.3.1/dependency/sambamba-0.8.2.sh +++ b/LifeSciences/Lumpy-0.3.1/dependency/sambamba-0.8.2.sh @@ -19,7 +19,15 @@ set -e yum install -y wget tar environment-modules \ lz4-devel.aarch64 -wget -t 10 -c -P $buildpath https://github.com/biod/sambamba/archive/refs/tags/v0.8.2.tar.gz +if `wget -t 40 -c -P $buildpath https://ghproxy.com/https://github.com/biod/sambamba/archive/refs/tags/v0.8.2.tar.gz` +then + echo "v0.8.2.tar.gz下载成功!(国内github加速下载)" +elif `wget -t 40 -c -P $buildpath https://github.com/biod/sambamba/archive/refs/tags/v0.8.2.tar.gz` +then + echo "v0.8.2.tar.gz下载成功!" +else + echo "v0.8.2.tar.gz下载失败!" +fi tar -zxvf $buildpath/v0.8.2.tar.gz -C $buildpath && rm -rf $buildpath/v0.8.2.tar.gz cd $buildpath/sambamba-0.8.2 sed -i "27c CC=clang" Makefile diff --git a/LifeSciences/Lumpy-0.3.1/dependency/samblaster-0.1.26.sh b/LifeSciences/Lumpy-0.3.1/dependency/samblaster-0.1.26.sh index 12e2613064ee8779ac23bdd27fadec70ddab99fe..1edb0a34d69b9f709a833020e628dfe91def5a6a 100644 --- a/LifeSciences/Lumpy-0.3.1/dependency/samblaster-0.1.26.sh +++ b/LifeSciences/Lumpy-0.3.1/dependency/samblaster-0.1.26.sh @@ -19,7 +19,15 @@ installpath=$2 set -e yum install -y wget tar environment-modules -wget -t 10 -c -P $buildpath https://github.com/GregoryFaust/samblaster/releases/download/v.0.1.26/samblaster-v.0.1.26.tar.gz +if `wget -t 40 -c -P $buildpath https://ghproxy.com/https://github.com/GregoryFaust/samblaster/releases/download/v.0.1.26/samblaster-v.0.1.26.tar.gz` +then + echo "samblaster-v.0.1.26.tar.gz下载成功!(国内github加速下载)" +elif `wget -t 40 -c -P $buildpath https://github.com/GregoryFaust/samblaster/releases/download/v.0.1.26/samblaster-v.0.1.26.tar.gz` +then + echo "samblaster-v.0.1.26.tar.gz下载成功!" +else + echo "samblaster-v.0.1.26.tar.gz下载失败!" +fi tar xf $buildpath/samblaster-v.0.1.26.tar.gz -C $buildpath && rm -rf $buildpath/samblaster-v.0.1.26.tar.gz cd $buildpath/samblaster-v.0.1.26 sed -i 's/gcc/clang/g' Makefile diff --git a/LifeSciences/Lumpy-0.3.1/dependency/samtools-1.15.1.sh b/LifeSciences/Lumpy-0.3.1/dependency/samtools-1.15.1.sh index f58b67cc4207c37aaf20ebfdbe76d8f6d9d964b3..5e0774d968c1368a3113da2f0b0f556722ee0e26 100644 --- a/LifeSciences/Lumpy-0.3.1/dependency/samtools-1.15.1.sh +++ b/LifeSciences/Lumpy-0.3.1/dependency/samtools-1.15.1.sh @@ -19,7 +19,15 @@ installpath=$2 set -e yum install -y wget tar environment-modules -wget -t 10 -c -P $buildpath https://github.com/samtools/samtools/releases/download/1.15.1/samtools-1.15.1.tar.bz2 +if `wget -t 40 -c -P $buildpath https://ghproxy.com/https://github.com/samtools/samtools/releases/download/1.15.1/samtools-1.15.1.tar.bz2` +then + echo "samtools-1.15.1.tar.bz2下载成功!(国内github加速下载)" +elif `wget -t 40 -c -P $buildpath https://github.com/samtools/samtools/releases/download/1.15.1/samtools-1.15.1.tar.bz2` +then + echo "samtools-1.15.1.tar.bz2下载成功!" +else + echo "samtools-1.15.1.tar.bz2下载失败!" +fi tar xf $buildpath/samtools-1.15.1.tar.bz2 -C $buildpath && rm -rf $buildpath/samtools-1.15.1.tar.bz2 cd $buildpath/samtools-1.15.1 ./configure --prefix=$installpath/samtools-1.15.1 CC=clang diff --git "a/LifeSciences/Lumpy-0.3.1/doc/Devkit\346\212\245\345\221\212/Lumpy-0.3.1 Devkit\350\277\201\347\247\273\344\270\216\350\260\203\344\274\230\346\212\245\345\221\212.docx" "b/LifeSciences/Lumpy-0.3.1/doc/Devkit\346\212\245\345\221\212/Lumpy-0.3.1 Devkit\350\277\201\347\247\273\344\270\216\350\260\203\344\274\230\346\212\245\345\221\212.docx" index d7a8d62fd81216f9dff4cef134ef279b937d7fb5..4d8d0422c55cb03009e4047b88176dd4a9404814 100644 Binary files "a/LifeSciences/Lumpy-0.3.1/doc/Devkit\346\212\245\345\221\212/Lumpy-0.3.1 Devkit\350\277\201\347\247\273\344\270\216\350\260\203\344\274\230\346\212\245\345\221\212.docx" and "b/LifeSciences/Lumpy-0.3.1/doc/Devkit\346\212\245\345\221\212/Lumpy-0.3.1 Devkit\350\277\201\347\247\273\344\270\216\350\260\203\344\274\230\346\212\245\345\221\212.docx" differ diff --git "a/LifeSciences/Lumpy-0.3.1/doc/Lumpy-0.3.1\345\272\224\347\224\250\347\247\273\346\244\215\346\214\207\345\215\227.docx" "b/LifeSciences/Lumpy-0.3.1/doc/Lumpy-0.3.1\345\272\224\347\224\250\347\247\273\346\244\215\346\214\207\345\215\227.docx" index 6fa421ec3912e89561730a1cd58e0e9f34e2bfbe..efd43104f5b7bf5ce18530e1a65c826534303311 100644 Binary files "a/LifeSciences/Lumpy-0.3.1/doc/Lumpy-0.3.1\345\272\224\347\224\250\347\247\273\346\244\215\346\214\207\345\215\227.docx" and "b/LifeSciences/Lumpy-0.3.1/doc/Lumpy-0.3.1\345\272\224\347\224\250\347\247\273\346\244\215\346\214\207\345\215\227.docx" differ diff --git a/LifeSciences/Lumpy-0.3.1/lumpy-0.3.1.sh b/LifeSciences/Lumpy-0.3.1/lumpy-0.3.1.sh index 4a8fd751dc5b0b4d7e8bbe439609dd834434db72..7e9811859e2cc0b99a6f6d60c13a0ecb660a7250 100644 --- a/LifeSciences/Lumpy-0.3.1/lumpy-0.3.1.sh +++ b/LifeSciences/Lumpy-0.3.1/lumpy-0.3.1.sh @@ -22,10 +22,33 @@ set -e yum install numpy zlib-devel autoconf automake openssl-devel -y cd $buildpath -wget -t 10 -c https://github.com/arq5x/lumpy-sv/archive/refs/tags/v0.3.1.tar.gz -wget -t 10 -c https://github.com/samtools/htslib/archive/d2d9c76ade2df2b63b9cf79ae8decda1dfadc042.zip -wget -t 10 -c https://github.com/hall-lab/bamkit/archive/148ef1d3ac05ef7a033ed5ef42749c21956718d6.zip - +if `wget -t 40 -c -P $buildpath https://ghproxy.com/https://github.com/arq5x/lumpy-sv/archive/refs/tags/v0.3.1.tar.gz` +then + echo "v0.3.1.tar.gz下载成功!(国内github加速下载)" +elif `wget -t 40 -c -P $buildpath https://github.com/arq5x/lumpy-sv/archive/refs/tags/v0.3.1.tar.gz` +then + echo "v0.3.1.tar.gz下载成功!" +else + echo "v0.3.1.tar.gz下载失败!" +fi +if `wget -t 40 -c -P $buildpath https://ghproxy.com/https://github.com/samtools/htslib/archive/d2d9c76ade2df2b63b9cf79ae8decda1dfadc042.zip` +then + echo "d2d9c76ade2df2b63b9cf79ae8decda1dfadc042.zip下载成功!(国内github加速下载)" +elif `wget -t 40 -c -P $buildpath https://github.com/samtools/htslib/archive/d2d9c76ade2df2b63b9cf79ae8decda1dfadc042.zip` +then + echo "d2d9c76ade2df2b63b9cf79ae8decda1dfadc042.zip下载成功!" +else + echo "d2d9c76ade2df2b63b9cf79ae8decda1dfadc042.zip下载失败!" +fi +if `wget -t 40 -c -P $buildpath https://ghproxy.com/https://github.com/hall-lab/bamkit/archive/148ef1d3ac05ef7a033ed5ef42749c21956718d6.zip` +then + echo "148ef1d3ac05ef7a033ed5ef42749c21956718d6.zip下载成功!(国内github加速下载)" +elif `wget -t 40 -c -P $buildpath https://github.com/hall-lab/bamkit/archive/148ef1d3ac05ef7a033ed5ef42749c21956718d6.zip` +then + echo "148ef1d3ac05ef7a033ed5ef42749c21956718d6.zip下载成功!" +else + echo "148ef1d3ac05ef7a033ed5ef42749c21956718d6.zip下载失败!" +fi tar xf v0.3.1.tar.gz && rm -rf v0.3.1.tar.gz unzip d2d9c76ade2df2b63b9cf79ae8decda1dfadc042.zip && rm -rf d2d9c76ade2df2b63b9cf79ae8decda1dfadc042.zip unzip 148ef1d3ac05ef7a033ed5ef42749c21956718d6.zip && rm -rf 148ef1d3ac05ef7a033ed5ef42749c21956718d6.zip @@ -35,6 +58,7 @@ cp -rf bamkit-148ef1d3ac05ef7a033ed5ef42749c21956718d6/* lumpy-sv-0.3.1/scripts/ cd lumpy-sv-0.3.1 sed -i 's/ g++/ clang++/g' Makefile +sed -i "25s/$/&-march=armv8.2-a -fsigned-char -ffp-contract=off/" Makefile make -j$(nproc) mkdir -p $installpath/lumpy-0.3.1 && cp -r $buildpath/lumpy-sv-0.3.1/* $installpath/lumpy-0.3.1 diff --git a/LifeSciences/README.md b/LifeSciences/README.md index acc5036769f1c71ecd051329466d6a94bec70592..ef2affc84d719048a6479642825adfa78c1a80a2 100644 --- a/LifeSciences/README.md +++ b/LifeSciences/README.md @@ -34,3 +34,4 @@ Life Sciences Software List: - repositories: graphmap-0.3.0 - repositories: wham-1.8.0 - repositories: GATK-4.0.0.0 +- repositories: Lumpy-0.3.1 diff --git a/README.md b/README.md index 6825790d79bf312c2307ec46fd544dbb0f1caddb..1a78357c59cad24219f0806c47f315a5545b672d 100644 --- a/README.md +++ b/README.md @@ -38,3 +38,4 @@ HPC Software List: - repositories: LifeSciences/graphmap-0.3.0 - repositories: LifeSciences/wham-1.8.0 - repositories: LifeSciences/GATK-4.0.0.0 +- repositories: LifeSciences/Lumpy-0.3.1