From 3f15e9a220318855a21735ae5163741dfb3e1557 Mon Sep 17 00:00:00 2001
From: cfmin <1163105507@qq.com>
Date: Fri, 13 Jun 2025 15:51:35 +0800
Subject: [PATCH 1/3] Add templates app CNVnator and package app cern_root

---
 package/cern_root/6.18.04/install.sh          | 26 ++++++++
 .../0.4.1/cnvnator.arm.kgcc.hmpi.config       | 59 +++++++++++++++++++
 templates/CNVnator/0.4.1/cnvnator_test.sh     | 22 +++++++
 3 files changed, 107 insertions(+)
 create mode 100644 package/cern_root/6.18.04/install.sh
 create mode 100755 templates/CNVnator/0.4.1/cnvnator.arm.kgcc.hmpi.config
 create mode 100755 templates/CNVnator/0.4.1/cnvnator_test.sh

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 0000000..c8ab9ae
--- /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 0000000..1c7dea8
--- /dev/null
+++ b/templates/CNVnator/0.4.1/cnvnator.arm.kgcc.hmpi.config
@@ -0,0 +1,59 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+CNVnator/0.4.1 ${JARVIS_PROXY}/abyzovlab/CNVnator/releases/download/v0.4.1/CNVnator_v0.4.1.zip
+samtools/1.10 ${JARVIS_PROXY}/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2
+
+[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 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}
+mkdir -p ${JARVIS_TMP_DOWNLOAD}/CNVnator_v0.4.1/src/samtools
+cd ${JARVIS_TMP_DOWNLOAD}/CNVnator_v0.4.1/src/samtools
+tar xvf ${JARVIS_DOWNLOAD}/samtools-1.10.tar.bz2 --strip-components=1
+./configure --prefix=$(pwd)
+make all all-htslib -j4
+make install install-htslib
+cp -a *.h $(pwd)/include
+cp -a *.a $(pwd)/lib
+
+[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 ${JARVIS_LIBS}/kgcc10.3.1/hmpi2.4.2/cern_root/6.18.04 cern_root
+sed -i '3a ROOTSYS = cern_root' Makefile
+sed -i '/^SAMLIB = .*/s/$/\ -lz -llzma -lbz2 -lreadline -lcurl/' 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
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 0000000..b0fec69
--- /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/samtools index NA12878_ali.bam
+../src/samtools/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
-- 
Gitee


From 923b6aad02975eceb91f54912ec157f93b1f42ba Mon Sep 17 00:00:00 2001
From: cfmin <1163105507@qq.com>
Date: Tue, 24 Jun 2025 02:04:44 +0000
Subject: [PATCH 2/3] update
 templates/CNVnator/0.4.1/cnvnator.arm.kgcc.hmpi.config.

Signed-off-by: cfmin <1163105507@qq.com>
---
 .../0.4.1/cnvnator.arm.kgcc.hmpi.config       | 23 ++++++++-----------
 1 file changed, 10 insertions(+), 13 deletions(-)

diff --git a/templates/CNVnator/0.4.1/cnvnator.arm.kgcc.hmpi.config b/templates/CNVnator/0.4.1/cnvnator.arm.kgcc.hmpi.config
index 1c7dea8..b86031c 100755
--- a/templates/CNVnator/0.4.1/cnvnator.arm.kgcc.hmpi.config
+++ b/templates/CNVnator/0.4.1/cnvnator.arm.kgcc.hmpi.config
@@ -3,7 +3,6 @@
 
 [DOWNLOAD]
 CNVnator/0.4.1 ${JARVIS_PROXY}/abyzovlab/CNVnator/releases/download/v0.4.1/CNVnator_v0.4.1.zip
-samtools/1.10 ${JARVIS_PROXY}/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2
 
 [DEPENDENCY]
 set -e
@@ -14,19 +13,13 @@ module use ./software/modulefiles
 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}
-mkdir -p ${JARVIS_TMP_DOWNLOAD}/CNVnator_v0.4.1/src/samtools
-cd ${JARVIS_TMP_DOWNLOAD}/CNVnator_v0.4.1/src/samtools
-tar xvf ${JARVIS_DOWNLOAD}/samtools-1.10.tar.bz2 --strip-components=1
-./configure --prefix=$(pwd)
-make all all-htslib -j4
-make install install-htslib
-cp -a *.h $(pwd)/include
-cp -a *.a $(pwd)/lib
 
 [ENV]
 module purge
@@ -38,13 +31,17 @@ module load cern_root/6.18.04
 [APP]
 app_name = cnvnator
 build_dir = ${JARVIS_TMP_DOWNLOAD}/CNVnator_v0.4.1/src
-binary_dir = 
+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 ${JARVIS_LIBS}/kgcc10.3.1/hmpi2.4.2/samtools/1.10 samtools
 sed -i '3a ROOTSYS = cern_root' Makefile
-sed -i '/^SAMLIB = .*/s/$/\ -lz -llzma -lbz2 -lreadline -lcurl/' 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
 
@@ -55,5 +52,5 @@ make clean
 
 [RUN]
 run = cp -ar ${JARVIS_ROOT}/templates/CNVnator/0.4.1/cnvnator_test.sh . && bash cnvnator_test.sh
-binary = 
-nodes = 1
+binary =
+nodes = 1
\ No newline at end of file
-- 
Gitee


From 644fa6e4d51ec4ddc56e60e19a5810c6174d6d8e Mon Sep 17 00:00:00 2001
From: cfmin <1163105507@qq.com>
Date: Tue, 24 Jun 2025 02:05:19 +0000
Subject: [PATCH 3/3] update templates/CNVnator/0.4.1/cnvnator_test.sh.

Signed-off-by: cfmin <1163105507@qq.com>
---
 templates/CNVnator/0.4.1/cnvnator_test.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/templates/CNVnator/0.4.1/cnvnator_test.sh b/templates/CNVnator/0.4.1/cnvnator_test.sh
index b0fec69..545f621 100755
--- a/templates/CNVnator/0.4.1/cnvnator_test.sh
+++ b/templates/CNVnator/0.4.1/cnvnator_test.sh
@@ -9,8 +9,8 @@ wget https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/NA12878/alignment/NA
 
 gunzip chr20.fa.gz
 mv NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam NA12878_ali.bam
-../src/samtools/samtools index NA12878_ali.bam
-../src/samtools/samtools faidx chr20.fa
+../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
-- 
Gitee