From de895a2a1ef262cfb3236d95bb003feba31f5afd Mon Sep 17 00:00:00 2001
From: limingyang <limingyang49@huawei.com>
Date: Wed, 12 Feb 2025 02:43:10 +0000
Subject: [PATCH 1/4] update package/petsc/3.19.6/install.sh.

Signed-off-by: limingyang <limingyang49@huawei.com>
---
 package/petsc/3.19.6/install.sh | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/package/petsc/3.19.6/install.sh b/package/petsc/3.19.6/install.sh
index 5e1e968..5f6c49c 100755
--- a/package/petsc/3.19.6/install.sh
+++ b/package/petsc/3.19.6/install.sh
@@ -2,12 +2,13 @@
 set -x
 set -e
 . ${DOWNLOAD_TOOL} -u https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.19.6.tar.gz
+. ${DOWNLOAD_TOOL} -u https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.11/src/hdf5-1.10.11.tar.bz2
 cd ${JARVIS_TMP}
 rm -rf petsc-3.19.6
 tar -xvf ${JARVIS_DOWNLOAD}/petsc-3.19.6.tar.gz
 cd petsc-3.19.6
 ./configure F77=$F77 --prefix=$1 --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpifort \
-	--download-parmetis=1 --download-metis=1 \
-	--download-hdf5=${JARVIS_DOWNLOAD} --force
+        --download-parmetis=1 --download-metis=1 \
+        --download-hdf5=${JARVIS_DOWNLOAD}/hdf5-1.10.11.tar.bz2 --force
 make PETSC_DIR=${JARVIS_TMP}/petsc-3.19.6 PETSC_ARCH=arch-linux-c-debug all -j
-make PETSC_DIR=${JARVIS_TMP}/petsc-3.19.6 PETSC_ARCH=arch-linux-c-debug install -j
+make PETSC_DIR=${JARVIS_TMP}/petsc-3.19.6 PETSC_ARCH=arch-linux-c-debug install -j
\ No newline at end of file
-- 
Gitee


From 3b1f0c3ce62963e1329fefd4f7cb8f65556eb595 Mon Sep 17 00:00:00 2001
From: limingyang <limingyang49@huawei.com>
Date: Wed, 12 Feb 2025 02:44:20 +0000
Subject: [PATCH 2/4] update package/boost/1.72.0/clang/install.sh.

Signed-off-by: limingyang <limingyang49@huawei.com>
---
 package/boost/1.72.0/clang/install.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package/boost/1.72.0/clang/install.sh b/package/boost/1.72.0/clang/install.sh
index 9f61ca8..06b1f1e 100755
--- a/package/boost/1.72.0/clang/install.sh
+++ b/package/boost/1.72.0/clang/install.sh
@@ -6,5 +6,5 @@ cd ${JARVIS_TMP}
 tar -xvf ${JARVIS_DOWNLOAD}/boost_1_72_0.tar.gz
 cd boost_1_72_0
 sed -i '60s/.*/#ifdef PTHREAD_STACK_MIN/' ./boost/thread/pthread/thread_data.hpp
-./bootstrap.sh --with-toolset=clang
+./bootstrap.sh --with-toolset=clang --with-libraries=system,serialization,program_options
 ./b2 toolset=clang cxxflags="-std=c++14 -stdlib=libc++ -Wno-error=enum-constexpr-conversion" linkflags="-std=c++14 -stdlib=libc++ -Wno-error=enum-constexpr-conversion" install --prefix=$1
\ No newline at end of file
-- 
Gitee


From e3b6b5fa4414524c81937fd3eca34b359890d6df Mon Sep 17 00:00:00 2001
From: limingyang <1016071721@qq.com>
Date: Wed, 12 Feb 2025 10:57:40 +0800
Subject: [PATCH 3/4] Add template for augustus.

---
 package/bamtools/2.5.0/install.sh             | 13 ++++
 package/mysql/3.3.0/install.sh                | 10 +++
 .../3.3.3/data.augustus.arm.cpu.config        | 71 +++++++++++++++++++
 .../3.5.0/data.augustus.arm.cpu.config        | 69 ++++++++++++++++++
 4 files changed, 163 insertions(+)
 create mode 100755 package/bamtools/2.5.0/install.sh
 create mode 100755 package/mysql/3.3.0/install.sh
 create mode 100644 templates/augustus/3.3.3/data.augustus.arm.cpu.config
 create mode 100644 templates/augustus/3.5.0/data.augustus.arm.cpu.config

diff --git a/package/bamtools/2.5.0/install.sh b/package/bamtools/2.5.0/install.sh
new file mode 100755
index 0000000..8fb49d3
--- /dev/null
+++ b/package/bamtools/2.5.0/install.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+set -x
+set -e
+. ${DOWNLOAD_TOOL} -u https://github.com/pezmaster31/bamtools/archive/refs/tags/v2.5.0.tar.gz -f bamtools-2.5.0.tar.gz
+cd ${JARVIS_TMP}
+rm -rf bamtools-2.5.0
+tar -xvf ${JARVIS_DOWNLOAD}/bamtools-2.5.0.tar.gz
+cd bamtools-2.5.0
+export CC=clang CXX=clang++ FC=flang
+mkdir build && cd build
+cmake -DCMAKE_INSTALL_PREFIX=$1 .. -DCMAKE_CXX_FLAGS="-std=c++14 -O3" ..
+make -j
+make install
diff --git a/package/mysql/3.3.0/install.sh b/package/mysql/3.3.0/install.sh
new file mode 100755
index 0000000..8b02ceb
--- /dev/null
+++ b/package/mysql/3.3.0/install.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+set -x
+set -e
+. ${DOWNLOAD_TOOL} -u https://tangentsoft.com/mysqlpp/releases/mysql++-3.3.0.tar.gz
+cd ${JARVIS_TMP}
+rm -rf mysql++-3.3.0
+tar -xvf ${JARVIS_DOWNLOAD}/mysql++-3.3.0.tar.gz
+cd mysql++-3.3.0
+./configure --prefix=$1
+make -j && make install
diff --git a/templates/augustus/3.3.3/data.augustus.arm.cpu.config b/templates/augustus/3.3.3/data.augustus.arm.cpu.config
new file mode 100644
index 0000000..d715359
--- /dev/null
+++ b/templates/augustus/3.3.3/data.augustus.arm.cpu.config
@@ -0,0 +1,71 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+augustus/3.3.3 https://github.com/Gaius-Augustus/Augustus/archive/refs/tags/v3.3.3.tar.gz Augustus-3.3.3.tar.gz
+
+[DEPENDENCY]
+set -x
+set -e
+yum install gsl* mysql-devel sqlite* suitesparse* -y
+pip3 install parallel_augustus -i https://mirrors.aliyun.com/pypi/simple
+. ${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
+. ${DOWNLOAD_TOOL} -u http://bioinf.uni-greifswald.de/augustus/datasets/sag178.fa.gz
+rpm -ivh ./${JARVIS_DOWNLOAD}/lpsolve-5.5.2.5-5.mga9.aarch64.rpm ./${JARVIS_DOWNLOAD}/lpsolve-devel-5.5.2.5-5.mga9.aarch64.rpm
+
+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
+./jarvis -install mysql/3.3.0 clang
+./jarvis -install boost-clang/1.72.0 clang
+./jarvis -install htslib/1.15 clang
+./jarvis -install samtools/1.15 clang
+./jarvis -install bamtools/2.5.0 clang
+
+tar -zxvf $JARVIS_DOWNLOAD/Augustus-3.3.3.tar.gz
+
+[ENV]
+module purge
+module use ./software/modulefiles
+module load bisheng/4.1.0
+module load mysql/3.3.0
+module load boost-clang/1.72.0
+module load htslib/1.15
+module load samtools/1.15
+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
+case_dir = ${JARVIS_ROOT}/Augustus-3.3.3/run
+
+[BUILD]
+rm -rf Augustus-3.3.3
+tar -zxvf ${JARVIS_DOWNLOAD}/Augustus-3.3.3.tar.gz
+cd Augustus-3.3.3
+
+AUGUSTUS_PATH=$(realpath ./install)
+sed -i "s|\/opt\/augustus|$AUGUSTUS_PATH|g" Makefile
+
+make -j CC=clang CXX=clang++ \
+      CFLAGS="-DCOMPGENEPRED -g -I${BAMTOOLS_PATH}/include/bamtools -I${BOOST_CLANG_PATH}/include -I${HTSLIB_PATH}/include/htslib -I${MYSQL_PATH}/include/mysql++ -L${BAMTOOLS_PATH}/lib64 -L${BOOST_CLANG_PATH}/lib -L${HTSLIB_PATH}/lib -L${MYSQL_PATH}/lib -L/usr/lib64/mysql" \
+      CXXFLAGS="-DCOMPGENEPRED -g -std=c++17 -lstdc++ -I${BAMTOOLS_PATH}/include/bamtools -I${BOOST_CLANG_PATH}/include -I${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"
+make install
+
+mkdir run
+cd ./run
+cp ${JARVIS_DOWNLOAD}/sag178.fa.gz .
+gzip -d sag178.fa.gz
+
+[CLEAN]
+make clean
+
+[RUN]
+run = time -p
+binary = parallel_augustus -g sag178.fa -o sag178.res -c 1024 -p 128 --extra '--species=human -UTR=on'
+nodes = 1
diff --git a/templates/augustus/3.5.0/data.augustus.arm.cpu.config b/templates/augustus/3.5.0/data.augustus.arm.cpu.config
new file mode 100644
index 0000000..e8a0c15
--- /dev/null
+++ b/templates/augustus/3.5.0/data.augustus.arm.cpu.config
@@ -0,0 +1,69 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+augustus/3.5.0 https://github.com/Gaius-Augustus/Augustus/archive/refs/tags/v3.5.0.tar.gz Augustus-3.5.0.tar.gz
+
+[DEPENDENCY]
+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
+./jarvis -install boost-clang/1.72.0 clang
+./jarvis -install htslib/1.15 clang
+./jarvis -install samtools/1.15 clang
+./jarvis -install bamtools/2.5.0 clang
+
+module load hmpi/2.4.2
+export CC=mpicc CXX=mpicxx FC=mpifort
+
+tar -zxvf $JARVIS_DOWNLOAD/Augustus-3.5.0.tar.gz
+
+[ENV]
+module purge
+module use ./software/modulefiles
+module load bisheng/4.1.0
+module load boost-clang/1.72.0
+module load htslib/1.15
+module load samtools/1.15
+module load bamtools/2.5.0
+#module load hmpi/2.4.2
+
+[APP]
+app_name = Augustus
+build_dir = ${JARVIS_ROOT}
+binary_dir = ${JARVIS_ROOT}/Augustus-3.5.0/install-3.5.0/bin
+case_dir = ${JARVIS_ROOT}/Augustus-3.5.0/run
+
+[BUILD]
+yum install mysql-devel sqlite* -y
+rm -rf Augustus-3.5.0
+tar -zxvf $JARVIS_DOWNLOAD/Augustus-3.5.0.tar.gz
+cd Augustus-3.5.0
+
+mkdir run
+AUGUSTUS_PATH=$(realpath ./install)
+
+sed -i 's|3\.4\.0|3\.5\.0|g' ./common.mk ./doxygen.conf
+sed -i "s|\/opt\/augustus|$AUGUSTUS_PATH|g" Makefile
+sed -i "15iMYSQL = false\nCOMPGENEPRED = false" common.mk
+
+make -j CC=clang CXX=clang++ \
+      CFLAGS="-g -I${BAMTOOLS_PATH}/include/bamtools -I${BOOST_CLANG_PATH}/include -I${HTSLIB_PATH}/include/htslib -L${BAMTOOLS_PATH}/lib64 -L${BOOST_CLANG_PATH}/lib -L${HTSLIB_PATH}/lib" \
+      CXXFLAGS="-g -std=c++17 -lstdc++ -I${BAMTOOLS_PATH}/include/bamtools -I${BOOST_CLANG_PATH}/include -I${HTSLIB_PATH}/include/htslib -L${BAMTOOLS_PATH}/lib64 -L${BOOST_CLANG_PATH}/lib -L${HTSLIB_PATH}/lib"
+make install
+cd ./run
+wget http://bioinf.uni-greifswald.de/augustus/datasets/sag178.gb.gz --no-check-certificate
+gzip -d sag178.gb.gz
+
+[CLEAN]
+make clean
+
+[RUN]
+run = time -p
+binary = augustus --species=human --UTR=on sag178.gb
+nodes = 1
-- 
Gitee


From e10bdb5ebffd5b0ecbf9ed1ffcdea56316d034dc Mon Sep 17 00:00:00 2001
From: limingyang <limingyang49@huawei.com>
Date: Wed, 12 Feb 2025 03:02:58 +0000
Subject: [PATCH 4/4] =?UTF-8?q?=E5=88=A0=E9=99=A4=E6=96=87=E4=BB=B6=20temp?=
 =?UTF-8?q?lates/augustus/3.5.0?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .../3.5.0/data.augustus.arm.cpu.config        | 69 -------------------
 1 file changed, 69 deletions(-)
 delete mode 100644 templates/augustus/3.5.0/data.augustus.arm.cpu.config

diff --git a/templates/augustus/3.5.0/data.augustus.arm.cpu.config b/templates/augustus/3.5.0/data.augustus.arm.cpu.config
deleted file mode 100644
index e8a0c15..0000000
--- a/templates/augustus/3.5.0/data.augustus.arm.cpu.config
+++ /dev/null
@@ -1,69 +0,0 @@
-[SERVER]
-11.11.11.11
-
-[DOWNLOAD]
-augustus/3.5.0 https://github.com/Gaius-Augustus/Augustus/archive/refs/tags/v3.5.0.tar.gz Augustus-3.5.0.tar.gz
-
-[DEPENDENCY]
-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
-./jarvis -install boost-clang/1.72.0 clang
-./jarvis -install htslib/1.15 clang
-./jarvis -install samtools/1.15 clang
-./jarvis -install bamtools/2.5.0 clang
-
-module load hmpi/2.4.2
-export CC=mpicc CXX=mpicxx FC=mpifort
-
-tar -zxvf $JARVIS_DOWNLOAD/Augustus-3.5.0.tar.gz
-
-[ENV]
-module purge
-module use ./software/modulefiles
-module load bisheng/4.1.0
-module load boost-clang/1.72.0
-module load htslib/1.15
-module load samtools/1.15
-module load bamtools/2.5.0
-#module load hmpi/2.4.2
-
-[APP]
-app_name = Augustus
-build_dir = ${JARVIS_ROOT}
-binary_dir = ${JARVIS_ROOT}/Augustus-3.5.0/install-3.5.0/bin
-case_dir = ${JARVIS_ROOT}/Augustus-3.5.0/run
-
-[BUILD]
-yum install mysql-devel sqlite* -y
-rm -rf Augustus-3.5.0
-tar -zxvf $JARVIS_DOWNLOAD/Augustus-3.5.0.tar.gz
-cd Augustus-3.5.0
-
-mkdir run
-AUGUSTUS_PATH=$(realpath ./install)
-
-sed -i 's|3\.4\.0|3\.5\.0|g' ./common.mk ./doxygen.conf
-sed -i "s|\/opt\/augustus|$AUGUSTUS_PATH|g" Makefile
-sed -i "15iMYSQL = false\nCOMPGENEPRED = false" common.mk
-
-make -j CC=clang CXX=clang++ \
-      CFLAGS="-g -I${BAMTOOLS_PATH}/include/bamtools -I${BOOST_CLANG_PATH}/include -I${HTSLIB_PATH}/include/htslib -L${BAMTOOLS_PATH}/lib64 -L${BOOST_CLANG_PATH}/lib -L${HTSLIB_PATH}/lib" \
-      CXXFLAGS="-g -std=c++17 -lstdc++ -I${BAMTOOLS_PATH}/include/bamtools -I${BOOST_CLANG_PATH}/include -I${HTSLIB_PATH}/include/htslib -L${BAMTOOLS_PATH}/lib64 -L${BOOST_CLANG_PATH}/lib -L${HTSLIB_PATH}/lib"
-make install
-cd ./run
-wget http://bioinf.uni-greifswald.de/augustus/datasets/sag178.gb.gz --no-check-certificate
-gzip -d sag178.gb.gz
-
-[CLEAN]
-make clean
-
-[RUN]
-run = time -p
-binary = augustus --species=human --UTR=on sag178.gb
-nodes = 1
-- 
Gitee