From 974ea32035e70ad61dfec29103a019ac79155188 Mon Sep 17 00:00:00 2001
From: xiaolinjunhao <981755938@qq.com>
Date: Mon, 17 Feb 2025 08:51:03 +0000
Subject: [PATCH 1/2] =?UTF-8?q?=E6=8F=8F=E8=BF=B0=EF=BC=9A=E6=96=B0?=
 =?UTF-8?q?=E5=A2=9E=E5=BA=94=E7=94=A8cufflinks2.2.1=EF=BC=8C=E4=BB=A5?=
 =?UTF-8?q?=E5=8F=8A=E5=85=B6=E4=BE=9D=E8=B5=96samtools1.10=20=E7=94=A8?=
 =?UTF-8?q?=E6=88=B7=EF=BC=9A=E8=82=96=E6=9E=97=E4=BF=8A=E6=B5=A9x00806476?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 package/boost/1.72.0/install.sh               |  3 +-
 package/samtools/1.10/install.sh              | 14 ++++
 .../2.2.1/data.cufflinks.arm.cpu.config       | 66 +++++++++++++++++++
 3 files changed, 82 insertions(+), 1 deletion(-)
 create mode 100755 package/samtools/1.10/install.sh
 create mode 100644 templates/cufflinks/2.2.1/data.cufflinks.arm.cpu.config

diff --git a/package/boost/1.72.0/install.sh b/package/boost/1.72.0/install.sh
index 0c8a87c..ef7f626 100755
--- a/package/boost/1.72.0/install.sh
+++ b/package/boost/1.72.0/install.sh
@@ -1,7 +1,8 @@
 #!/bin/bash
 set -x
 set -e
-. ${DOWNLOAD_TOOL} -u https://boostorg.jfrog.io/artifactory/main/release/1.72.0/source/boost_1_72_0.tar.gz
+. ${DOWNLOAD_TOOL} -u https://archives.boost.io/release/1.72.0/source/boost_1_72_0.tar.gz
+#https://boostorg.jfrog.io/artifactory/main/release/1.72.0/source/boost_1_72_0.tar.gz
 cd ${JARVIS_TMP}
 rm -rf boost_1_72_0
 tar -xvf ${JARVIS_DOWNLOAD}/boost_1_72_0.tar.gz
diff --git a/package/samtools/1.10/install.sh b/package/samtools/1.10/install.sh
new file mode 100755
index 0000000..0b9d4a7
--- /dev/null
+++ b/package/samtools/1.10/install.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+set -x
+set -e
+. ${DOWNLOAD_TOOL} -u $JARVIS_PROXY/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2
+cd ${JARVIS_TMP}
+tar xvf ${JARVIS_DOWNLOAD}/samtools-1.10.tar.bz2
+cd samtools-1.10
+./configure --prefix=$1
+make all all-htslib
+make install install-htslib
+mkdir $1/include/bam
+cp *.h $1/include/bam
+cp *.a $1/lib
+
diff --git a/templates/cufflinks/2.2.1/data.cufflinks.arm.cpu.config b/templates/cufflinks/2.2.1/data.cufflinks.arm.cpu.config
new file mode 100644
index 0000000..44f5da5
--- /dev/null
+++ b/templates/cufflinks/2.2.1/data.cufflinks.arm.cpu.config
@@ -0,0 +1,66 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+cufflinks/2.2.1 $JARVIS_PROXY/cole-trapnell-lab/cufflinks/archive/refs/tags/v2.2.1.tar.gz cufflinks-2.2.1.tar.gz
+
+[DEPENDENCY]
+set -e
+set -x
+./jarvis -install kgcc/10.3.1 com
+module purge
+module use ./software/modulefiles
+module load kgcc/10.3.1
+export CC=`which gcc`
+export CXX=`which g++`
+export FC=`which gfortran`
+
+./jarvis -install boost/1.72.0 gcc
+./jarvis -install samtools/1.10 gcc
+./jarvis -install eigen3/3.4.0 gcc
+
+module use ./software/modulefiles
+module load boost/1.72.0
+module load samtools/1.10
+module load eigen3/3.4.0
+
+rm -rf cufflinks-2.2.1
+tar -xzvf ${JARVIS_DOWNLOAD}/cufflinks-2.2.1.tar.gz
+
+[ENV]
+module purge
+module use ./software/modulefiles
+module load kgcc/10.3.1
+module load boost/1.72.0
+module load samtools/1.10
+module load eigen3/3.4.0
+cd ${JARVIS_ROOT}/software/libs/kgcc10.3.1/eigen3/3.4.0/include
+cp -rf eigen3/Eigen .
+
+[APP]
+app_name = cufflinks
+build_dir = ${JARVIS_ROOT}/cufflinks-2.2.1
+binary_dir = 
+case_dir = 
+
+[BUILD]
+sed -i '16s/^/#/' configure.ac
+autoreconf --install
+sed -i 's/-lbam/-lbam -lhts/g' configure
+sed -i 's/#include <boost\/tr1\/unordered_map.hpp>/#include<boost\/unordered_map.hpp>/g' src/biascorrection.h
+sed -i 's/hash\[pos\].hash/(hash\[pos\].hash)/g' src/GHash.hh
+sed -i '70s/return;/return *this;/;72s/return;/return *this;/' src/lemon/error.h
+sed -i 's/curwin/curwins/g' src/locfit/c_plot.c
+./configure --with-boost=${BOOST_PATH} --with-eigen=${EIGEN3_PATH} --with-bam=${SAMTOOLS_PATH}
+make
+make install
+
+[CLEAN]
+make clean
+
+[RUN]
+run = 
+binary = 
+nodes = 1
+
+
-- 
Gitee


From 7b34e4e51a9e92846611084a54b61f5de919e00b Mon Sep 17 00:00:00 2001
From: xiaolinjunhao <981755938@qq.com>
Date: Sat, 22 Feb 2025 06:24:22 +0000
Subject: [PATCH 2/2] =?UTF-8?q?=E6=8F=8F=E8=BF=B0=EF=BC=9A=E6=96=B0?=
 =?UTF-8?q?=E5=A2=9E=E5=BA=94=E7=94=A8ecFlow5.5.2=E6=9E=81=E5=85=B6?=
 =?UTF-8?q?=E4=BE=9D=E8=B5=96boost-python?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 package/boost-python/1.72.0/install.sh        | 11 ++++
 .../ecFlow/5.5.2/data.ecFlow.arm.cpu.config   | 64 +++++++++++++++++++
 2 files changed, 75 insertions(+)
 create mode 100755 package/boost-python/1.72.0/install.sh
 create mode 100644 templates/ecFlow/5.5.2/data.ecFlow.arm.cpu.config

diff --git a/package/boost-python/1.72.0/install.sh b/package/boost-python/1.72.0/install.sh
new file mode 100755
index 0000000..ae2843d
--- /dev/null
+++ b/package/boost-python/1.72.0/install.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+set -x
+set -e
+. ${DOWNLOAD_TOOL} -u https://archives.boost.io/release/1.72.0/source/boost_1_72_0.tar.gz
+cd ${JARVIS_TMP}
+rm -rf boost_1_72_0
+tar -xvf ${JARVIS_DOWNLOAD}/boost_1_72_0.tar.gz
+cd boost_1_72_0
+sed -i '60s/.*/#ifdef PTHREAD_STACK_MIN/' ./boost/thread/pthread/thread_data.hpp
+./bootstrap.sh --with-python=`which python3`
+./b2 cxxflags="$(python3-config --includes) -Wno-deprecated-builtins -Wno-enum-constexpr-conversion -fPIC" linkflags="$(python3-config --ldflags)" install --prefix=$1
diff --git a/templates/ecFlow/5.5.2/data.ecFlow.arm.cpu.config b/templates/ecFlow/5.5.2/data.ecFlow.arm.cpu.config
new file mode 100644
index 0000000..8a13cf7
--- /dev/null
+++ b/templates/ecFlow/5.5.2/data.ecFlow.arm.cpu.config
@@ -0,0 +1,64 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+ecFlow/5.5.2 https://confluence.ecmwf.int/download/attachments/8650755/ecFlow-5.5.2-Source.tar.gz
+
+[DEPENDENCY]
+set -e
+set -x
+./jarvis -install kgcc/10.3.1 com
+module purge
+module use ./software/modulefiles
+module load kgcc/10.3.1
+export CC=`which gcc`
+export CXX=`which g++`
+export FC=`which gfortran`
+
+yum install -y python3
+yum install -y qt5 qt5-devel
+
+./jarvis -install boost-python/1.72.0 gcc
+
+rm -rf ecFlow-5.5.2-Source
+tar -xzvf ${JARVIS_DOWNLOAD}/ecFlow-5.5.2-Source.tar.gz
+
+[ENV]
+module purge
+module use ./software/modulefiles
+module load kgcc/10.3.1
+#module load boost-python/1.72.0
+
+[APP]
+app_name = ecFlow
+build_dir = 
+binary_dir = 
+case_dir = 
+
+[BUILD]
+export BOOST_ROOT=${JARVIS_TMP}/boost_1_72_0
+export WK=${JARVIS_ROOT}/ecFlow-5.5.2-Source
+export BOOST_PATH=${JARVIS_ROOT}/software/libs/kgcc10.3.1/boost-python/1.72.0
+
+cd ${JARVIS_TMP}/boost_1_72_0
+$WK/build_scripts/boost_build.sh
+
+cd ${WK}
+mkdir build
+cd build
+cmake .. -DENABLE_UI=ON -DENABLE_PYTHON=ON -DBoost_INCLUDE_DIR=${BOOST_PATH}/include -DCMAKE_CXX_FLAGS="-Wno-enum-constexpr-conversion -fPIC" -DBoost_PYTHON3_LIBRARY_RELEASE=${BOOST_PATH}/lib/libboost_python39.a -DBoost_PYTHON_LIBRARY_RELEASE=${BOOST_PATH}/lib/libboost_python39.a
+make
+make install
+
+[CLEAN]
+make clean
+
+[RUN]
+run =
+binary = 
+nodes = 1
+
+[PERF]
+perf=
+nsys=
+ncu=--target-processes all
-- 
Gitee