From 95ba019b0151cba11d6cc792d62f8f2ae8f1a1ac Mon Sep 17 00:00:00 2001
From: cgnfs <1014153531@qq.com>
Date: Mon, 11 Apr 2022 17:31:48 +0800
Subject: [PATCH] add some scripts and some templates

---
 package/R/3.6.3/install.sh                    | 12 +++++++
 package/automake/1.16.5/install.sh            | 11 +++++++
 package/blas/3.10.0/bisheng/install.sh        | 12 +++++++
 package/blas/3.10.0/install.sh                |  0
 package/git/2.35.1/install.sh                 | 12 +++++++
 package/htslib/1.15/install.sh                | 11 +++++++
 package/python3/3.7.10/install.sh             |  7 ++--
 package/samtools/1.15/install.sh              | 10 ++++++
 package/szip/2.1.1/install.sh                 | 10 ++++++
 templates/R/3.6.3/data.R.arm.bisheng.config   | 32 +++++++++++++++++++
 .../1.16.5/data.automake.arm.bisheng.config   | 32 +++++++++++++++++++
 .../blas/3.10.0/data.blas.arm.bisheng.config  | 32 +++++++++++++++++++
 .../git/2.35.1/data.git.arm.bisheng.config    | 32 +++++++++++++++++++
 .../1.15/data.htslib.arm.bisheng.config       | 32 +++++++++++++++++++
 .../3.7.10/data.python3.arm.bisheng.config    | 32 +++++++++++++++++++
 .../1.15/data.samtools.arm.bisheng.config     | 32 +++++++++++++++++++
 .../szip/2.1.1/data.szip.arm.bisheng.config   | 32 +++++++++++++++++++
 17 files changed, 338 insertions(+), 3 deletions(-)
 create mode 100644 package/R/3.6.3/install.sh
 create mode 100644 package/automake/1.16.5/install.sh
 create mode 100644 package/blas/3.10.0/bisheng/install.sh
 create mode 100644 package/blas/3.10.0/install.sh
 create mode 100644 package/git/2.35.1/install.sh
 create mode 100644 package/htslib/1.15/install.sh
 create mode 100644 package/samtools/1.15/install.sh
 create mode 100644 package/szip/2.1.1/install.sh
 create mode 100644 templates/R/3.6.3/data.R.arm.bisheng.config
 create mode 100644 templates/automake/1.16.5/data.automake.arm.bisheng.config
 create mode 100644 templates/blas/3.10.0/data.blas.arm.bisheng.config
 create mode 100644 templates/git/2.35.1/data.git.arm.bisheng.config
 create mode 100644 templates/htslib/1.15/data.htslib.arm.bisheng.config
 create mode 100644 templates/python3/3.7.10/data.python3.arm.bisheng.config
 create mode 100644 templates/samtools/1.15/data.samtools.arm.bisheng.config
 create mode 100644 templates/szip/2.1.1/data.szip.arm.bisheng.config

diff --git a/package/R/3.6.3/install.sh b/package/R/3.6.3/install.sh
new file mode 100644
index 0000000..daa865d
--- /dev/null
+++ b/package/R/3.6.3/install.sh
@@ -0,0 +1,12 @@
+#!/bin/bash
+
+#wget https://cloud.r-project.org/src/base/R-3/R-3.6.3.tar.gz
+#yum install libXt-devel.aarch64 readline-devel.aarch64
+set -x
+set -e
+cd ${JARVIS_TMP}
+tar -xvf ${JARVIS_DOWNLOAD}/R-3.6.3.tar.gz
+cd R-3.6.3
+./configure -enable-R-shlib -enable-R-static-lib --with-libpng --with-jpeglib --prefix=$1
+make all -j
+make install
diff --git a/package/automake/1.16.5/install.sh b/package/automake/1.16.5/install.sh
new file mode 100644
index 0000000..3ef8673
--- /dev/null
+++ b/package/automake/1.16.5/install.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+#wget https://ftp.gnu.org/gnu/automake/automake-1.16.5.tar.gz
+set -x
+set -e
+cd ${JARVIS_TMP}
+tar -xvf ${JARVIS_DOWNLOAD}/automake-1.16.5.tar.gz
+cd automake-1.16.5
+./configure --prefix=$1
+make -j
+make install
diff --git a/package/blas/3.10.0/bisheng/install.sh b/package/blas/3.10.0/bisheng/install.sh
new file mode 100644
index 0000000..4bceade
--- /dev/null
+++ b/package/blas/3.10.0/bisheng/install.sh
@@ -0,0 +1,12 @@
+#!/bin/bash
+#http://www.netlib.org/blas/blas-3.10.0.tgz
+set -x
+set -e
+cd ${JARVIS_TMP}
+rm -rf BLAS-3.10.0
+tar -xvf ${JARVIS_DOWNLOAD}/blas-3.10.0.tgz
+cd BLAS-3.10.0
+`which flang` -c -O3 -fomit-frame-pointer -funroll-loops *.f
+ar rv libblas.a *.o
+mkdir $1/lib
+cp libblas.a $1/lib
diff --git a/package/blas/3.10.0/install.sh b/package/blas/3.10.0/install.sh
new file mode 100644
index 0000000..e69de29
diff --git a/package/git/2.35.1/install.sh b/package/git/2.35.1/install.sh
new file mode 100644
index 0000000..9993f8b
--- /dev/null
+++ b/package/git/2.35.1/install.sh
@@ -0,0 +1,12 @@
+#!/bin/bash
+#wget https://github.com/git/git/archive/refs/tags/v2.35.1.tar.gz -O git-2.35.1.tar.gz
+set -x
+set -e
+cd ${JARVIS_TMP}
+tar -xvf ${JARVIS_DOWNLOAD}/git-2.35.1.tar.gz
+cd git-2.35.1
+autoconf
+./configure --prefix=$1
+make -j
+make install
+#export PATH=${JARVIS_COMPILER}/git/2.35.1/bin:$PATH
diff --git a/package/htslib/1.15/install.sh b/package/htslib/1.15/install.sh
new file mode 100644
index 0000000..c9d1359
--- /dev/null
+++ b/package/htslib/1.15/install.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+#wget https://github.com/samtools/htslib/releases/download/1.15/htslib-1.15.tar.bz2
+set -x
+set -e
+cd ${JARVIS_TMP}
+tar -xvf ${JARVIS_DOWNLOAD}/htslib-1.15.tar.bz2
+cd htslib-1.15 
+autoreconf -i
+./configure --prefix=$1
+make -j
+make install
diff --git a/package/python3/3.7.10/install.sh b/package/python3/3.7.10/install.sh
index 49f88a7..2dd773f 100644
--- a/package/python3/3.7.10/install.sh
+++ b/package/python3/3.7.10/install.sh
@@ -3,10 +3,11 @@
 set -x
 set -e
 cd ${JARVIS_TMP}
-yum -y install zlib-devel bzip2-devel openssl-devel ncurses-devel sqlite-devel readline-devel tk-devel gcc make libffi-devel
+#yum -y install zlib-devel bzip2-devel openssl-devel ncurses-devel sqlite-devel readline-devel tk-devel gcc make libffi-devel
 tar -zxvf ${JARVIS_DOWNLOAD}/Python-3.7.10.tgz
 cd Python-3.7.10
-./configure --prefix=${JARVIS_COMPILER}/python3
+./configure --prefix=$1
 make
 make install
-ln -s ${JARVIS_COMPILER}/python3/bin/python3.7 /usr/local/bin/python3
\ No newline at end of file
+#ln -s $1/python3/3.7.10/bin/python3.7 /usr/local/bin/python3
+#ln -s $1/python3/3.7.10/bin/pip3.7 /usr/local/bin/pip3
diff --git a/package/samtools/1.15/install.sh b/package/samtools/1.15/install.sh
new file mode 100644
index 0000000..c275133
--- /dev/null
+++ b/package/samtools/1.15/install.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+#wget https://github.com/samtools/samtools/releases/download/1.15/samtools-1.15.tar.bz2
+set -x
+set -e
+cd ${JARVIS_TMP}
+tar xvf ${JARVIS_DOWNLOAD}/samtools-1.15.tar.bz2
+cd samtools-1.15
+./configure --prefix=$1
+make -j
+make install
diff --git a/package/szip/2.1.1/install.sh b/package/szip/2.1.1/install.sh
new file mode 100644
index 0000000..12191e7
--- /dev/null
+++ b/package/szip/2.1.1/install.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+#wget https://distfiles.macports.org/szip/szip-2.1.1.tar.gz
+set -x
+set -e
+cd ${JARVIS_TMP}
+tar xvf ${JARVIS_DOWNLOAD}/szip-2.1.1.tar.gz
+cd szip-2.1.1
+./configure --prefix=$1
+make -j
+make install
diff --git a/templates/R/3.6.3/data.R.arm.bisheng.config b/templates/R/3.6.3/data.R.arm.bisheng.config
new file mode 100644
index 0000000..9f7779a
--- /dev/null
+++ b/templates/R/3.6.3/data.R.arm.bisheng.config
@@ -0,0 +1,32 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+R/3.6.3 https://cloud.r-project.org/src/base/R-3/R-3.6.3.tar.gz
+bisheng/2.1.0 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz
+
+[DEPENDENCY]
+./jarvis -install bisheng/2.1.0 com
+
+[ENV]
+module purge
+module use ./software/modulefiles
+module load bisheng2/2.1.0
+export CC=`which clang`
+export CXX=`which clang++`
+export FC=`which flang`
+
+[APP]
+app_name = R
+build_dir = $JARVIS_ROOT
+binary_dir =
+case_dir =
+
+[BUILD]
+./jarvis -install R/3.6.3 clang
+
+
+[RUN]
+run =
+binary =
+node = 1
diff --git a/templates/automake/1.16.5/data.automake.arm.bisheng.config b/templates/automake/1.16.5/data.automake.arm.bisheng.config
new file mode 100644
index 0000000..32ba035
--- /dev/null
+++ b/templates/automake/1.16.5/data.automake.arm.bisheng.config
@@ -0,0 +1,32 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+automake/1.16.5 https://ftp.gnu.org/gnu/automake/automake-1.16.5.tar.gz
+bisheng/2.1.0 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz
+
+[DEPENDENCY]
+./jarvis -install bisheng/2.1.0 com
+
+[ENV]
+module purge
+module use ./software/modulefiles
+module load bisheng2/2.1.0
+export CC=`which clang`
+export CXX=`which clang++`
+export FC=`which flang`
+
+[APP]
+app_name = automake
+build_dir = $JARVIS_ROOT
+binary_dir =
+case_dir =
+
+[BUILD]
+./jarvis -install automake/1.16.5 clang
+
+
+[RUN]
+run =
+binary =
+node = 1
diff --git a/templates/blas/3.10.0/data.blas.arm.bisheng.config b/templates/blas/3.10.0/data.blas.arm.bisheng.config
new file mode 100644
index 0000000..96edb25
--- /dev/null
+++ b/templates/blas/3.10.0/data.blas.arm.bisheng.config
@@ -0,0 +1,32 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+blas/3.10.0 http://www.netlib.org/blas/blas-3.10.0.tgz
+bisheng/2.1.0 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz
+
+[DEPENDENCY]
+./jarvis -install bisheng/2.1.0 com
+
+[ENV]
+module purge
+module use ./software/modulefiles
+module load bisheng2/2.1.0
+export CC=`which clang`
+export CXX=`which clang++`
+export FC=`which flang`
+
+[APP]
+app_name = blas
+build_dir = $JARVIS_ROOT
+binary_dir =
+case_dir =
+
+[BUILD]
+./jarvis -install blas/3.10.0/bisheng clang
+
+
+[RUN]
+run =
+binary =
+node = 1
diff --git a/templates/git/2.35.1/data.git.arm.bisheng.config b/templates/git/2.35.1/data.git.arm.bisheng.config
new file mode 100644
index 0000000..ace25fa
--- /dev/null
+++ b/templates/git/2.35.1/data.git.arm.bisheng.config
@@ -0,0 +1,32 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+git/2.35.1 https://github.com/git/git/archive/refs/tags/v2.35.1.tar.gz git-2.35.1.tar.gz
+bisheng/2.1.0 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz
+
+[DEPENDENCY]
+./jarvis -install bisheng/2.1.0 com
+
+[ENV]
+module purge
+module use ./software/modulefiles
+module load bisheng2/2.1.0
+export CC=`which clang`
+export CXX=`which clang++`
+export FC=`which flang`
+
+[APP]
+app_name = git
+build_dir = $JARVIS_ROOT
+binary_dir =
+case_dir =
+
+[BUILD]
+./jarvis -install git/2.35.1 clang
+
+
+[RUN]
+run =
+binary =
+node = 1
diff --git a/templates/htslib/1.15/data.htslib.arm.bisheng.config b/templates/htslib/1.15/data.htslib.arm.bisheng.config
new file mode 100644
index 0000000..452779d
--- /dev/null
+++ b/templates/htslib/1.15/data.htslib.arm.bisheng.config
@@ -0,0 +1,32 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+htslib/1.15 https://github.com/samtools/htslib/releases/download/1.15/htslib-1.15.tar.bz2
+bisheng/2.1.0 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz
+
+[DEPENDENCY]
+./jarvis -install bisheng/2.1.0 com
+
+[ENV]
+module purge
+module use ./software/modulefiles
+module load bisheng2/2.1.0
+export CC=`which clang`
+export CXX=`which clang++`
+export FC=`which flang`
+
+[APP]
+app_name = htslib
+build_dir = $JARVIS_ROOT
+binary_dir =
+case_dir =
+
+[BUILD]
+./jarvis -install htslib/1.15 clang
+
+
+[RUN]
+run =
+binary =
+node = 1
diff --git a/templates/python3/3.7.10/data.python3.arm.bisheng.config b/templates/python3/3.7.10/data.python3.arm.bisheng.config
new file mode 100644
index 0000000..0796dbf
--- /dev/null
+++ b/templates/python3/3.7.10/data.python3.arm.bisheng.config
@@ -0,0 +1,32 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+python3/3.7.10 https://repo.huaweicloud.com/python/3.7.10/Python-3.7.10.tgz
+bisheng/2.1.0 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz
+
+[DEPENDENCY]
+./jarvis -install bisheng/2.1.0 com
+
+[ENV]
+module purge
+module use ./software/modulefiles
+module load bisheng2/2.1.0
+export CC=`which clang`
+export CXX=`which clang++`
+export FC=`which flang`
+
+[APP]
+app_name = python3
+build_dir = $JARVIS_ROOT
+binary_dir =
+case_dir =
+
+[BUILD]
+./jarvis -install python3/3.7.10 clang
+
+
+[RUN]
+run =
+binary =
+node = 1
diff --git a/templates/samtools/1.15/data.samtools.arm.bisheng.config b/templates/samtools/1.15/data.samtools.arm.bisheng.config
new file mode 100644
index 0000000..8dac01a
--- /dev/null
+++ b/templates/samtools/1.15/data.samtools.arm.bisheng.config
@@ -0,0 +1,32 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+samtools/1.15 https://github.com/samtools/samtools/releases/download/1.15/samtools-1.15.tar.bz2
+bisheng/2.1.0 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz
+
+[DEPENDENCY]
+./jarvis -install bisheng/2.1.0 com
+
+[ENV]
+module purge
+module use ./software/modulefiles
+module load bisheng2/2.1.0
+export CC=`which clang`
+export CXX=`which clang++`
+export FC=`which flang`
+
+[APP]
+app_name = samtools
+build_dir = $JARVIS_ROOT
+binary_dir =
+case_dir =
+
+[BUILD]
+./jarvis -install samtools/1.15 clang
+
+
+[RUN]
+run =
+binary =
+node = 1
diff --git a/templates/szip/2.1.1/data.szip.arm.bisheng.config b/templates/szip/2.1.1/data.szip.arm.bisheng.config
new file mode 100644
index 0000000..03c22f2
--- /dev/null
+++ b/templates/szip/2.1.1/data.szip.arm.bisheng.config
@@ -0,0 +1,32 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+szip/2.1.1 https://distfiles.macports.org/szip/szip-2.1.1.tar.gz
+bisheng/2.1.0 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz
+
+[DEPENDENCY]
+./jarvis -install bisheng/2.1.0 com
+
+[ENV]
+module purge
+module use ./software/modulefiles
+module load bisheng2/2.1.0
+export CC=`which clang`
+export CXX=`which clang++`
+export FC=`which flang`
+
+[APP]
+app_name = szip
+build_dir = $JARVIS_ROOT
+binary_dir =
+case_dir =
+
+[BUILD]
+./jarvis -install szip/2.1.1 clang
+
+
+[RUN]
+run =
+binary =
+node = 1
-- 
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