From a552d030b548ff063ecf743957e7f86a3f4cd9b7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E6=B1=82=E7=9F=A5=E8=B7=AF?=
 <11884013+lu-liaojunhao@user.noreply.gitee.com>
Date: Tue, 4 Mar 2025 21:34:54 +0800
Subject: [PATCH 1/3] templates/FastTree/ templates/deeptools/ templates/fasta/
 templates/fastp/ templates/featurecounts/

---
 .../2.1.11/data.fasttree.arm.cpu.config       | 78 +++++++++++++++
 .../3.5.1/data.deeptools.arm.cpu.config       | 72 ++++++++++++++
 .../fasta/36.3.8/data.fasta.arm.cpu.config    | 99 +++++++++++++++++++
 .../fastp/0.20.1/data.fastp.arm.cpu.config    | 80 +++++++++++++++
 .../2.0.3/data.featurecounts.arm.cpu.config   | 70 +++++++++++++
 5 files changed, 399 insertions(+)
 create mode 100644 templates/FastTree/2.1.11/data.fasttree.arm.cpu.config
 create mode 100644 templates/deeptools/3.5.1/data.deeptools.arm.cpu.config
 create mode 100644 templates/fasta/36.3.8/data.fasta.arm.cpu.config
 create mode 100644 templates/fastp/0.20.1/data.fastp.arm.cpu.config
 create mode 100644 templates/featurecounts/2.0.3/data.featurecounts.arm.cpu.config

diff --git a/templates/FastTree/2.1.11/data.fasttree.arm.cpu.config b/templates/FastTree/2.1.11/data.fasttree.arm.cpu.config
new file mode 100644
index 0000000..2b9e796
--- /dev/null
+++ b/templates/FastTree/2.1.11/data.fasttree.arm.cpu.config
@@ -0,0 +1,78 @@
+[SERVER]
+11.11.11.11
+
+
+[DOWNLOAD]
+FastTree/2.1.11  http://meta.microbesonline.org/fasttree/FastTree.c 
+FastTree/case http://morgannprice.org/16S/403K/all.masked.gz
+
+
+[DEPENDENCY]
+set -e
+set -x
+module purge 
+
+./jarvis -install bisheng/4.1.0 com
+module use ./software/modulefiles
+module load bisheng/4.1.0
+export CC=`which clang`
+export CXX=`which clang++`
+export FC=`which flang`
+
+echo "Check the source code"
+if [ -d FastTree-2.1.11 ];then
+        rm -rf FastTree-2.1.11
+fi
+if [ -d workloads/FastTree ];then
+        rm -rf workloads/FastTree
+fi
+
+mkdir -p FastTree-2.1.11
+mkdir -p workloads/FastTree/fasttree-test
+cp ${JARVIS_DOWNLOAD}/FastTree.c FastTree-2.1.11/
+cd workloads/FastTree/fasttree-test
+cp ${JARVIS_DOWNLOAD}/all.masked.gz .
+gzip -dk all.masked.gz
+
+
+[ENV]
+set -e
+set -x
+module purge
+module use ./software/modulefiles
+module load bisheng/4.1.0
+export CC=`which clang`
+export CXX=`which clang++`
+export FC=`which flang`
+
+
+[APP]
+app_name = FastTree
+build_dir = ${JARVIS_ROOT}/FastTree-2.1.11
+binary_dir = ${JARVIS_ROOT}/FastTree-2.1.11
+case_dir = ${JARVIS_ROOT}/workloads/FastTree/fasttree-test
+
+
+[BUILD]
+set -e
+set -x
+clang -DOPENMP -DUSE_DOUBLE -fopenmp -O3 -march=armv8.2-a -mtune=tsv110 -finline-functions -funroll-loops -Wall -o FastTreePar-2.1.11 FastTree.c -lm
+
+
+[CLEAN]
+set -e
+set -x
+rm -f FastTreePar-2.1.11
+
+
+[RUN]
+run = 
+binary = FastTreePar-2.1.11 -fastest -noml -gtr -nt all.masked > `hostname`_`date '+%Y%m%d%H%M%S'`.masked.ft.rooted
+nodes = 1
+
+
+[PERF]
+perf=
+nsys=
+ncu=--target-processes all
+
diff --git a/templates/deeptools/3.5.1/data.deeptools.arm.cpu.config b/templates/deeptools/3.5.1/data.deeptools.arm.cpu.config
new file mode 100644
index 0000000..cc3f508
--- /dev/null
+++ b/templates/deeptools/3.5.1/data.deeptools.arm.cpu.config
@@ -0,0 +1,72 @@
+[SERVER]
+11.11.11.11
+
+
+[DOWNLOAD]
+deeptools/3.5.1 https://github.com/deeptools/deepTools/archive/refs/tags/3.5.1.tar.gz deepTools-3.5.1.tar.gz
+
+
+[DEPENDENCY]
+set -e
+set -x
+module purge 
+
+./jarvis -install bisheng/4.1.0 com
+module use ./software/modulefiles
+module load bisheng/4.1.0
+export CC=`which clang`
+export CXX=`which clang++`
+export FC=`which flang`
+
+./jarvis -install python3/3.9.9 clang
+module use ./software/moduledeps/bisheng4.1.0
+module load python3/3.9.9
+
+echo "Check the source code"
+if [ -d deepTools-3.5.1 ];then
+        rm -rf deepTools-3.5.1
+fi
+
+tar -xvzf ${JARVIS_DOWNLOAD}/deepTools-3.5.1.tar.gz
+
+
+[ENV]
+set -e
+set -x
+module purge
+module use ./software/modulefiles
+module load bisheng/4.1.0
+export CC=`which clang`
+export CXX=`which clang++`
+export FC=`which flang`
+module use ./software/moduledeps/bisheng4.1.0
+module load python3/3.9.9
+
+
+[APP]
+app_name = deeptools
+build_dir = ${JARVIS_ROOT}/deepTools-3.5.1
+binary_dir =
+case_dir =
+
+
+[BUILD]
+set -e
+set -x
+python3 setup.py install
+
+
+[CLEAN]
+
+
+[RUN]
+run = 
+binary = deeptools
+nodes = 1
+
+
+[PERF]
+perf=
+nsys=
+ncu=--target-processes all
+
diff --git a/templates/fasta/36.3.8/data.fasta.arm.cpu.config b/templates/fasta/36.3.8/data.fasta.arm.cpu.config
new file mode 100644
index 0000000..a3f8da6
--- /dev/null
+++ b/templates/fasta/36.3.8/data.fasta.arm.cpu.config
@@ -0,0 +1,99 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+fasta/36.3.8 https://github.com/wrpearson/fasta36/archive/v36.3.8h_04-May-2020.tar.gz fasta36-36.3.8h_04-May-2020.tar.gz 
+sse2neon/master https://github.com/DLTcollab/sse2neon/archive/refs/heads/master.zip sse2neon-master.zip
+
+
+[DEPENDENCY]
+set -e
+set -x
+module purge 
+
+./jarvis -install kgcc/10.3.1 com
+module use software/modulefiles
+module load kgcc/10.3.1
+export CC=`which gcc`
+export CXX=`which g++`
+export FC=`which gfortran`
+
+#./jarvis -install cmake/3.28.2 any
+#module load cmake/3.28.2
+
+./jarvis -install hmpi/2.4.2 gcc
+module use ./software/moduledeps/kgcc10.3.1
+module load hmpi/2.4.2
+
+echo "Check the source code"
+if [ -d fasta36-36.3.8h_04-May-2020 ];then
+	rm -rf fasta36-36.3.8h_04-May-2020
+fi
+if [ -d sse2neon-master ];then
+        rm -rf sse2neon-master
+fi
+
+tar -xvzf ${JARVIS_DOWNLOAD}/fasta36-36.3.8h_04-May-2020.tar.gz
+unzip ${JARVIS_DOWNLOAD}/sse2neon-master.zip
+
+cp sse2neon-master/sse2neon.h fasta36-36.3.8h_04-May-2020/src/
+
+cd fasta36-36.3.8h_04-May-2020/make
+cp Makefile.linux64_sse2 Makefile.linux64_sse2.bak
+sed -i "15s/.*/CC = gcc -g -O2 -march=armv8.2-a/" Makefile.linux64_sse2
+sed -i "29s/$/ -I. /" Makefile.linux64_sse2
+
+cd ../src
+cp smith_waterman_sse2.c smith_waterman_sse2.c-bak
+cp global_sse2.c global_sse2.c-bak
+cp glocal_sse2.c glocal_sse2.c-bak
+sed -i '23s/<emmintrin.h>/"sse2neon.h"/' smith_waterman_sse2.c
+sed -i '22s/<emmintrin.h>/"sse2neon.h"/' global_sse2.c
+sed -i '22s/<emmintrin.h>/"sse2neon.h"/' glocal_sse2.c
+
+
+[ENV]
+set -e
+set -x
+
+module use software/modulefiles
+module load kgcc/10.3.1
+export CC=`which gcc`
+export CXX=`which g++`
+export FC=`which gfortran`
+
+module use ./software/moduledeps/kgcc10.3.1
+module load hmpi/2.4.2
+
+export PATH=${JARVIS_ROOT}/fasta36-36.3.8h_04-May-2020/bin:$PATH
+
+[APP]
+app_name = fasta
+build_dir = ${JARVIS_ROOT}/fasta36-36.3.8h_04-May-2020/src
+binary_dir =
+case_dir = ${JARVIS_ROOT}/fasta36-36.3.8h_04-May-2020/data
+
+
+[BUILD]
+set -e
+set -x
+make -f ../make/Makefile.linux64_sse2
+
+
+[CLEAN]
+set -e
+set -x
+
+
+[RUN]
+run = mpirun --allow-run-as-root -np 12 ../bin/fasta36 -q ../seq/titin_hum.seq ../seq/prot_test.lseg
+#run = ../bin/fasta36 -q ../seq/titin_hum.seq ../seq/prot_test.lseg
+binary = 
+nodes = 1
+
+
+[PERF]
+perf=
+nsys=
+ncu=--target-processes all
+
diff --git a/templates/fastp/0.20.1/data.fastp.arm.cpu.config b/templates/fastp/0.20.1/data.fastp.arm.cpu.config
new file mode 100644
index 0000000..ec13718
--- /dev/null
+++ b/templates/fastp/0.20.1/data.fastp.arm.cpu.config
@@ -0,0 +1,80 @@
+[SERVER]
+11.11.11.11
+
+
+[DOWNLOAD]
+fastp/0.20.1 https://github.com/OpenGene/fastp/archive/v0.20.1.tar.gz fastp-0.20.1.tar.gz
+fastp/case1 http://ftp.sra.ebi.ac.uk/vol1/fastq/ERR104/008/ERR1044518/ERR1044518_1.fastq.gz
+fastp/case2 http://ftp.sra.ebi.ac.uk/vol1/fastq/ERR104/008/ERR1044518/ERR1044518_2.fastq.gz
+
+
+[DEPENDENCY]
+set -e
+set -x
+module purge 
+./jarvis -install bisheng/4.1.0 com
+module use ./software/modulefiles
+module load bisheng/4.1.0
+export CC=`which clang`
+export CXX=`which clang++`
+export FC=`which flang`
+
+echo "Check the source code"
+if [ -d fastp-0.20.1 ];then
+        rm -rf fastp-0.20.1
+fi
+if [ -d ${JARVIS_ROOT}/workloads/fastp ];then
+        rm -rf ${JARVIS_ROOT}/workloads/fastp
+fi
+
+tar -xvzf ${JARVIS_DOWNLOAD}/fastp-0.20.1.tar.gz
+
+mkdir -p ${JARVIS_ROOT}/workloads/fastp/fastp-test
+cd ${JARVIS_ROOT}/workloads/fastp/fastp-test
+cp ${JARVIS_DOWNLOAD}/ERR1044518_1.fastq.gz .
+cp ${JARVIS_DOWNLOAD}/ERR1044518_2.fastq.gz .
+gunzip -k ERR1044518_1.fastq.gz
+gunzip -k ERR1044518_2.fastq.gz
+
+
+[ENV]
+set -e
+set -x
+module purge
+module use ./software/modulefiles
+module load bisheng/4.1.0
+export CC=`which clang`
+export CXX=`which clang++`
+export FC=`which flang`
+
+
+[APP]
+app_name = fastp
+build_dir = ${JARVIS_ROOT}/fastp-0.20.1
+binary_dir = ${JARVIS_ROOT}/fastp-0.20.1
+case_dir = ${JARVIS_ROOT}/workloads/fastp/fastp-test
+
+
+[BUILD]
+set -e
+set -x
+make -j
+
+
+[CLEAN]
+set -e
+set -x
+make clean
+
+
+[RUN]
+run = 
+binary = fastp -i ERR1044518_1.fastq -I ERR1044518_2.fastq -w 16
+nodes = 1
+
+
+[PERF]
+perf=
+nsys=
+ncu=--target-processes all
+
diff --git a/templates/featurecounts/2.0.3/data.featurecounts.arm.cpu.config b/templates/featurecounts/2.0.3/data.featurecounts.arm.cpu.config
new file mode 100644
index 0000000..3fc8961
--- /dev/null
+++ b/templates/featurecounts/2.0.3/data.featurecounts.arm.cpu.config
@@ -0,0 +1,70 @@
+[SERVER]
+11.11.11.11
+
+
+[DOWNLOAD]
+featurecounts/2.0.3 https://sourceforge.net/projects/subread/files/subread-2.0.3/subread-2.0.3-source.tar.gz
+
+
+[DEPENDENCY]
+set -e
+set -x
+./jarvis -install bisheng/4.1.0 com
+module purge
+module use ./software/modulefiles
+module load bisheng/4.1.0
+export CC=`which clang`
+export CXX=`which clang++`
+export FC=`which flang`
+
+echo "Check the source code"
+if [ -d subread-2.0.3-source ];then
+        rm -rf subread-2.0.3-source
+fi
+
+tar -xzvf ${JARVIS_DOWNLOAD}/subread-2.0.3-source.tar.gz
+
+
+[ENV]
+module purge
+module use ./software/modulefiles
+module load bisheng/4.1.0 
+
+
+[APP]
+app_name = featurecounts
+build_dir = ${JARVIS_ROOT}/subread-2.0.3-source/src/
+binary_dir =
+case_dir = ${JARVIS_ROOT}/subread-2.0.3-source/test/featureCounts/
+
+
+[BUILD]
+sed -i 's/^CC_EXEC = gcc$/CC_EXEC = clang/' Makefile.Linux longread-one/Makefile
+sed -i "s/\(-mtune=core2\)/-march=native/" Makefile.Linux longread-one/Makefile
+echo "The compiler has been changed to Bisheng."
+
+# Output the first 14 lines of the Makefile.Linux for review.
+echo "Output the first 14 lines of the Makefile.Linux for review."
+head -n 14 Makefile.Linux
+
+# Output the first 10 lines of the longread-one/Makefile for review.
+echo "Output the first 10 lines of the longread-one/Makefile for review."
+head -n 10 longread-one/Makefile
+
+make -f Makefile.Linux
+
+
+[CLEAN]
+make -f Makefile.Linux clean
+
+
+[RUN]
+run = sh featureCounts-test.sh
+binary = 
+nodes = 1
+
+
+[PERF]
+perf= 
+nsys=
+ncu=--target-processes all
-- 
Gitee


From 3211455ad21e3633823210a457dc86b6944b7692 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E6=B1=82=E7=9F=A5=E8=B7=AF?=
 <11884013+lu-liaojunhao@user.noreply.gitee.com>
Date: Tue, 4 Mar 2025 23:07:45 +0800
Subject: [PATCH 2/3] RSEM

---
 templates/RSEM/1.3.3/data.rsem.arm.cpu.config | 98 +++++++++++++++++++
 1 file changed, 98 insertions(+)
 create mode 100644 templates/RSEM/1.3.3/data.rsem.arm.cpu.config

diff --git a/templates/RSEM/1.3.3/data.rsem.arm.cpu.config b/templates/RSEM/1.3.3/data.rsem.arm.cpu.config
new file mode 100644
index 0000000..0b4dc3b
--- /dev/null
+++ b/templates/RSEM/1.3.3/data.rsem.arm.cpu.config
@@ -0,0 +1,98 @@
+[SERVER]
+11.11.11.11
+
+
+[DOWNLOAD]
+RSEM/1.3.3 https://github.com/deweylab/RSEM/archive/refs/tags/v1.3.3.tar.gz RSEM-v1.3.3.tar.gz 
+RSEM/case https://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
+RSEM/case https://ftp.ensembl.org/pub/release-104/gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz
+
+[DEPENDENCY]
+set -e
+set -x
+module purge 
+
+./jarvis -install bisheng/4.1.0 com
+module use ./software/modulefiles
+module load bisheng/4.1.0
+export CC=`which clang`
+export CXX=`which clang++`
+export FC=`which flang`
+
+echo "Check the source code"
+if [ -d RSEM-1.3.3 ];then
+        rm -rf RSEM-1.3.3
+fi
+if [ -d workloads/RSEM ];then
+        rm -rf workloads/RSEM
+fi
+
+tar -xvzf ${JARVIS_DOWNLOAD}/RSEM-v1.3.3.tar.gz
+cp RSEM-1.3.3/Makefile RSEM-1.3.3/Makefile.bak
+mkdir -p RSEM-1.3.3/RSEM
+
+mkdir -p workloads/RSEM/rsem-test
+cd workloads/RSEM/rsem-test
+cp ${JARVIS_DOWNLOAD}/Homo_sapiens.GRCh38.104.gtf.gz .
+cp ${JARVIS_DOWNLOAD}/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz .
+gunzip -k Homo_sapiens.GRCh38.104.gtf.gz
+gunzip -k Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
+
+echo "Check the execution dependency “STAR” of the example "
+if [ ! -d STAR-2.7.1a ];then
+	echo "Please install the execution dependency “STAR”"
+else 
+	echo "Already install the execution dependency “STAR”"
+fi
+
+
+[ENV]
+set -e
+set -x
+module purge
+module use ./software/modulefiles
+module load bisheng/4.1.0
+export CC=`which clang`
+export CXX=`which clang++`
+export FC=`which flang`
+
+export PATH=${JARVIS_ROOT}/RSEM-1.3.3/RSEM/bin:$PATH
+export PATH=${JARVIS_ROOT}/STAR-2.7.1a/source:$PATH
+
+
+[APP]
+app_name = RSEM
+build_dir = ${JARVIS_ROOT}/RSEM-1.3.3
+binary_dir =
+case_dir = ${JARVIS_ROOT}/workloads/RSEM/rsem-test
+
+
+[BUILD]
+set -e
+set -x
+
+sed -i '14s|CXX = g++|CXX = clang++|' Makefile
+sed -i "28s|prefix ?= \/usr/local|prefix ?=${JARVIS_ROOT}/RSEM-1.3.3/RSEM|" Makefile
+
+make -j
+make install
+
+
+[CLEAN]
+set -e
+set -x
+make clean
+
+
+[RUN]
+run = rsem-prepare-reference --gtf Homo_sapiens.GRCh38.104.gtf --star Homo_sapiens.GRCh38.dna.primary_assembly.fa ./rsem_ref
+#run = rsem-prepare-reference --help
+binary =
+nodes = 1
+
+
+[PERF]
+perf=
+nsys=
+ncu=--target-processes all
+
-- 
Gitee


From ddfbb6fdf0262d2b82c2fc63fb3175b03d8b59de Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E6=B1=82=E7=9F=A5=E8=B7=AF?=
 <11884013+lu-liaojunhao@user.noreply.gitee.com>
Date: Wed, 5 Mar 2025 00:11:37 +0800
Subject: [PATCH 3/3] rsem1

---
 templates/RSEM/1.3.3/data.rsem.arm.cpu.config | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/templates/RSEM/1.3.3/data.rsem.arm.cpu.config b/templates/RSEM/1.3.3/data.rsem.arm.cpu.config
index 0b4dc3b..72f7e62 100644
--- a/templates/RSEM/1.3.3/data.rsem.arm.cpu.config
+++ b/templates/RSEM/1.3.3/data.rsem.arm.cpu.config
@@ -39,10 +39,10 @@ gunzip -k Homo_sapiens.GRCh38.104.gtf.gz
 gunzip -k Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
 
 echo "Check the execution dependency “STAR” of the example "
-if [ ! -d STAR-2.7.1a ];then
-	echo "Please install the execution dependency “STAR”"
+if command -v STAR; then
+	echo "Already install the execution dependency “STAR”."
 else 
-	echo "Already install the execution dependency “STAR”"
+	echo "Please install the execution dependency “STAR” in ${JARVIS_ROOT} or configure the STAR executable file environment variables after installation."
 fi
 
 
-- 
Gitee