From 08f6804d26e39e3b25144dc63972e9003280b640 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com>
Date: Fri, 9 May 2025 18:00:24 +0800
Subject: [PATCH 1/3] diamond

---
 .../2.0.4/diamond.arm.cpu.bisheng.hmpi.config | 69 +++++++++++++++++++
 1 file changed, 69 insertions(+)
 create mode 100644 templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config

diff --git a/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config b/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config
new file mode 100644
index 0000000..b82edfe
--- /dev/null
+++ b/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config
@@ -0,0 +1,69 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+diamond/2.0.4 https://github.com/bbuchfink/diamond/archive/v2.0.4.tar.gz diamond-2.0.4.tar.gz
+swissprot http://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/swissprot.gz swissprot.gz
+human_g1k_v37 http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz human_g1k_v37.fasta.gz
+
+[DEPENDENCY]
+set -e
+set -x
+
+yum install -y vim tar git wget make cmake
+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 hmpi/2.4.2 clang
+module use ./software/moduledeps/bisheng4.1.0
+module load hmpi/2.4.2
+tar -vzxf ${JARVIS_DOWNLOAD}/diamond-2.0.4.tar.gz
+mkdir -p DIAMOND
+mkdir -p TESTCASE
+cp -r ${JARVIS_DOWNLOAD}/swissprot.gz ./TESTCASE
+cp -r ${JARVIS_DOWNLOAD}/human_g1k_v37.fasta.gz ./TESTCASE
+cd ./TESTCASE
+gzip -dk swissprot.gz
+gzip -dk human_g1k_v37.fasta.gz
+split -l 1000000 human_g1k_v37.fasta human_g1k_part_
+cd ..
+
+[ENV]
+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 hmpi/2.4.2
+
+[APP]
+app_name = diamond
+build_dir = ${JARVIS_ROOT}/diamond-2.0.4/
+binary_dir = ${JARVIS_ROOT}/DIAMOND/bin/
+case_dir = ${JARVIS_ROOT}/TESTCASE/
+
+[BUILD]
+mkdir build
+cd build
+cmake -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/DIAMOND ../
+make -j 16
+make install
+
+[CLEAN]
+make clean
+
+[RUN]
+run =
+binary = diamond blastp -p 16 -q human_g1k_part_aa -d swissprot -o out_part_aa.tsv --very-sensitive
+nodes = 1
+
+[PERF]
+perf= 
+nsys=
+ncu=--target-processes all
-- 
Gitee


From 1c9acc06c697ed47a6d3d07a0681d1888b72c7bf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com>
Date: Fri, 9 May 2025 18:10:50 +0800
Subject: [PATCH 2/3] diamond

---
 templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config b/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config
index b82edfe..d2da120 100644
--- a/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config
+++ b/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config
@@ -28,7 +28,7 @@ cp -r ${JARVIS_DOWNLOAD}/swissprot.gz ./TESTCASE
 cp -r ${JARVIS_DOWNLOAD}/human_g1k_v37.fasta.gz ./TESTCASE
 cd ./TESTCASE
 gzip -dk swissprot.gz
-gzip -dk human_g1k_v37.fasta.gz
+gzip -dk human_g1k_v37.fasta.gz || true
 split -l 1000000 human_g1k_v37.fasta human_g1k_part_
 cd ..
 
-- 
Gitee


From 7cc0ba68ec557add0651b682cfd41b8e8c777281 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com>
Date: Mon, 12 May 2025 14:30:47 +0800
Subject: [PATCH 3/3] diamond

---
 templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config b/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config
index d2da120..33619c3 100644
--- a/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config
+++ b/templates/diamond/2.0.4/diamond.arm.cpu.bisheng.hmpi.config
@@ -56,6 +56,7 @@ make -j 16
 make install
 
 [CLEAN]
+cd build
 make clean
 
 [RUN]
-- 
Gitee