From 3a2bb5997ace85b87966bd9ec17b7cc50e503936 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com>
Date: Tue, 13 May 2025 16:42:23 +0800
Subject: [PATCH 1/2] hmmer

---
 .../3.3.2/hmmer.arm.cpu.bisheng.hmpi.config   | 67 +++++++++++++++++++
 1 file changed, 67 insertions(+)
 create mode 100644 templates/hmmer/3.3.2/hmmer.arm.cpu.bisheng.hmpi.config

diff --git a/templates/hmmer/3.3.2/hmmer.arm.cpu.bisheng.hmpi.config b/templates/hmmer/3.3.2/hmmer.arm.cpu.bisheng.hmpi.config
new file mode 100644
index 0000000..971b6f5
--- /dev/null
+++ b/templates/hmmer/3.3.2/hmmer.arm.cpu.bisheng.hmpi.config
@@ -0,0 +1,67 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+hmmer/3.3.2 $JARVIS_PROXY/EddyRivasLab/hmmer/archive/refs/heads/h3-arm.zip hmmer-h3-arm.zip
+master $JARVIS_PROXY/EddyRivasLab/easel/archive/refs/heads/master.zip master.zip
+
+[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 hmpi/2.4.2 clang
+module use ./software/moduledeps/bisheng4.1.0
+module load hmpi/2.4.2
+yum install -y environment-modules csh time patch libatomic perl-Data-Dumper autoconf automake libtool numactl binutils systemd-devel valgrind flex wget
+mkdir -p hmmer
+unzip ${JARVIS_DOWNLOAD}/hmmer-h3-arm.zip
+mv hmmer-h3-arm/ hmmer-3.3.2/
+cd hmmer-3.3.2/
+#wget https://github.com/EddyRivasLab/easel/archive/refs/heads/master.zip
+unzip ${JARVIS_DOWNLOAD}/master.zip
+mv easel-master/ easel/
+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}/hmmer-3.3.2/
+binary_dir = ${JARVIS_ROOT}/hmmer/bin/
+case_dir = ${JARVIS_ROOT}/hmmer-3.3.2/tutorial/
+
+[BUILD]
+autoconf
+./configure --prefix=${JARVIS_ROOT}/hmmer --enable-mpi --enable-neon CC=$MPICC CXX=$MPICXX FC=$MPIFC F77=$MPIFC
+make -j
+make check
+make -j install
+cd easel/
+make install
+
+[CLEAN]
+make clean
+
+[RUN]
+run =
+binary = hmmbuild globins4.hmm globins4.sto
+nodes = 1
+
+[PERF]
+perf= 
+nsys=
+ncu=--target-processes all
-- 
Gitee


From e399352ea6974d4d8c32b6676c6dd23966b1a414 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E9=AB=98=E6=96=87=E5=B0=A7?= <18848977154@163.com>
Date: Tue, 13 May 2025 17:31:23 +0800
Subject: [PATCH 2/2] hmmer

---
 templates/hmmer/3.3.2/hmmer.arm.cpu.bisheng.hmpi.config | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/templates/hmmer/3.3.2/hmmer.arm.cpu.bisheng.hmpi.config b/templates/hmmer/3.3.2/hmmer.arm.cpu.bisheng.hmpi.config
index 971b6f5..52510f1 100644
--- a/templates/hmmer/3.3.2/hmmer.arm.cpu.bisheng.hmpi.config
+++ b/templates/hmmer/3.3.2/hmmer.arm.cpu.bisheng.hmpi.config
@@ -2,8 +2,8 @@
 11.11.11.11
 
 [DOWNLOAD]
-hmmer/3.3.2 $JARVIS_PROXY/EddyRivasLab/hmmer/archive/refs/heads/h3-arm.zip hmmer-h3-arm.zip
-master $JARVIS_PROXY/EddyRivasLab/easel/archive/refs/heads/master.zip master.zip
+hmmer/3.3.2 https://github.com/EddyRivasLab/hmmer/archive/refs/heads/h3-arm.zip hmmer-h3-arm.zip
+master https://github.com/EddyRivasLab/easel/archive/refs/heads/master.zip master.zip
 
 [DEPENDENCY]
 set -e
@@ -18,7 +18,7 @@ export FC=`which flang`
 ./jarvis -install hmpi/2.4.2 clang
 module use ./software/moduledeps/bisheng4.1.0
 module load hmpi/2.4.2
-yum install -y environment-modules csh time patch libatomic perl-Data-Dumper autoconf automake libtool numactl binutils systemd-devel valgrind flex wget
+yum install -y environment-modules csh time patch libatomic perl-Data-Dumper autoconf automake libtool numactl binutils systemd-devel valgrind flex wget cmake make
 mkdir -p hmmer
 unzip ${JARVIS_DOWNLOAD}/hmmer-h3-arm.zip
 mv hmmer-h3-arm/ hmmer-3.3.2/
-- 
Gitee