From 073119341097ac57d4359788864eaa6425421e68 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, 6 May 2025 11:38:43 +0800
Subject: [PATCH 1/2] abyss

---
 .../data.abyss.arm.cpu.bisheng.hmpi.config    | 71 +++++++++++++++++++
 1 file changed, 71 insertions(+)
 create mode 100644 templates/abyss/2.2.4/data.abyss.arm.cpu.bisheng.hmpi.config

diff --git a/templates/abyss/2.2.4/data.abyss.arm.cpu.bisheng.hmpi.config b/templates/abyss/2.2.4/data.abyss.arm.cpu.bisheng.hmpi.config
new file mode 100644
index 0000000..52d94b9
--- /dev/null
+++ b/templates/abyss/2.2.4/data.abyss.arm.cpu.bisheng.hmpi.config
@@ -0,0 +1,71 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+abyss/2.2.4 https://github.com/bcgsc/abyss/archive/2.2.4.tar.gz abyss-2.2.4.tar.gz
+test-data https://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.3.4/test-data.tar.gz test-data.tar.gz
+
+[DEPENDENCY]
+set -e
+set -x
+yum install -y vim tar git wget automake autoconf libtool make cmake
+./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`
+./jarvis -install hmpi/2.4.2 clang
+module use ./software/moduledeps/bisheng4.1.0
+module load hmpi/2.4.2
+./jarvis -install boost/1.72.0/clang bisheng
+module load boost-clang/1.72.0
+yum install libomp  -y
+tar -vzxf ${JARVIS_DOWNLOAD}/abyss-2.2.4.tar.gz
+mkdir -p ABYSS
+tar xvf ${JARVIS_DOWNLOAD}/test-data.tar.gz
+
+[ENV]
+yum install -y vim tar git wget automake autoconf libtool make cmake
+module purge
+module use ./software/modulefiles
+module load bisheng/4.1.0
+module use ./software/moduledeps/bisheng4.1.0
+module load hmpi/2.4.2
+yum install libomp  -y
+export CC=`which clang`
+export CXX=`which clang++`
+export FC=`which flang`
+module use ./software/moduledeps/bisheng4.1.0
+module load boost-clang/1.72.0
+
+[APP]
+app_name = abyss
+build_dir = ${JARVIS_ROOT}/abyss-2.2.4/
+binary_dir = ${JARVIS_ROOT}/ABYSS/bin
+case_dir = ${JARVIS_ROOT}/test-data/
+
+[BUILD]
+./autogen.sh
+export CURRENT_MPI_PATH=`which mpirun | sed 's/\/bin\/mpirun//g'`
+./configure --prefix=${JARVIS_ROOT}/ABYSS --with-boost=${BOOST_PATH} --without-sparsehash --with-mpi=$CURRENT_MPI_PATH
+make -j 32 AM_CXXFLAGS=-Wall
+make install AM_CXXFLAGS=-Wall
+sed -i '543s/\$(mpirun)/\$(mpirun) --allow-run-as-root -mca coll_hcoll_enable 0/' "${JARVIS_ROOT}/ABYSS/bin/abyss-pe"
+sed -i '551s/\$(mpirun)/\$(mpirun) --allow-run-as-root -mca coll_hcoll_enable 0/' "${JARVIS_ROOT}/ABYSS/bin/abyss-pe"
+
+
+
+[CLEAN]
+make clean
+
+[RUN]
+run =
+binary = abyss-pe k=25 name=test in="reads1.fastq reads2.fastq"
+nodes = 1
+
+[PERF]
+perf= 
+nsys=
+ncu=--target-processes all
-- 
Gitee


From ca8d7f05fa6e9ad69480b6eafaf761c0e83618f1 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, 6 May 2025 20:11:22 +0800
Subject: [PATCH 2/2] abyss

---
 templates/abyss/2.2.4/data.abyss.arm.cpu.bisheng.hmpi.config | 2 --
 1 file changed, 2 deletions(-)

diff --git a/templates/abyss/2.2.4/data.abyss.arm.cpu.bisheng.hmpi.config b/templates/abyss/2.2.4/data.abyss.arm.cpu.bisheng.hmpi.config
index 52d94b9..0363a04 100644
--- a/templates/abyss/2.2.4/data.abyss.arm.cpu.bisheng.hmpi.config
+++ b/templates/abyss/2.2.4/data.abyss.arm.cpu.bisheng.hmpi.config
@@ -27,13 +27,11 @@ mkdir -p ABYSS
 tar xvf ${JARVIS_DOWNLOAD}/test-data.tar.gz
 
 [ENV]
-yum install -y vim tar git wget automake autoconf libtool make cmake
 module purge
 module use ./software/modulefiles
 module load bisheng/4.1.0
 module use ./software/moduledeps/bisheng4.1.0
 module load hmpi/2.4.2
-yum install libomp  -y
 export CC=`which clang`
 export CXX=`which clang++`
 export FC=`which flang`
-- 
Gitee