From 97bd36c37b5c86b5614e775c341f770f0e5cca9f Mon Sep 17 00:00:00 2001
From: cfmin <1163105507@qq.com>
Date: Tue, 22 Apr 2025 16:53:57 +0800
Subject: [PATCH] Add templates app wtdbg2-2.5

---
 .../wtdbg2/2.5/wtdbg.arm.kgcc.hmpi.config     | 59 +++++++++++++++++++
 1 file changed, 59 insertions(+)
 create mode 100644 templates/wtdbg2/2.5/wtdbg.arm.kgcc.hmpi.config

diff --git a/templates/wtdbg2/2.5/wtdbg.arm.kgcc.hmpi.config b/templates/wtdbg2/2.5/wtdbg.arm.kgcc.hmpi.config
new file mode 100644
index 0000000..a96679f
--- /dev/null
+++ b/templates/wtdbg2/2.5/wtdbg.arm.kgcc.hmpi.config
@@ -0,0 +1,59 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+wtdbg2/2.5 ${JARVIS_PROXY}/ruanjue/wtdbg2/archive/refs/tags/v2.5.tar.gz wtdbg2-2.5.tar.gz
+sse2neon/ ${JARVIS_PROXY}/jratcliff63367/sse2neon/archive/master.zip sse2neon-master.zip
+case/E.coli http://www.cbcb.umd.edu/software/PBcR/data/selfSampleData.tar.gz
+
+[DEPENDENCY]
+module purge
+module use ./software/modulefiles
+./jarvis -install kgcc/10.3.1 com
+module load kgcc/10.3.1
+./jarvis -install hmpi/2.4.2 gcc
+module load hmpi/2.4.2
+
+mkdir -p ${JARVIS_ROOT}/software/apps/wtdbg2/bin
+tar -zxvf ${JARVIS_DOWNLOAD}/wtdbg2-2.5.tar.gz -C ${JARVIS_TMP_DOWNLOAD}
+unzip -j ${JARVIS_DOWNLOAD}/sse2neon-master.zip 'sse2neon-master/SSE2NEON.h' -d ${JARVIS_TMP_DOWNLOAD}/wtdbg2-2.5/
+
+[ENV]
+module purge
+module use ./software/modulefiles
+module load kgcc/10.3.1
+module load hmpi/2.4.2
+
+[APP]
+app_name = wtdbg2
+build_dir = ${JARVIS_TMP_DOWNLOAD}/wtdbg2-2.5
+binary_dir = ${JARVIS_ROOT}/software/apps/wtdbg2/bin
+case_dir = ${JARVIS_TMP_DOWNLOAD}/wtdbg2-2.5/wtdbg2_test
+
+[BUILD]
+mv SSE2NEON.h sse2neon.h
+sed -i 's/^CC  :=.*/CC  := mpicc/' Makefile
+sed -i 's/^BIN :=.*/BIN := \${JARVIS_ROOT}\/software\/apps\/wtdbg2\/bin/' Makefile
+sed -i 's/\-mpopcnt \-msse4.2/\-march=armv8-a/' Makefile
+sed -i '/^GENERIC_SRC=.*/s/$/\ sse2neon.h/' Makefile
+sed -i '/^#include <emmintrin.h>/a #include \"sse2neon.h\"' ksw.c
+sed -i '/^#include <emmintrin.h>/s/^/\/\//' ksw.c
+sed -i '/^#include <tmmintrin.h>/a #include \"sse2neon.h\"' poacns.h
+sed -i '/^#include <emmintrin.h>/s/^/\/\//' poacns.h
+sed -i '/^#include <tmmintrin.h>/s/^/\/\//' poacns.h
+sed -i '/SMASK =.*/s/^/\/\//' poacns.h
+make
+make install
+cp -ar wtdbg2.pl ${JARVIS_ROOT}/software/apps/wtdbg2/bin
+
+mkdir -p wtdbg2_test
+cd wtdbg2_test/
+cp -ar ${JARVIS_DOWNLOAD}/selfSampleData.tar.gz .
+
+[CLEAN]
+make clean
+
+[RUN]
+run = ${JARVIS_ROOT}/software/apps/wtdbg2/bin/wtdbg2 -x rs -g 4.6m -t $(nproc) -i selfSampleData.tar.gz -fo ecoli &&
+binary = wtpoa-cns -t $(nproc) -i ecoli.ctg.lay.gz -fo ecoli.ctg.fa
+nodes = 1
-- 
Gitee