From a40fd66e64bbbd5e9b3f3aeed6091e77d337aade Mon Sep 17 00:00:00 2001
From: jsfhd <2162443403@qq.com>
Date: Fri, 11 Apr 2025 14:49:59 +0800
Subject: [PATCH] add tophat2-2.1.1 templates

---
 .../tophat2/2.1.1/data.tophat2.arm.cpu.config | 100 ++++++++++++++++++
 1 file changed, 100 insertions(+)
 create mode 100644 templates/tophat2/2.1.1/data.tophat2.arm.cpu.config

diff --git a/templates/tophat2/2.1.1/data.tophat2.arm.cpu.config b/templates/tophat2/2.1.1/data.tophat2.arm.cpu.config
new file mode 100644
index 0000000..1bb7008
--- /dev/null
+++ b/templates/tophat2/2.1.1/data.tophat2.arm.cpu.config
@@ -0,0 +1,100 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+tophat2/2.1.1 https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.tar.gz
+case1 http://opengene.org/data/R1.fq.gz
+case2 http://opengene.org/data/R2.fq.gz
+case3 http://ftp.ensembl.org/pub/release-84/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.dna.toplevel.fa.gz
+
+[DEPENDENCY]
+set -e
+set -x
+module purge
+./jarvis -install package/anaconda3/2023.3 any
+source ${JARVIS_ROOT}/software/utils/anaconda3/2023.3/etc/profile.d/conda.sh
+./jarvis -install package/hpckit/2024.12.30 any
+module use software/utils/hpckit/2024.12.30/HPCKit/latest/modulefiles
+module add bisheng/compiler4.1.0/bishengmodule
+./jarvis -install package/boost/1.72.0/clang clang
+module use software/moduledeps
+module add bisheng4.1.0/boost-clang/1.72.0
+
+[ENV]
+module purge
+source ${JARVIS_ROOT}/software/utils/anaconda3/2023.3/etc/profile.d/conda.sh
+module use software/utils/hpckit/2024.12.30/HPCKit/latest/modulefiles
+module add bisheng/compiler4.1.0/bishengmodule
+module use software/moduledeps
+module add bisheng4.1.0/boost-clang/1.72.0
+module add bisheng4.1.0/bowtie2/2.4.1
+export PATH=${JARVIS_ROOT}/software/apps/bisheng/tophat2/2.1.1/bin:$PATH
+mkdir -p ${JARVIS_ROOT}/case
+
+[APP]
+app_name = tophat2
+build_dir = ${JARVIS_ROOT}
+binary_dir = 
+case_dir = ${JARVIS_ROOT}/case
+
+[BUILD]
+rm -rf ${JARVIS_ROOT}/software/utils/anaconda3/2023.3/envs/tophat2
+conda create -n tophat2 -y
+conda activate tophat2
+conda install python=2.7.15 -c conda-forge -y
+cd ${JARVIS_TMP}
+rm -rf tophat-2.1.1
+tar -xf ${JARVIS_DOWNLOAD}/tophat-2.1.1.tar.gz
+cd tophat-2.1.1
+sed -i "341s/<Junction, JunctionStats>//g" src/juncs_db.cpp
+sed -i "2708s/<Junction, JunctionStats>//g" src/tophat_reports.cpp
+./configure --prefix=${JARVIS_ROOT}/software/apps/bisheng/tophat2/2.1.1 --with-boost=${JARVIS_LIBS}/bisheng4.1.0/boost-clang/1.72.0
+sed -i "263s/CXXFLAGS = /CXXFLAGS = -std=c++14 /g" src/Makefile
+sed -i "152s/CXXFLAGS = /CXXFLAGS = -std=c++14 /g" Makefile
+sed -i "2s/-g/-g -fPIC/g" src/samtools-0.1.18/Makefile
+sed -i "2s/-g/-g -fPIC/g" src/samtools-0.1.18/bcftools/Makefile
+make -j
+make install
+conda deactivate
+rm -rf ${JARVIS_TMP}/tophat-2.1.1
+
+[RUN]
+run = 
+binary = 
+nodes = 1
+
+[BATCH]
+#定义日志文件
+LOG_FILE="tophat2-performance.log"
+
+#清空日志文件
+> "$LOG_FILE"
+
+#执行命令并统计性能
+#待补充
+
+[JOB]
+#!/bin/sh
+#DSUB -n tophat2_test
+#DSUB --mpi hmpi
+#DSUB -q default
+#DSUB -N 1
+#DSUB -R cpu =128
+#DSUB -oo tophat2_$J.out
+#DSUB -eo tophat2.$J.err
+
+conda activate tophat2
+
+#生成算例
+cd ${JARVIS_ROOT}/case
+if [ ! -f "R1.fa" ];then
+ gzip -d ${JARVIS_DOWNLOAD}/R1.fq.gz
+ gzip -d ${JARVIS_DOWNLOAD}/R2.fq.gz
+ gzip -d ${JARVIS_DOWNLOAD}/Drosophila_melanogaster.BDGP6.dna.toplevel.fa.gz
+ mv Drosophila_melanogaster.BDGP6.dna.toplevel.fa genome.fa
+fi
+
+#运行
+#待补充
+#bowtie2-build genome.fa genome
+#tophat2 -p 128 genome R1.fq R2.fq
-- 
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