kallisto-hpcrunner-AtomGit

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kallisto #925

gao-wenyao123创建于 2025年12月17日关闭于 1月6日从refs/pull/925/head 合入到 master

kallisto #925

已关闭

gao-wenyao123创建于 2025年12月17日关闭于 1月6日

从refs/pull/925/head合入到master

共 2 个文件变更+13-9

Mtemplates/kallisto-bustools_python/0.51.1/data.kallisto.arm.cpu.kgcc.config+6-4

	@@ -14,19 +14,20 @@ yum install libarchive -y
14	module purge	14	module purge
15	./jarvis -install hpckit/${HPCKIT_VERSION} any	15	./jarvis -install hpckit/${HPCKIT_VERSION} any
16	module use ./software/utils/hpckit/${HPCKIT_VERSION}/HPCKit/${HPCKIT_VERSION}/modulefiles	16	module use ./software/utils/hpckit/${HPCKIT_VERSION}/HPCKit/${HPCKIT_VERSION}/modulefiles
17	-module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi	17	+module add gcc/compiler12.3.1/gccmodule gcc/hmpi${HPCKIT_VERSION}/release
18	export CC=`which gcc`	18	export CC=`which gcc`
19	export CXX=`which g++`	19	export CXX=`which g++`
20	export FC=`which gfortran`	20	export FC=`which gfortran`
21	./jarvis -install htslib/1.11 gcc	21	./jarvis -install htslib/1.11 gcc
22	module use software/moduledeps/gcc12.3.1	22	module use software/moduledeps/gcc12.3.1
23	module load htslib/1.11	23	module load htslib/1.11
		24	+rm -rf kallisto-0.51.1
24	tar -xzvf ${JARVIS_DOWNLOAD}/kallisto-0.51.1.tar.gz	25	tar -xzvf ${JARVIS_DOWNLOAD}/kallisto-0.51.1.tar.gz
25		26
26	[ENV]	27	[ENV]
27	module purge	28	module purge
28	module use ./software/utils/hpckit/${HPCKIT_VERSION}/HPCKit/${HPCKIT_VERSION}/modulefiles	29	module use ./software/utils/hpckit/${HPCKIT_VERSION}/HPCKit/${HPCKIT_VERSION}/modulefiles
29	-module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi	30	+module add gcc/compiler12.3.1/gccmodule gcc/hmpi${HPCKIT_VERSION}/release
30	export CC=`which gcc`	31	export CC=`which gcc`
31	export CXX=`which g++`	32	export CXX=`which g++`
32	export FC=`which gfortran`	33	export FC=`which gfortran`
	@@ -37,7 +38,7 @@ module load htslib/1.11
37	app_name = kallisto	38	app_name = kallisto
38	build_dir = ${JARVIS_ROOT}/kallisto-0.51.1/	39	build_dir = ${JARVIS_ROOT}/kallisto-0.51.1/
39	binary_dir =	40	binary_dir =
40	-case_dir = ${JARVIS_ROOT}/kallisto-0.51.1/	41	+case_dir = ${JARVIS_ROOT}/kallisto-0.51.1/build/src/
41		42
42	[BUILD]	43	[BUILD]
43	mkdir build	44	mkdir build
	@@ -50,7 +51,7 @@ make install
50	make clean	51	make clean
51		52
52	[RUN]	53	[RUN]
53	-run = kallisto	54	+run = ./kallisto
54	binary =	55	binary =
55	nodes = 1	56	nodes = 1
56		57
	@@ -58,3 +59,4 @@ nodes = 1
58	perf=	59	perf=
59	nsys=	60	nsys=
60	ncu=--target-processes all	61	ncu=--target-processes all
		62	+

Mtemplates/kallisto-bustools_python/0.51.1/kallisto.arm.bisheng.hmpi.config+7-5

	@@ -7,15 +7,15 @@ kallisto/0.51.1 ${JARVIS_PROXY}/pachterlab/kallisto/archive/refs/tags/v0.51.1.ta
7	[DEPENDENCY]	7	[DEPENDENCY]
8	set -e	8	set -e
9	module purge	9	module purge
10	-
11	./jarvis -install hpckit/${HPCKIT_VERSION} any	10	./jarvis -install hpckit/${HPCKIT_VERSION} any
12	module use ./software/utils/hpckit/${HPCKIT_VERSION}/HPCKit/${HPCKIT_VERSION}/modulefiles	11	module use ./software/utils/hpckit/${HPCKIT_VERSION}/HPCKit/${HPCKIT_VERSION}/modulefiles
13	module load bisheng/compiler${BISHENG_VERSION}/bishengmodule	12	module load bisheng/compiler${BISHENG_VERSION}/bishengmodule
14	-module load bisheng/hmpi${HMPI_VERSION}	13	+module load bisheng/hmpi${HMPI_VERSION}/release
15	-
16	./jarvis -install hdf5/1.12.1/clang bisheng+mpi	14	./jarvis -install hdf5/1.12.1/clang bisheng+mpi
		15	+module use ./software/moduledeps/bisheng${BISHENG_VERSION}-hmpi${HPCKIT_VERSION}
17	module load hdf5-clang/1.12.1	16	module load hdf5-clang/1.12.1
18	-	17	+rm -rf ${JARVIS_ROOT}/software/apps/kallisto
		18	+rm -rf ${JARVIS_TMP_DOWNLOAD}/kallisto-0.51.1
19	mkdir -p ${JARVIS_ROOT}/software/apps/kallisto	19	mkdir -p ${JARVIS_ROOT}/software/apps/kallisto
20	tar -zxf ${JARVIS_DOWNLOAD}/kallisto-0.51.1.tar.gz -C ${JARVIS_TMP_DOWNLOAD}	20	tar -zxf ${JARVIS_DOWNLOAD}/kallisto-0.51.1.tar.gz -C ${JARVIS_TMP_DOWNLOAD}
21		21
	@@ -23,7 +23,8 @@ tar -zxf ${JARVIS_DOWNLOAD}/kallisto-0.51.1.tar.gz -C ${JARVIS_TMP_DOWNLOAD}
23	module purge	23	module purge
24	module use ./software/utils/hpckit/${HPCKIT_VERSION}/HPCKit/${HPCKIT_VERSION}/modulefiles	24	module use ./software/utils/hpckit/${HPCKIT_VERSION}/HPCKit/${HPCKIT_VERSION}/modulefiles
25	module load bisheng/compiler${BISHENG_VERSION}/bishengmodule	25	module load bisheng/compiler${BISHENG_VERSION}/bishengmodule
26	-module load bisheng/hmpi${HMPI_VERSION}	26	+module load bisheng/hmpi${HMPI_VERSION}/release
		27	+module use ./software/moduledeps/bisheng${BISHENG_VERSION}-hmpi${HPCKIT_VERSION}
27	module load hdf5-clang/1.12.1	28	module load hdf5-clang/1.12.1
28		29
29	[APP]	30	[APP]
	@@ -47,3 +48,4 @@ make clean
47	run = ${JARVIS_ROOT}/software/apps/kallisto/bin/kallisto index -i transcripts.idx transcripts.fasta.gz &&	48	run = ${JARVIS_ROOT}/software/apps/kallisto/bin/kallisto index -i transcripts.idx transcripts.fasta.gz &&
48	binary = kallisto quant -i transcripts.idx -o reads-ouput -b 100 reads_1.fastq.gz reads_2.fastq.gz && head -n 20 reads-ouput/abundance.tsv	49	binary = kallisto quant -i transcripts.idx -o reads-ouput -b 100 reads_1.fastq.gz reads_2.fastq.gz && head -n 20 reads-ouput/abundance.tsv
49	nodes = 1	50	nodes = 1
		51	+