From 65d6d1b12b3028c16217c498e6f7ce7c2b419be1 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, 3 Jun 2025 15:32:55 +0800
Subject: [PATCH 1/4] kallisto-bustools_python

---
 .../0.51.1/data.kallisto.arm.cpu.kgcc.config  | 59 +++++++++++++++++++
 1 file changed, 59 insertions(+)
 create mode 100644 templates/kallisto-bustools_python/0.51.1/data.kallisto.arm.cpu.kgcc.config

diff --git a/templates/kallisto-bustools_python/0.51.1/data.kallisto.arm.cpu.kgcc.config b/templates/kallisto-bustools_python/0.51.1/data.kallisto.arm.cpu.kgcc.config
new file mode 100644
index 0000000..86e4daa
--- /dev/null
+++ b/templates/kallisto-bustools_python/0.51.1/data.kallisto.arm.cpu.kgcc.config
@@ -0,0 +1,59 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD]
+kallisto/0.51.1 https://github.com/pachterlab/kallisto/archive/refs/tags/v0.51.1.tar.gz kallisto-0.51.1.tar.gz 
+htslib/1.22 https://github.com/samtools/htslib/releases/download/1.22/htslib-1.22.tar.bz2
+
+[DEPENDENCY]
+set -e
+set -x
+yum install -y make cmake
+yum install -y autoconf automake libtool
+yum -y install xz-devel
+yum install libarchive -y
+module purge
+./jarvis -install hpckit/2024.12.30 any
+module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles
+module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi
+export CC=`which gcc`
+export CXX=`which g++`
+export FC=`which gfortran`
+tar -xjf ${JARVIS_DOWNLOAD}/htslib-1.22.tar.bz2
+tar -xzvf ${JARVIS_DOWNLOAD}/kallisto-0.51.1.tar.gz
+cd htslib-1.22
+autoreconf -i
+./configure
+make
+make install
+[ENV]
+module purge
+module use ./software/modulefiles
+module load kgcc/9.3.1
+module load openmpi/4.1.2
+
+[APP]
+app_name = QE
+build_dir = ${JARVIS_ROOT}/kallisto-0.51.1/
+binary_dir = 
+case_dir = ${JARVIS_ROOT}/kallisto-0.51.1/
+
+[BUILD]
+mkdir build
+cd build
+cmake ..
+make
+make install
+
+[CLEAN]
+make clean
+
+[RUN]
+run = kallisto 
+binary = 
+nodes = 1
+
+[PERF]
+perf= 
+nsys=
+ncu=--target-processes all
-- 
Gitee


From 7939c3576b0f60c3dd86225b251fb21507611d56 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, 3 Jun 2025 15:52:17 +0800
Subject: [PATCH 2/4] kallisto-bustools_python

---
 .../0.51.1/data.kallisto.arm.cpu.kgcc.config             | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/templates/kallisto-bustools_python/0.51.1/data.kallisto.arm.cpu.kgcc.config b/templates/kallisto-bustools_python/0.51.1/data.kallisto.arm.cpu.kgcc.config
index 86e4daa..af092e4 100644
--- a/templates/kallisto-bustools_python/0.51.1/data.kallisto.arm.cpu.kgcc.config
+++ b/templates/kallisto-bustools_python/0.51.1/data.kallisto.arm.cpu.kgcc.config
@@ -26,11 +26,14 @@ autoreconf -i
 ./configure
 make
 make install
+
 [ENV]
 module purge
-module use ./software/modulefiles
-module load kgcc/9.3.1
-module load openmpi/4.1.2
+module use software/utils/hpckit/2024.12.30/HPCKit/24.12.30/modulefiles
+module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi
+export CC=`which gcc`
+export CXX=`which g++`
+export FC=`which gfortran`
 
 [APP]
 app_name = QE
-- 
Gitee


From 202674b4de15cab85ad02b844c807e0b53dbe774 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, 10 Jun 2025 11:21:18 +0800
Subject: [PATCH 3/4] kallisto-bustools_python

---
 .../0.51.1/data.kallisto.arm.cpu.kgcc.config  | 22 +++++++++----------
 1 file changed, 10 insertions(+), 12 deletions(-)

diff --git a/templates/kallisto-bustools_python/0.51.1/data.kallisto.arm.cpu.kgcc.config b/templates/kallisto-bustools_python/0.51.1/data.kallisto.arm.cpu.kgcc.config
index af092e4..08b44df 100644
--- a/templates/kallisto-bustools_python/0.51.1/data.kallisto.arm.cpu.kgcc.config
+++ b/templates/kallisto-bustools_python/0.51.1/data.kallisto.arm.cpu.kgcc.config
@@ -2,8 +2,7 @@
 11.11.11.11
 
 [DOWNLOAD]
-kallisto/0.51.1 https://github.com/pachterlab/kallisto/archive/refs/tags/v0.51.1.tar.gz kallisto-0.51.1.tar.gz 
-htslib/1.22 https://github.com/samtools/htslib/releases/download/1.22/htslib-1.22.tar.bz2
+kallisto/0.51.1 https://github.com/pachterlab/kallisto/archive/refs/tags/v0.51.1.tar.gz kallisto-0.51.1.tar.gz
 
 [DEPENDENCY]
 set -e
@@ -19,13 +18,10 @@ module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi
 export CC=`which gcc`
 export CXX=`which g++`
 export FC=`which gfortran`
-tar -xjf ${JARVIS_DOWNLOAD}/htslib-1.22.tar.bz2
+./jarvis -install htslib/1.11 gcc
+module use software/moduledeps/gcc12.3.1
+module load htslib/1.11
 tar -xzvf ${JARVIS_DOWNLOAD}/kallisto-0.51.1.tar.gz
-cd htslib-1.22
-autoreconf -i
-./configure
-make
-make install
 
 [ENV]
 module purge
@@ -34,11 +30,13 @@ module add gcc/compiler12.3.1/gccmodule gcc/hmpi2.4.3/hmpi
 export CC=`which gcc`
 export CXX=`which g++`
 export FC=`which gfortran`
+module use software/moduledeps/gcc12.3.1
+module load htslib/1.11
 
 [APP]
 app_name = QE
 build_dir = ${JARVIS_ROOT}/kallisto-0.51.1/
-binary_dir = 
+binary_dir =
 case_dir = ${JARVIS_ROOT}/kallisto-0.51.1/
 
 [BUILD]
@@ -52,11 +50,11 @@ make install
 make clean
 
 [RUN]
-run = kallisto 
-binary = 
+run = kallisto
+binary =
 nodes = 1
 
 [PERF]
-perf= 
+perf=
 nsys=
 ncu=--target-processes all
-- 
Gitee


From 4f97219b04b3b40c08e3579d9d929b0465b5e564 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, 10 Jun 2025 15:38:41 +0800
Subject: [PATCH 4/4] kallisto-bustools_python

---
 .../0.51.1/data.kallisto.arm.cpu.kgcc.config                    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/templates/kallisto-bustools_python/0.51.1/data.kallisto.arm.cpu.kgcc.config b/templates/kallisto-bustools_python/0.51.1/data.kallisto.arm.cpu.kgcc.config
index 08b44df..4038fd5 100644
--- a/templates/kallisto-bustools_python/0.51.1/data.kallisto.arm.cpu.kgcc.config
+++ b/templates/kallisto-bustools_python/0.51.1/data.kallisto.arm.cpu.kgcc.config
@@ -34,7 +34,7 @@ module use software/moduledeps/gcc12.3.1
 module load htslib/1.11
 
 [APP]
-app_name = QE
+app_name = kallisto 
 build_dir = ${JARVIS_ROOT}/kallisto-0.51.1/
 binary_dir =
 case_dir = ${JARVIS_ROOT}/kallisto-0.51.1/
-- 
Gitee