From cf81e99dcb76c555a7a71b228c7406df877d7b68 Mon Sep 17 00:00:00 2001
From: cfmin <1163105507@qq.com>
Date: Thu, 24 Apr 2025 15:34:53 +0800
Subject: [PATCH] Add templates app monocle3-1.3.7

---
 .../1.3.7/monocle3.arm.bisheng.hmpi.R.config  | 75 +++++++++++++++++++
 1 file changed, 75 insertions(+)
 create mode 100644 templates/monocle3/1.3.7/monocle3.arm.bisheng.hmpi.R.config

diff --git a/templates/monocle3/1.3.7/monocle3.arm.bisheng.hmpi.R.config b/templates/monocle3/1.3.7/monocle3.arm.bisheng.hmpi.R.config
new file mode 100644
index 0000000..6508de5
--- /dev/null
+++ b/templates/monocle3/1.3.7/monocle3.arm.bisheng.hmpi.R.config
@@ -0,0 +1,75 @@
+[SERVER]
+11.11.11.11
+
+[DOWNLOAD] 
+monocle3/master ${JARVIS_PROXY}/cole-trapnell-lab/monocle3/archive/refs/heads/master.zip monocle3-master.zip
+
+[DEPENDENCY]
+yum install -y libgit2-devel freetype-devel fontconfig-devel libtiff-devel geos-devel libXext-devel harfbuzz-devel fribidi-devel libjpeg-turbo-devel
+module purge
+module use ./software/modulefiles
+./jarvis -install bisheng/4.1.0 com
+module load bisheng/4.1.0
+./jarvis -install hmpi/2.4.2 bisheng
+module load hmpi/2.4.2
+./jarvis -install libjpeg/v9b bisheng+mpi
+module load libjpeg/v9b
+./jarvis -install libpng/1.6.37 bisheng+mpi
+module load libpng/1.6.37
+./jarvis -install proj/5.2.0 bisheng+mpi
+module load proj/5.2.0
+./jarvis -install gdal/2.2.4 bisheng+mpi
+module load gdal/2.2.4
+./jarvis -install udunits/2.2.28 bisheng+mpi
+module load udunits/2.2.28
+./jarvis -install pixman/0.38.0 bisheng+mpi
+module load pixman/0.38.0
+export PKG_CONFIG_PATH=${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.2/pixman/0.38.0/lib/pkgconfig:$PKG_CONFIG_PATH
+./jarvis -install cairo/1.16.0 bisheng+mpi
+module load cairo/1.16.0
+export PKG_CONFIG_PATH=${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.2/cairo/1.16.0/lib/pkgconfig:$PKG_CONFIG_PATH
+./jarvis -install R/4.4.3 bisheng+mpi
+module load R/4.4.3
+
+unzip ${JARVIS_DOWNLOAD}/monocle3-master.zip -d ${JARVIS_TMP_DOWNLOAD}
+
+[ENV]
+module purge
+module use ./software/modulefiles
+module load bisheng/4.1.0
+module load hmpi/2.4.2
+module load libjpeg/v9b
+module load libpng/1.6.37
+module load proj/5.2.0
+module load gdal/2.2.4
+module load udunits/2.2.28
+module load pixman/0.38.0
+export PKG_CONFIG_PATH=${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.2/pixman/0.38.0/lib/pkgconfig:$PKG_CONFIG_PATH
+module load cairo/1.16.0
+export PKG_CONFIG_PATH=${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.2/cairo/1.16.0/lib/pkgconfig:$PKG_CONFIG_PATH
+module load R/4.4.3
+
+[APP]
+app_name = monocle3
+build_dir = ${JARVIS_TMP_DOWNLOAD}/monocle3-master
+binary_dir = 
+case_dir = ${JARVIS_TMP_DOWNLOAD}/monocle3-master/tests
+
+[BUILD]
+R --vanilla -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager", repos="https://cloud.r-project.org/"); q()'
+R --vanilla -e 'BiocManager::install(version = "3.20", ask=FALSE, update=TRUE); q()'
+R --vanilla -e 'BiocManager::install("terra", configure.args="--with-proj-include=${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.2/proj/5.2.0/include --with-proj-lib=${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.2/proj/5.2.0/lib"); q()'
+R --vanilla -e 'BiocManager::install("units", configure.args="--with-udunits2-lib=${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.2/udunits/2.2.28/lib --with-udunits2-include=${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.2/udunits/2.2.28/include"); q()'
+R --vanilla -e 'BiocManager::install("sf", configure.args="--with-proj-include=${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.2/proj/5.2.0/include --with-proj-lib=${JARVIS_LIBS}/bisheng4.1.0/hmpi2.4.2/proj/5.2.0/lib"); q()'
+R --vanilla -e 'BiocManager::install(c("BiocGenerics", "DelayedArray", "DelayedMatrixStats", "limma", "lme4", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment", "batchelor", "HDF5Array", "ggrastr")); q()'
+R --vanilla -e 'install.packages(c("devtools", "testthat"), repos="https://cloud.r-project.org/"); q()'
+R CMD INSTALL .
+
+[CLEAN]
+detach("package:monocle3", unload = T)
+remove.packages("monocle3")
+
+[RUN]
+run = R --vanilla -e "testthat::test_file(\"testthat.R\"); q()"
+binary =
+nodes = 1
-- 
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