Overview
Introduction¶
The Joint High Performance Computing Exchange (JHPCE) offers a variety of software for use on the cluster. They are installed and running on Rocky Linux 9.4. We use Lmod module system to manage the installed software. You can run module aval at the cluster prompt for the available software.
Current available software¶
[test@compute-110 ~]$ module avail
--------------------------------------------------------------------------------- /jhpce/shared/jhpce/modulefiles ---------------------------------------------------------------------------------
JHPCE_ROCKY9_DEFAULT_ENV (L) bcl2fastq/2.17.1 freesurfer/7.4.1 gmp/6.2.1 mathematica/13.3 python/3.11.8 stata/17
JHPCE_tools/3.0 (L) bowtie/2.5.1 fsl/6.0.6.5 go/20.6 matlab/R2023a (D) rstudio/2023.06.1 tex/20240117
R_test/4.3.2 conda/3-23.3.1-testing gcc/9.5.0 helix/23.10.0 matlab/R2023b rust/1.76.0 wine/7.11
afni/23.3.09 conda/3-23.3.1 (D) gcc/13.1.0 (D) java/19 (D) mpc/1.3.1 sas/9.0
alphafold/4.3.1 dcmtk/3.6.7 gdal/3.6.0 julia/1.9.2 mpfr/4.2.0 sas/9.4 (D)
anaconda/2023.03 encfs/1.9.5 ghostscript/10.02.1 kakoune/2023-08-05 python/3.9.14 (D) shapeit/5.1.1
aws/2.12.7 ffmpeg/6.0 glpk/5.0 latex/20240117 python/3.10.13 singularity/3.11.4
------------------------------------------------------------------------------- /jhpce/shared/community/modulefiles -------------------------------------------------------------------------------
R/4.3 bedtools/2.31.0 conda_R/devel conda_R/test conda_R/4.3.x (D) conda_R/4.3
--------------------------------------------------------------------------------- /jhpce/shared/libd/modulefiles ----------------------------------------------------------------------------------
PRSice/2.2.13 cell2location/0.1.3 fusion_twas/github java/17 plink/1.90b samtools/1.18 (D) trimgalore/0.6.6
Salmon/1.2.1 cell2location/0.8a0 (D) gatk/4.2.0.0 java/18 plink/2.00a4.6 (D) samui/1.0.0-next.24 trimmomatic/0.39
Salmon/1.10.1 (D) cellpose/2.2.2 gffread/github kallisto/0.46.1 qctool/2.0.7 samui/1.0.0-next.45 (D) vampire/3.4.4
arioc/1.51 cellprofiler/4.2.6 gffread/0.12.7 (D) ldsc/1.0.1 qtl_gtex/dae3369 spaceranger/2.1.0 vcftools/0.1.16
bamtofastq/1.4.1 cellranger/7.0.0 git-lfs/3.4.0 magma/1.10 r_nac/1.0 spagcn/1.2.0 wiggletools/1.2.1
bcftools/1.10.2 cellranger/7.2.0 (D) git-status-size/github methyldackel/0.5.2 regtools/0.5.33g star/2.7.8a wigtobigwig/2.9
bcftools/1.18 (D) cellranger_arc/2.0.2 graphst/da29b75 methylpy/1.4.3 resept/1.0.0 subread/2.0.0
bfg/1.13.0 cibersortx/04_04_2020 hipstr/0.7 nextflow/20.01.0 rmate/1.5.10 synapse/2.7.2
bismark/0.23.0 dissect/dc45940c hisat2/2.2.1 nextflow/22.10.7 rseqc/3.0.1 synapse/3.1.1 (D)
bs/1.3.0 fastqc/0.11.8 htslib/1.10.2 nextflow/23.10.0 (D) samblaster/0.1.26 tangram/1.0.4
bustools/0.39.3 fastqc/0.12.1 (D) htslib/1.18 (D) paste/1.3.0 samtools/1.10 tensorqtl/1.0.8