Overview
Introduction¶
The Joint High Performance Computing Exchange (JHPCE) offers a variety of software applications for use on the clusters. Please see the "Software" section of the navigation bar for more info.
Resources for software packages¶
We have web pages for some of the primary applications:
We use the Lmod module system to manage some of the installed software packages - you can run module avail at the cluster prompt to list them. For more info about using modules, please consult man module and our page.
Listing currently-available software¶
System administrators place locally-written programs in a "tools" directory, /jhpce/shared/jhpce/core/JHPCE_tools/3.0/bin/ Most of them are shell scripts, so you can inspect them with a text editor. You can also copy them and edit them to suite your needs.
You'll notice that the modules are divided up into groups. These divisions are due to the fact that their are multiple people/organizations who create and maintain the modules.
- "jhpce" modules are provided by the cluster maintainers.
- "libd" ones are from the Lieber Institute for Brain Development.
- The "community" ones are supported by volunteers from the broader JHPCE community.
For more-involved issues with "libd" and "community", please contact the bitsupport@lists.jh.edu mailing list. Those maintainers are members of that list.
For "jhpce" modules, contact bithelp@lists.jh.edu.
Of course, the modules you will see are the latest ones.
[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