Software installation services（Update）

The computing center is equipped with a wealth of software resources. In order to better use the software between users, the computing center uses the module environment management software, which can be loaded and unloaded at any time. Freely switch between different versions. This can make the kernel size and communication. The amount is minimized, and the computing center also supports parallel computing. It can organize disks on multiple nodes into one large storage system, providing greater storage capacity and aggregated I/O bandwidth, and as the system scales up. Expansion, playing an important role in a variety of storage environments, especially in the high-performance computing field of cluster structure, also provides services such as parallel programming consultation, parallel program debugging, and serial parallel program performance optimization to help users solve software problems and optimize Program design significantly improves program performance and results in faster and better results.

List of installed software：《bwa, cactus, cuda10.0/10.1/9.1, cutadapt /2.8, dock6, dsq, CNVnator, GATK3/4 , ImageJ/2.0.0, MATLAB/R2018b, OPtiType/1.3.2., R3.5/3.6/, RSEM, STAR/2.5.3 ,anaconda3, SRAtoolkit, augustus, bcftools, blast, bowtie, intel-compiler/2018|2019, kobas, Kyoto, openmpi, openbabel,perl, openblas/0.3.7, samtools/1.9, tophat/1.3.2|2.1.0, subread, python3, hdf5/1.10.6, sambamba/0.7., samblaster/0.1.24, platypus , scanorama/1.4 ,hisat2, fastp, ffmpeg, NextDenovo，cudamat，htseq/0.11.2 ,htslib/1.9 ,fsl/6.3.0 , jellyfish/2.3.0, bcftools/1.9, bedToGenePred, bedtools/2.29.2, MaSuRCA，trinity，HiC-Pro/2.11.1, rstudio, masurca/3.3.5,TensorRT/6.0.1.5, vaa3d/2.921, apbs/1.5, blasr/5.3.3, bustools/0.39.3, centrifuge/1.0.4, clustalw2, cufflinks/2.2.1, delly/0.8.2 , emboss/6.6.0, fastqc/0.11.7, fftw/3.3.8 , flappie/2.1.0, g_mmpbsa/5.1.2, gdc/1.4.0, genePredToBed, genePredToGtf, genomestrip/2.00.1949, genompy/0.5.2, gff3ToGenePred, gmap, gnuplot/5.2.8 , gromacs-cpu/2020,201905 , gromacs-gpu/2020, gtfToGenePred , guppy/3.4.4, hyphy/2.5.2，kallisto/0.46.1，kraken/2.0.8，macs2/2.2.6，manta/1.6.0，minimap2/2.17，mummer/4.0.0，nanopack，，openblas/0.3.7，popins/popins，salmon/0.13.1，speedseq/0.1.2，sratoolkit/2.9.6，,trf/4.09，trim_galore/0.6.5，wham/1.7.0，homer，seqtk, plink, vcftools, svtk, svtools, sratoolkit, pycoQC, blat, bismark,  bs-seeker2, stap, smrtanalysis, gdc, PEGASAS, circis, lastz, RepeatMasker, GenomeAlignmentTools, kentUtils, bioawk, magma, bioawk, multiqc , seqkit, stringtie, velvet, sickle, gffcompare, featurecounts, mageck，gffread，cpat，pfam-scan，Hermite,admixture , FastTree, FigTree，phylowgs，bamtools，deeptools，gsl，lima ,pbccs ,isoseq , MATLAB/R2019a，cupcak，lr2rmats，rMATS, DeepMod, albacore,nanopolish, hdfview, deepsignal，REDItools2，genblasta，tablet，openbabel，ont_fast5_api，graphmap，canu ,pilon, NanoFilt, Trimmomatic, RAGOO, PyMOL. Pycharm,fast5-to-fastq, RagTag, raxml-ng, phydl，ensembl-vep，Graphtyper2，KING，MUSCE，dnaml，Snphylo，EIGENSOFT， PBSuite，VG，BreakDancer，svimmer，VaPoR ，GRIDSS，Lumpy，Manta，Wham，SVseq2，SoftSV，BayesTyper，toil-vg，iqtree,  seqwish,primer3, physpetools,  pySCENIC,HAL ，phast，AFNI , Freesurfer ,FSL, Mricron, Diffusion,  Trackvis, Mrtrix，Pytorch, FreeCAD,HIRise, Meraculous, Falcon, LACHESIS,  diamond , Rhapsody,genewise，SolexaQA，deepmind,ALLHIC, gdal , AnnoLnc, 3d-dna, sratoolkit, Fmripre, ANTs, C3D, ICA-AROMA ,bids-validator, connectome-workbench , Nipype ,juicer, datalad，raxml,  smcpp , psmc, braker , prothint, VCF-kit, busco ,metaeuk, piodigal, hmmer, sepp ,SV-plaudit , NGSadmix，pyclone, flye，SNPEff, spark，PSITE，edirect，MS,expect， RevTrans，SPOT-RNA，xcp_abcd，acpype，xcpEngine，jo，hcp2bids,ProteinGAN, QSIprep, datamash, nanocompore, rosetta,cuda/10.1,RepeatModeler, megax, RepeatScout,TRF, GeneMark-ES/ET, fastclone_guanlab, hexedit，mugsy，jvarkit，czplib，gvst,fastx, paup, Nextstrain，tabix，Sequenza,AlphaFold，juicebox，Sailor，redundans，wtdbg2，RoseTTAFold，pipelines, ClipKIT，genomescope，jellyfish，trimal，pyclone-vi，quast，hifiasm，bandage，PSiTE，snakemake，nextflow，simpleelastix，treebest, Porechop, bedGraphToBigWig, Haploview，Autodock4，denovogear，forestdnm，LiteCall，g-phocs，r-sctransform，dv_trio/1.0.0，famsep/1.0.3，gsutil/5.6，vt/0.57，rstudio/1.1.463，R/4.1.0，denovogear/dev，ffmpeg/4.2.1_gpu，varscan/2.3.9，stereopy/0.2.2，velocyto/0.17.17，bam-readcount/1.0.1，rclone/1.58.0，julia/1.7.2，salmon 1.8.0，guppy 6.1.2/cpu、guppy 6.1.2/gpu,napari/0.4.15，cell2location/0.1、SpaGCN/1.2.5,opencv/3.4.1, openpose/1.4.0, caffe/1.0, protobuf/3.13.0, google-glog/0.6.0, google-gflags/2.2.2, mtag/0.9.0, gwas/0.21, deeplabcut/2.2.1.1, rtg-tools/3.12.1, ldsc/1.0.0, velocyto/0.17.17, dynamo/0.7.17, clairvoyante，stack，alphafold/2.2.2，bamdst，spateo，anndata，scanpy, spateo, hicexplorer, Bullseye，inferCNV，fastcsr，DPAM，dnbc4tools，MNI_N3，copykat，BioImageIT，pySCENIC，CCP4，phenix，chimera，Relion， Cryosparc，ZDOCK，fusion，LOGODetect，micro-manager, exonerate, zrank, xvfb-ru, igv-snapshot-automator, Lightgbm，pbmm2，ReditoolsV1，MeRIPseqPipe，depict，scdrs，rpy2，hap.py，VarBen，IsoSeq3，LongQC,purge_haplotigs,mitoz,alphafold/2.3.0, Margin, medaka, PEPPER, detalad, vaa3d_tools, stitching-spark, GenomeTools, gemoma, SNAP, EVM (Evidence Moduler), mmseqs,miropeats, smashpp,PASA,cDNA_Cupcake TransDecoder, truvari, svviz, MitoFinder,LTR_FINDER,LTR_retriever, nvidia-cuda-runtime, antismash,sqanti3, TOSICA, MAKER, swan_vis》

contact:

Yanmin Wang

HPC Core

wangyanmin@cibr.ac.cn