MODULE-INSTALLS

Section: User Commands (1)
Last updated: Wed 10 Jan 16:53:42 GMT 2024 2023-12-13
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DEPRECATION NOTICE

This CCB documentation has been superseded by our new website: https://lumin.imm.ox.ac.uk  

CHANGES (LAST 90 DAYS)

2023-12-13: new: py-capcruncher/0.3.8

2023-12-13: downgrades: python-base/3.10.13

2023-12-06: new: R-base-lapack/4.3.0

2023-12-04: new: py-mira/2.1.0

2023-11-24: new: TEpeaks/0.1

2023-11-22: new: cnvkit/0.9.10 ; tensorflow2-cpu/2.14.0

2023-11-21: new: R-base/4.3.0

2023-11-17: updates: cellranger/7.2.0

2023-11-16: new: cuDNN/8.9.6 ; tensorflow2-gpu/2.15.0

2023-11-16: updates: cuda/12.2v2

2023-11-03: updates: rna-star/2.7.11a ; STAR/2.7.11a

2023-10-20: updates: cuda/12.2

2023-10-11: new: py-cellbender/0.3.0

2023-09-28: updates: spaceranger/2.1.0

2023-09-20: new: fastq-tools/0.8.3

2023-09-19: new: geos/3.10.1 ; openjdk/10.0.2

2023-09-14: updates: annovar/20191024

 

MODULE INSTALLS

alicevision/2.2.0        cellranger-atac/1.2.0   htslib/1.10                pandaseq/2.11          sratoolkit/2.10.8     
annovar/20180416                        /2.1.0         /1.10.2              pear/20210121                    /2.9.6      
       /20191024         cellsnp-lite/20210816         /1.18                perl/5.36.1                      /3.0.0      
       /20230914         cellxgene/20230703            /1.3                 phylip/3.697           STAR/2.6.0c           
aspera/3.9.8             chips/2.1                     /1.5                 picard-tools/2.18.17       /2.6.1d           
      /3.9.9             circos/0.69-9                 /1.8                             /2.3.0         /2.7.11a          
atacqc/20170728          clustalw/2.1                  /1.9                 plink/1.07                 /2.7.3a           
avocato-deps/20221121    cnvkit/0.9.10           igblast/1.16.0                  /1.90b6.24            /2.7.8a           
            /20230726    cuda/10.0                      /1.19.0                  /1.90b7           star-fusion/1.11.0    
aws-cli/20220822             /10.1               igor/1.4.0                      /2.00a4.6         stringtie/2.1.4       
bam-readcount/20201113       /12.2               igv/2.14.1                 pod5/0.2.4             subread/2.0.0         
bamscale/0.0.5               /12.2v2                /2.4.11                 proj/7.2.1                    /2.0.3         
        /1.0                 /8.0                ilastik/1.3.3post3             /8.1.1                    /2.0.6         
bamtools/2.5.1               /9.0                imacyte/20200929           py-capcruncher/0.3.8   subset-bam/1.1.0      
bamutil/1.0.14           cuDNN/8.9.6             impute2/2.3.2              py-cellbender/0.3.0    tdrmapper/20210407    
barcounter/20211216      cufflinks/2.2.1         index-hopping-filter/1.1   py-mira/2.1.0          tensorflow2-cpu/2.14.0
basespace-cli/1.4.0      cytoscape/3.6.1         jags/4.3.0                 pycharm/2020.1.3                      /202311
bbtools/38.90            demuxlet/20210816       java/11.0.2                python-base/3.10.13    tensorflow2-gpu/2.15.0
bcftools/1.17            dorado/0.3.3                /17.0.1                           /3.11.3     TEpeaks/0.1           
bcl2fastq/2.20.0.422     dropEst/20201211            /7u80                  pytorch-gpu/2.0.1      tophat/2.1.1          
bedops/2.4.40            eagle/2.4.1                 /8u131                 qctool/2.0.7           trf/4.09.1            
bedtools/2.25.0          edlib/1.2.6                 /8u171                 qtltools/1.2           trim_galore/0.6.10    
        /2.26.0          emboss/6.6.0                /8u191                         /1.3.1         trimmomatic/0.39      
        /2.27.1          ensembl-vep/102.0           /8u311                 qupath/0.2.3           trinityrnaseq/2.11.0  
        /2.29.2          fastp/0.23.4            jellyfish/2.3.0            R-base/4.3.0                        /2.14.0  
bedtools2/2.25.0         fastq-pair/1.0          jq/1.6                     R-base-lapack/4.3.0    ucsctools/369         
         /2.26.0         fastq-tools/0.8.3       juicebox/1.9.8             R-natverse/20230822             /385         
         /2.27.1         fastq_screen/0.14.1             /2.10.01           repeatmasker/4.1.2     unet/20190409         
         /2.29.2         fastqc/0.11.5           julia/1.4.1                rmblast/2.10.0         urlwrap/1.0.0         
blast/2.11.0                   /0.11.9           kallisto/0.46.1            rna-star/2.6.0c        vardictjava/1.8.2     
bowtie/1.2.1.1           fftw/3.3.10             lanceotron/20230726                /2.6.1d        varscan/2.4.2         
      /1.2.3             fgbio/20210122          libBigWig/0.4.4                    /2.7.11a       vartrix/1.1.20        
bowtie2/2.3.2            fiji/20190409           linasm/1.13                        /2.7.3a               /1.1.22        
       /2.3.4.3          flash/1.2.11            longranger/2.2.2                   /2.7.8a        vcflib/20201113       
       /2.4.1            flexbar/3.5.0           mallet/202108              rsem/1.2.31            vcftools/0.1.16       
       /2.4.2            freebayes/1.3.4         manta/1.6.0                    /1.3.3             vdjtools/1.2.1        
bwa/0.7.17               freesasa/2.0.3          mathematica/11.3.0         salmon/1.3.0           velvet/1.2.10         
bwa-mem2/2.2.1           gatk/4.4.0.0            matlab/r2018b                    /1.8.0           verifybamid/1.0.6     
caveman/1.14.0           gctree/20210514               /r2019b              sambamba/0.8.0         wxpython/4.0.7post2   
ccs/4.2.0                genrich/0.6.1                 /r2020a              samblaster/0.1.24      zumis/20220222        
cdhit/4.8.1              geos/3.10.1             matlab-ubuntu/r2020a       samtools/1.17                                
cellpose/20200526            /3.9.0              meme/5.5.3                 sbt/1.4.5                                    
        /20210122        go/1.18                 meshroom/2019.2.0          schlacount/0.1.0                             
cellranger/2.1.1         gsea/3.0                methpipe/4.1.1             seqkit/0.12.1                                
          /3.0.1         gsl/2.6                 minimap2/2.17              seqmonk/1.47.1                               
          /3.1.0         gtool/0.7.5             miranda/3.3a               seqtk/20201102                               
          /4.0.0         guppy/3.3.3             mixcr/3.0.13               sevenbridges/0.18.2                          
          /5.0.0              /4.2.2             mosdepth/0.3.1             snpeff/5.0                                   
          /6.0.1         guppy-gpu/3.3.3         mpileup2readcounts/1.0     SNPsplit/0.3.2                               
          /6.1.1                  /4.2.2                           /1.0a    snptest/2.5.2                                
          /6.1.2         hdf5/1.10.7             netMHCpan/4.1b             snver/0.5.3                                  
          /7.0.0             /1.12.1             nextflow/23.04.1           sortmerna/2.1b                               
          /7.0.1         hdfview/3.1.1           octopus/20200902           spaceranger/1.2.2                            
          /7.1.0         hisat2/20201102         omero/5.2.4                           /1.3.1                            
          /7.2.0         hmmer/3.3.2             onetbb/2021.3.0                       /2.1.0                            
cellranger-arc/1.0.1     homer/20201202          openjdk/10.0.2             sqlite/3.35.0                                
              /2.0.0                                    /11.0.2                   /3.36.0                                
              /2.0.2                                    /12.0.2                   /3.37.2                                
                                                        /13.0.2                                                          
                                                        /14.0.2                                                          
                                                        /15.0.2                                                          
                                                        /16.0.2                                                          
                                                        /17.0.2                                                          
                                                        /18.0.2                                                          
                                                        /19.0.1                                                          
                                                        /20.0.2                                                          
                                                        /9.0.4                                                           


 

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DEPRECATION NOTICE
CHANGES (LAST 90 DAYS)
MODULE INSTALLS