Available Software

From wiki
Jump to: navigation, search

Introduction

The cluster uses the widely used Environment Modules system to manage the wide range of software available for Bioinformatics. It attempts to take care of the necessary environment for running the software, and so minmise (although not erradicate) errors.

To see all the available software, the command to type is:

moduleav

This is a fast wrapper command for the underlying slower:

module available

Categorised Listing

Sw2.png

Raw Listing 07 Dec 2016

--------------------------------- /usr/local/Modules/versions -----------------------------------------------------
3.2.10

---------------------------- /usr/local/Modules/3.2.10/modulefiles ------------------------------------------------
 AdapterRemoval/gitv0_abe4a3e(default)         
ArtificialFastqGenerator/1.0.0(default)       AsperaConnect/3.6.2                           BAPS/6.0                                      
BUSCO/1.22                                    BamQC/gitv0_480c091                           BayeScEnv/1.0                                 
BayeScEnv/gitv0_beb60d2(default)              BayeScan/2.1(default)                         CAFE/3.1                                      
CEGMA/2.5(default)                            CRISP/2                                       CRISP/5                                       
CRISP/gitv0_7bfcd34(default)                  EIGENSOFT/6.0.1(default)                      EMBOSS/6.6.0(default)                         
FASTQC/0.11.5(default)                        FastML/3.1                                    FastML/gitv0_bb5d761                          
FastTree/2.1.8(default)                       GapFiller/v1-10                               GeneMark_ES/3.48(default)                     
HTSlib/1.3                                    HTSlib/1.3.1(default)                         HTSlib/gitv1_0de7fe5                          
MCR/v713                                      MUMmer/3.23                                   MUMmer/3.23b(default)                         
Mash/gitv0_2edc42                             Mash/v1.1.1(default)                          Mauve/2015-02-13                              
NGSToolsApp/2.1.5(default)                    OpenBLAS/0.2.14                               OpenBLAS/0.2.18                               
OpenBLAS/0.2.19(default)                      OrthoFinder/0.6.0                             PAGIT/1(default)                              
PEAR/gitv0_a37a84b(default)                   PEAT/gitv0_27981d7(default)                   PGAP/1.2.1                                    
PGDSpider/2.0.8.2(default)                    Prodigal/gitv0_004218f                        R/3.2.1(default)                              
R/3.2.3                                       R/3.3.1                                       RAxML/gitv0_4692545(default)                  
RSEM/1.2.25(default)                          RSEM/1.2.27                                   SPAdes/3.9.0(default)                         
SSPACE/3.0                                    STAR/2.4.2a(default)                          T-COFFEE/11.00.8                              
VarScan/2.3.7(default)                        VelvetOptimiser/2.2.5(default)                abacas/1.3.1(default)                         
abyss/1.9.0                                   act/v1                                        allpathslg/52488                              
angsd/gitv0_212d58                            angsd/gitv1_89d8fa9(default)                  arlequin/3.5.2(default)                       
artemis/16.0.0(default)                       assembly-stats/gitv0_003a372                  augustus/3.0.3                                
augustus/3.2.2(default)                       bamtools/gitv0_02c2be8(default)               bcftools/gitv0_47e811c                        
bedtools/2.23.0                               bedtools/2.25.0(default)                      bioawk/gitv0_5e8b41d(default)                 
blastScripts/1.0.0(default)                   blastScripts/1.0.1                            blastall/2.2.26(default)                      
blat/35                                       boost/1.60.0(default)                         boost/1.61.0                                  
bowtie/1.0.0                                  bowtie2/2.1.0(default)                        bowtie2/2.2.4                                 
bwa/0.7.12(default)                           bwa/0.7.7                                     bzip2/1.0.6                                   
capnproto/0.5.3                               cd-hit/gitv0_5acf038(default)                 clustalx/2.1                                  
crimap/2.504(default)                         cufflinks/2.2.1(default)                      dDocent/gitv0_7dea314                         
diamond/gitv0_39f2a71                         dot                                           ea-utils/gitv0_88c9ad5                        
ensembl-git-tools/gitv0_68ac669(default)      ensembl/gitv0_bb48912(default)                exonerate/2.2.0(default)                      
fastSTRUCTURE/1.0                             fastSTRUCTURE/190315(default)                 fastsimcoal2/2.5.2.21                         
fastsimcoal2/2.5.2.8(default)                 freebayes/gitv0_dbb6160                       gatk/3.4.0                                    
gatk/3.5.0                                    gatk/3.6.0(default)                           gcc/4.9.3                                     
geneid/1.4.4(default)                         general_script_tools/(default)                gnuparallel/20160422                          
gsea/2.2.2(default)                           gsl/2.1                                       gubbins/gitv0_fe094b0                         
gubbins/gitv1_8a12ae7(default)                gwas                                          harvest-tools/gitv0_ebf7ecc                   
hdf5/1.8.15-patch1(default)                   hdf5/1.8.16                                   hmmer/2.3.2                                   
hmmer/3.1b1                                   hmmer/3.1b2(default)                          interproscan/5.4-47.0(default)                
kallisto/git0_f0678a2                         lamarc/2.1.10(default)                        lpsolve/5.5.2.3                               
mafft/7.147(default)                          maker/2.31.8(default)                         masurca/2.3.2(default)                        
mcl/14-137(default)                           mdb/0.6(default)                              merlin/1.1.2(default)                         
module-info                                   modules                                       mpifast/gitrev2(default)                      
mrbayes/3.2.6                                 muscle/3.7                                    newick_utils/4.9.3                            
newick_utils/gitv0_614bf6c(default)           ngs/gitv0_aef5f50                             null                                          
openmpi/1.10.2                                openmpi/1.6.5                                 openmpi/2.0.0(default)                        
oraclejava/jdk1.8.0_74                        paml/4.7a(default)                            parsnp/gitv0_63bea13                          
pblat/1.6.0(default)                          perl/5.20.2(default)                          perl/5.24.0                                   
phylip/3.696(default)                         phyml/gitv0_0f6d745                           picard-tools/1.119                            
picard-tools/2.1.0                            picard-tools/2.1.1                            picard-tools/2.7.1(default)                   
prank-msa/gitv0_3e44771(default)              prokka/1.11                                   prokka/gitv1_8f07048(default)                 
prosite/1.79.1                                protobuf/gitv0_0622030                        psmc/gitv0_e5f7df5(default)                   
pyrad/gitv0_704ffbf                           python/2.7(default)                           python/2.7.12                                 
python/3.4                                    qtdt/2.6.1(default)                           quast/4.1                                     
rainbow/2.0.4                                 rapsearch/gitv0_95c866e(default)              readseq/2.1.30(default)                       
repeatmasker/4.0.5(default)                   rmblastn/2.2.28(default)                      rnammer/1.2(default)                          
roary/gitv0_c4d9b77(default)                  samtools/0.1.18                               samtools/0.1.19(default)                      
samtools/0.1.19b                              samtools/1.2                                  samtools/1.3.1                                
scalaBLAST/2.0(default)                       scipio/1.4.1(default)                         script_tools/1.0(default)                     
seqtk/gitv0_1a8319b(default)                  sickle/gitv0_f3d6ae3(default)                 signalp/4.1(default)                          
smalt/0.7.6(default)                          snap_alignment/1.0beta.17(default)            snap_hmm/11_29_2013(default)                  
snape-pooled/31(default)                      snippy/gitv0_848a62e                          snpcallphylo/0.7                              
sparsehash/gitv0_4cb9240                      sra-tools/gitv0_814d6f7(default)              srst2/gitv1_e30dd01(default)                  
srst2/gitv2_41b3f46                           stacks/1.35                                   stacks/1.37                                   
stacks/1.40(default)                          stacks/1.41                                   stampy/1.0.23(default)                        
structure/2.3.4(default)                      tRNAscan-SE/1.3.1(default)                    tabix/gitv0_1ae158a                           
tabtk/gitv0_741f3f0                           tophat/2.0.10(default)                        treemix/gitv0_23c15a2(default)                
trimmomatic/0.32                              trinity/2.2.0(default)                        trinity/20140717                              
use.own                                       vcflib/gitv0_e3ab177                          vcftools/0.1.11                               
vcftools/0.1.12a                              vcftools/gitv0_4fce995(default)               vdb/gitv0_f1497a1                             
velvet/1.2.10(default)                        velvet/gitv0_9adf09f                          vsearch/gitv0_174f810(default)