Available Software

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, all its dependencies and their versions and some of its documentation.

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

module available

A short cut for this is:

module av

Raw Listing 01 Sep 2016

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

---------------------------- /usr/local/Modules/3.2.10/modulefiles ------------------------------------------------
abacas/1.3.1(default)                    capnproto/0.5.3                          gsl/2.1                               
abyss/1.9.0                              cd-hit/gitv0_5acf038(default)            gubbins/gitv0_fe094b0                 
act/v1                                   CEGMA/2.5(default)                       gubbins/gitv1_8a12ae7(default)        
AdapterRemoval/gitv0_abe4a3e(default)    crimap/2.504(default)                    gwas                                  
angsd/gitv0_212d58                       CRISP/2                                  harvest-tools/gitv0_ebf7ecc           
angsd/gitv1_89d8fa9(default)             CRISP/5(default)                         hdf5/1.8.15-patch1(default)           
arlequin/3.5.2(default)                  cufflinks/2.2.1(default)                 hdf5/1.8.16                           
artemis/16.0.0(default)                  dDocent/gitv0_7dea314                    hmmer/2.3.2                           
ArtificialFastqGenerator/1.0.0(default)  diamond/gitv0_39f2a71                    hmmer/3.1b1                           
AsperaConnect/3.6.2                      dot                                      hmmer/3.1b2(default)                  
assembly-stats/gitv0_003a372             ea-utils/gitv0_88c9ad5                   HTSlib/1.3                            
augustus/3.0.3                           EIGENSOFT/6.0.1(default)                 HTSlib/1.3.1(default)                 
augustus/3.2.2(default)                  EMBOSS/6.6.0(default)                    HTSlib/gitv1_0de7fe5                  
BamQC/gitv0_480c091                      ensembl/gitv0_bb48912(default)           interproscan/5.4-47.0(default)        
bamtools/gitv0_02c2be8(default)          ensembl-git-tools/gitv0_68ac669(default) kallisto/git0_f0678a2                 
BayeScan/2.1(default)                    exonerate/2.2.0(default)                 lamarc/2.1.10(default)                
BayeScEnv/1.0                            FastML/3.1                               lpsolve/5.5.2.3                       
BayeScEnv/gitv0_beb60d2(default)         FastML/gitv0_bb5d761                     mafft/7.147(default)                  
bcftools/gitv0_47e811c                   FASTQC/0.11.5(default)                   maker/2.31.8(default)                 
bedtools/2.25.0(default)                 fastsimcoal2/2.5.2.21                    Mash/gitv0_2edc42                     
bioawk/gitv0_5e8b41d(default)            fastsimcoal2/2.5.2.8(default)            masurca/2.3.2(default)                
blastall/2.2.26(default)                 fastSTRUCTURE/1.0                        Mauve/2015-02-13                      
blastScripts/1.0.0(default)              fastSTRUCTURE/190315(default)            mcl/14-137(default)                   
blastScripts/1.0.1                       FastTree/2.1.8(default)                  mdb/0.6(default)                      
blat/35                                  freebayes/gitv0_dbb6160                  merlin/1.1.2(default)                 
boost/1.60.0(default)                    GapFiller/v1-10                          module-info                           
boost/1.61.0                             gatk/3.4.0                               modules                               
bowtie/1.0.0                             gatk/3.5.0                               mpifast/gitrev2(default)              
bowtie2/2.1.0(default)                   gatk/3.6.0(default)                      mrbayes/3.2.6                         
bowtie2/2.2.4                            gcc/4.9.3                                MUMmer/3.23                           
BUSCO/1.22                               geneid/1.4.4(default)                    MUMmer/3.23b(default)                 
bwa/0.7.12(default)                      GeneMark_ES/3.48(default)                muscle/3.7                            
bwa/0.7.7                                general_script_tools/(default)           newick_utils/4.9.3                    
CAFE/3.1                                 gsea/2.2.2(default)                      newick_utils/gitv0_614bf6c(default)   

ngs/gitv0_aef5f50                        python/2.7.12                            sra-tools/gitv0_814d6f7(default)
NGSToolsApp/2.1.5(default)               python/3.4                               srst2/gitv1_e30dd01(default)
null                                     qtdt/2.6.1(default)                      srst2/gitv2_41b3f46
OpenBLAS/0.2.14                          quast/4.1                                SSPACE/3.0
OpenBLAS/0.2.18                          R/3.2.1(default)                         stacks/1.35
openmpi/1.10.2                           R/3.2.3                                  stacks/1.37
openmpi/1.6.5                            rainbow/2.0.4                            stacks/1.40(default)
openmpi/2.0.0(default)                   rapsearch/gitv0_95c866e(default)         stacks/1.41
oraclejava/jdk1.8.0_74                   RAxML/gitv0_4692545(default)             stampy/1.0.23(default)
OrthoFinder/0.6.0                        readseq/2.1.30(default)                  STAR/2.4.2a(default)
PAGIT/1(default)                         repeatmasker/4.0.5(default)              structure/2.3.4(default)
paml/4.7a(default)                       rmblastn/2.2.28(default)                 tabix/gitv0_1ae158a
parsnp/gitv0_63bea13                     rnammer/1.2(default)                     tabtk/gitv0_741f3f0
pblat/1.6.0(default)                     roary/gitv0_c4d9b77(default)             tophat/2.0.10(default)
PEAR/gitv0_a37a84b(default)              RSEM/1.2.25(default)                     treemix/gitv0_23c15a2(default)
PEAT/gitv0_27981d7(default)              RSEM/1.2.27                              trimmomatic/0.32
perl/5.20.2(default)                     samtools/0.1.18                          trinity/20140717
perl/5.24.0                              samtools/0.1.19(default)                 trinity/2.2.0(default)
PGAP/1.2.1                               samtools/0.1.19b                         tRNAscan-SE/1.3.1(default)
PGDSpider/2.0.8.2(default)               samtools/1.2                             use.own
phylip/3.696(default)                    scalaBLAST/2.0(default)                  VarScan/2.3.7(default)
picard-tools/1.119                       scipio/1.4.1(default)                    vcflib/gitv0_e3ab177
picard-tools/2.1.0                       script_tools/1.0(default)                vcftools/0.1.12a
picard-tools/2.1.1(default)              seqtk/gitv0_1a8319b(default)             vcftools/gitv0_4fce995(default)
prank-msa/gitv0_3e44771(default)         sickle/gitv0_f3d6ae3(default)            vdb/gitv0_f1497a1
Prodigal/gitv0_004218f                   signalp/4.1(default)                     velvet/1.2.10(default)
prokka/1.11                              smalt/0.7.6(default)                     velvet/gitv0_9adf09f
prokka/gitv1_8f07048(default)            snap_alignment/1.0beta.17(default)       VelvetOptimiser/2.2.5(default)
prosite/1.79.1                           snape-pooled/31(default)                 vsearch/gitv0_174f810(default)
protobuf/gitv0_0622030                   snap_hmm/11_29_2013(default)             wise/2.4.1(default)
psmc/gitv0_e5f7df5(default)              snippy/gitv0_848a62e                     zlib/1.2.8
pyrad/gitv0_704ffbf                      snpcallphylo/0.7
python/2.7(default)                      SPAdes/3.9.0(default)
python/2.7.11                            sparsehash/gitv0_4cb9240