Available Software

From wiki
Revision as of 13:54, 1 September 2016 by Rf (talk | contribs) (Created page with "= 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 th...")
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
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, 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

Categorised Listing

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                                  ngs/gitv0_aef5f50                        python/2.7.12                            sra-tools/gitv0_814d6f7(default)
abyss/1.9.0                              cd-hit/gitv0_5acf038(default)            gubbins/gitv0_fe094b0                    NGSToolsApp/2.1.5(default)               python/3.4                               srst2/gitv1_e30dd01(default)
act/v1                                   CEGMA/2.5(default)                       gubbins/gitv1_8a12ae7(default)           null                                     qtdt/2.6.1(default)                      srst2/gitv2_41b3f46
AdapterRemoval/gitv0_abe4a3e(default)    crimap/2.504(default)                    gwas                                     OpenBLAS/0.2.14                          quast/4.1                                SSPACE/3.0
angsd/gitv0_212d58                       CRISP/2                                  harvest-tools/gitv0_ebf7ecc              OpenBLAS/0.2.18                          R/3.2.1(default)                         stacks/1.35
angsd/gitv1_89d8fa9(default)             CRISP/5(default)                         hdf5/1.8.15-patch1(default)              openmpi/1.10.2                           R/3.2.3                                  stacks/1.37
arlequin/3.5.2(default)                  cufflinks/2.2.1(default)                 hdf5/1.8.16                              openmpi/1.6.5                            rainbow/2.0.4                            stacks/1.40(default)
artemis/16.0.0(default)                  dDocent/gitv0_7dea314                    hmmer/2.3.2                              openmpi/2.0.0(default)                   rapsearch/gitv0_95c866e(default)         stacks/1.41
ArtificialFastqGenerator/1.0.0(default)  diamond/gitv0_39f2a71                    hmmer/3.1b1                              oraclejava/jdk1.8.0_74                   RAxML/gitv0_4692545(default)             stampy/1.0.23(default)
AsperaConnect/3.6.2                      dot                                      hmmer/3.1b2(default)                     OrthoFinder/0.6.0                        readseq/2.1.30(default)                  STAR/2.4.2a(default)
assembly-stats/gitv0_003a372             ea-utils/gitv0_88c9ad5                   HTSlib/1.3                               PAGIT/1(default)                         repeatmasker/4.0.5(default)              structure/2.3.4(default)
augustus/3.0.3                           EIGENSOFT/6.0.1(default)                 HTSlib/1.3.1(default)                    paml/4.7a(default)                       rmblastn/2.2.28(default)                 tabix/gitv0_1ae158a
augustus/3.2.2(default)                  EMBOSS/6.6.0(default)                    HTSlib/gitv1_0de7fe5                     parsnp/gitv0_63bea13                     rnammer/1.2(default)                     tabtk/gitv0_741f3f0
BamQC/gitv0_480c091                      ensembl/gitv0_bb48912(default)           interproscan/5.4-47.0(default)           pblat/1.6.0(default)                     roary/gitv0_c4d9b77(default)             tophat/2.0.10(default)
bamtools/gitv0_02c2be8(default)          ensembl-git-tools/gitv0_68ac669(default) kallisto/git0_f0678a2                    PEAR/gitv0_a37a84b(default)              RSEM/1.2.25(default)                     treemix/gitv0_23c15a2(default)
BayeScan/2.1(default)                    exonerate/2.2.0(default)                 lamarc/2.1.10(default)                   PEAT/gitv0_27981d7(default)              RSEM/1.2.27                              trimmomatic/0.32
BayeScEnv/1.0                            FastML/3.1                               lpsolve/5.5.2.3                          perl/5.20.2(default)                     samtools/0.1.18                          trinity/20140717
BayeScEnv/gitv0_beb60d2(default)         FastML/gitv0_bb5d761                     mafft/7.147(default)                     perl/5.24.0                              samtools/0.1.19(default)                 trinity/2.2.0(default)
bcftools/gitv0_47e811c                   FASTQC/0.11.5(default)                   maker/2.31.8(default)                    PGAP/1.2.1                               samtools/0.1.19b                         tRNAscan-SE/1.3.1(default)
bedtools/2.25.0(default)                 fastsimcoal2/2.5.2.21                    Mash/gitv0_2edc42                        PGDSpider/2.0.8.2(default)               samtools/1.2                             use.own
bioawk/gitv0_5e8b41d(default)            fastsimcoal2/2.5.2.8(default)            masurca/2.3.2(default)                   phylip/3.696(default)                    scalaBLAST/2.0(default)                  VarScan/2.3.7(default)
blastall/2.2.26(default)                 fastSTRUCTURE/1.0                        Mauve/2015-02-13                         picard-tools/1.119                       scipio/1.4.1(default)                    vcflib/gitv0_e3ab177
blastScripts/1.0.0(default)              fastSTRUCTURE/190315(default)            mcl/14-137(default)                      picard-tools/2.1.0                       script_tools/1.0(default)                vcftools/0.1.12a
blastScripts/1.0.1                       FastTree/2.1.8(default)                  mdb/0.6(default)                         picard-tools/2.1.1(default)              seqtk/gitv0_1a8319b(default)             vcftools/gitv0_4fce995(default)
blat/35                                  freebayes/gitv0_dbb6160                  merlin/1.1.2(default)                    prank-msa/gitv0_3e44771(default)         sickle/gitv0_f3d6ae3(default)            vdb/gitv0_f1497a1
boost/1.60.0(default)                    GapFiller/v1-10                          module-info                              Prodigal/gitv0_004218f                   signalp/4.1(default)                     velvet/1.2.10(default)
boost/1.61.0                             gatk/3.4.0                               modules                                  prokka/1.11                              smalt/0.7.6(default)                     velvet/gitv0_9adf09f
bowtie/1.0.0                             gatk/3.5.0                               mpifast/gitrev2(default)                 prokka/gitv1_8f07048(default)            snap_alignment/1.0beta.17(default)       VelvetOptimiser/2.2.5(default)
bowtie2/2.1.0(default)                   gatk/3.6.0(default)                      mrbayes/3.2.6                            prosite/1.79.1                           snape-pooled/31(default)                 vsearch/gitv0_174f810(default)
bowtie2/2.2.4                            gcc/4.9.3                                MUMmer/3.23                              protobuf/gitv0_0622030                   snap_hmm/11_29_2013(default)             wise/2.4.1(default)
BUSCO/1.22                               geneid/1.4.4(default)                    MUMmer/3.23b(default)                    psmc/gitv0_e5f7df5(default)              snippy/gitv0_848a62e                     zlib/1.2.8
bwa/0.7.12(default)                      GeneMark_ES/3.48(default)                muscle/3.7                               pyrad/gitv0_704ffbf                      snpcallphylo/0.7
bwa/0.7.7                                general_script_tools/(default)           newick_utils/4.9.3                       python/2.7(default)                      SPAdes/3.9.0(default)
CAFE/3.1                                 gsea/2.2.2(default)                      newick_utils/gitv0_614bf6c(default)      python/2.7.11                            sparsehash/gitv0_4cb9240
Retrieved from "http://stab.st-andrews.ac.uk/wiki/index.php?title=Available_Software&oldid=625"