Difference between revisions of "Available Software"
(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...") |
(No difference)
|
Revision as of 13:54, 1 September 2016
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
