Difference between revisions of "Available Software"
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---------------------------- /usr/local/Modules/3.2.10/modulefiles ------------------------------------------------ | ---------------------------- /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 | |
| − | blastScripts/1.0.1 | + | bedtools/2.23.0 bedtools/2.25.0(default) bioawk/gitv0_5e8b41d(default) |
| − | blat/35 | + | 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) | ||
Revision as of 13:04, 7 December 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 ------------------------------------------------ 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)
