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...") |
|||
| Line 14: | Line 14: | ||
= Raw Listing 01 Sep 2016 = | = Raw Listing 01 Sep 2016 = | ||
| − | + | --------------------------------- /usr/local/Modules/versions ----------------------------------------------------- | |
3.2.10 | 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 | ||
Revision as of 14:20, 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 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
