文件列表:

beagle (0, 2018-08-24)
beagle\.shed.yml (195, 2018-08-24)
beagle\execute_beagle.sh (236, 2018-08-24)
beagle\execute_beagle.xml (3228, 2018-08-24)
beagle\test-data (0, 2018-08-24)
beagle\test-data\Annotated_VCF.vcf (3606183, 2018-08-24)
beagle\test-data\filelog.txt (2885, 2018-08-24)
beagle\test-data\output.vcf (10675075, 2018-08-24)
cytoscape (0, 2018-08-24)
cytoscape\.shed.yml (131, 2018-08-24)
cytoscape\Cytoscape.pl (2534, 2018-08-24)
cytoscape\Cytoscape.sh (166, 2018-08-24)
cytoscape\Cytoscape.xml (4051, 2018-08-24)
cytoscape\static (0, 2018-08-24)
cytoscape\static\images (0, 2018-08-24)
cytoscape\static\images\network.png (15156, 2018-08-24)
cytoscape\test-data (0, 2018-08-24)
cytoscape\test-data\input.json (1392, 2018-08-24)
cytoscape\test-data\network.html (4298, 2018-08-24)
fastme (0, 2018-08-24)
fastme\.shed.yml (122, 2018-08-24)
fastme\fastme.xml (14746, 2018-08-24)
fastme\test-data (0, 2018-08-24)
fastme\test-data\TreeTn93BionjSpr.nwk (4849, 2018-08-24)
fastme\test-data\newick (4849, 2018-08-24)
fastme\test-data\newick.log (146, 2018-08-24)
fastme\test-data\phylip (1172420, 2018-08-24)
haplophyle (0, 2018-08-24)
haplophyle\.shed.yml (127, 2018-08-24)
haplophyle\Haplophyle.pl (3873, 2018-08-24)
haplophyle\Haplophyle.sh (810, 2018-08-24)
haplophyle\Haplophyle.xml (6523, 2018-08-24)
haplophyle\HaplophyleInBatch.pl (1829, 2018-08-24)
haplophyle\NetworkCreator_fat.jar (24495, 2018-08-24)
haplophyle\test-data (0, 2018-08-24)
haplophyle\test-data\cytoscape.html (2590, 2018-08-24)
haplophyle\test-data\dotfile.txt (1520, 2018-08-24)
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# GFLS (Galaxy For Life Science) :heavy_minus_sign::sparkles::sparkles::four::herb::microscope::heavy_minus_sign: SNiPlay This repository concern the **SNiPlay** part of the GFLS project ([website](http://sniplay.southgreen.fr/cgi-bin/home.cgi)). It is made in collaboration with Alexis Dereeper from the 'Institut de Recherche pour le Developpement' (IRD). All the **XML** files (Wrappers) are made by his team. #### :file_folder: Content The repository contain all the wrappers for the workflow SNiPlay. - admixture [deprecated] - fastme - plink - readseq - snmf - snpeff_from_gff_vcf - tassel5 - vcftools_filter_stats_diversity (vcftoolsFilter,vcftoolsStats,vcftoolsSlidingWindow) - mlmm Wrappers for the Haplotype analysis workflow. - Beagle - Haplophyle It contain also wrappers for SNP analysis (in Sniplay repo.). - AnnotationStatsFromVCF - check_gwas_inputs - egglib - GetHaplotypesFromPhasedVCF - hapmap2mlmm - MDSplot - ped2bed - PedToFasta - Rooting - SNP_density - VCF2Hapmap The sniplay3_complete_workflow repository. ~~And the Haplotype_analysis workflow repository.~~ #### :page_with_curl: Publications Alexis Dereeper, Felix Homa, Gwendoline Andres, Guilhem Sempere, Gautier Sarah, Yann Hueber, Jean-Francois Dufayard, Manuel Ruiz; SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations, Nucleic Acids Research, Volume 43, Issue W1, 1 July 2015, Pages W295–W300, https://doi.org/10.1093/nar/gkv351 Alexis Dereeper, Stephane Nicolas, Loic Le Cunff, Roberto Bacilieri, Agnes Doligez, Jean-Pierre Peros, Manuel Ruiz and Patrice This; SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects, BMC Bioinformatics, Volume 12, 5 May 2011, Page 134, https://doi.org/10.1186/1471-2105-12-134 #### :pencil: Use tools These tools are available in a docker container: - https://quay.io/repository/valentinmarcon/docker-galaxy-sniplay - https://github.com/ValentinMarcon/docker-galaxy-sniplay

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