On 2019-10-19, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #146
Gemini Tools
- gemini_actionable_mutations was updated to a0379503290f
- gemini_amend was updated to 2281967e7bc3
- gemini_amend was updated to bff8fad3fb69
- gemini_annotate was updated to 3859552a63d8
- gemini_annotate was updated to 8da05bf2b1d1
- gemini_burden was updated to c70d79e0eed7
- gemini_comp_hets was updated to 62647e2637f6
- gemini_db_info was updated to f3cc64057b4e
- gemini_de_novo was updated to 9db3e299b1c8
- gemini_fusions was updated to 6e3d2bd01a96
- gemini_fusions was updated to 8295781a3c27
- gemini_inheritance was updated to 3123ce7acd0e
- gemini_interactions was updated to 4234e3248f4d
- gemini_interactions was updated to 7028ca3cac1c
- gemini_load was updated to 5c5cdbdc3534
- gemini_load was updated to 993ccb45326b
- gemini_load was updated to b5b53c27baca
- gemini_lof_sieve was updated to be7ac09bc2fa
- gemini_lof_sieve was updated to e1920f41a1ca
- gemini_pathways was updated to 2bce41988d8e
- gemini_pathways was updated to 69b5327a1f88
- gemini_pathways was updated to c63b7eefb07a
- gemini_qc was updated to 8414eecc3828
- gemini_qc was updated to a875f940d8fd
- gemini_query was updated to 18f459744a97
- gemini_query was updated to ab195e756e5e
- gemini_recessive_and_dominant was updated to 05124dc72dba
- gemini_region was updated to 601b70d10d92
- gemini_roh was updated to 91b4db3e6df4
- gemini_set_somatic was updated to 230c975e7759
- gemini_set_somatic was updated to 7b031989ea12
- gemini_stats was updated to a0ee6874a23b
- gemini_stats was updated to ac761838cdaf
- gemini_windower was updated to 9b462be5a604
Expression Tools
- compose_text_param was updated to feb3acba1e0a
Phylogenetics
- hyphy_bgm was updated to bf97cacc1a55
- hyphy_fubar was updated to 0f108ee932ea
Get Data
- unipept was updated to 34758ab8aaa4
- ebi_search_rest_results was updated to b6029f2c71cb
- sra_tools was updated to 1790dcf3c32d
Multiple Alignments
- compalignp was updated to 7e55ac3bd458
Quality Control
- fastx_nucleotides_distribution was updated to 63d6e2daad48
- multiqc was updated to e4574a4d09d8
Extract Features
- length_and_gc_content was updated to f088370d2a3c
Phenotype Association
- ctd_batch was updated to 4a32700dcaa2
Assembly
- sopra was updated to 87ffe493b6c1
- disco was updated to 6d447ebb2bf4
- metaspades was updated to 05c394313b1c
Mothur
- mothur_align_seqs was updated to 5d134e0b31fd
- mothur_chimera_perseus was updated to 29412cc05a3d
- mothur_chimera_slayer was updated to a899cc1416bc
- mothur_chimera_uchime was updated to 4e3780d096af
- mothur_chop_seqs was updated to 35a4e758bbed
- mothur_chop_seqs was updated to 6e1047fa1a51
- mothur_classify_otu was updated to c384c39c9c27
- mothur_clearcut was updated to 20e764494303
- mothur_cluster_fragments was updated to 978cdd9b48d3
- mothur_cluster_split was updated to a29ac7993cb0
- mothur_collect_shared was updated to fd3fedbebdab
- mothur_cooccurrence was updated to 5076b26f99d0
- mothur_cooccurrence was updated to f83d1ed69978
- mothur_count_groups was updated to dc02f3831a1a
- mothur_count_seqs was updated to f00841c6fc14
- mothur_degap_seqs was updated to bd09ab148632
- mothur_dist_shared was updated to 3e2ca0c67e9d
- mothur_dist_shared was updated to bba3c4af4982
- mothur_filter_seqs was updated to a0ce9fb3f260
- mothur_get_dists was updated to 6936b18e2a9e
- mothur_get_otulabels was updated to 56b4c4b3ce7c
- mothur_get_oturep was updated to 782220733828
- mothur_get_otus was updated to 971ab18e74d7
- mothur_get_rabund was updated to abe4ffadab83
- mothur_get_relabund was updated to 7756edb68ddc
- mothur_get_relabund was updated to e034a3d4b6c7
- mothur_get_seqs was updated to 32a95d4cd850
- mothur_get_seqs was updated to 9cefa4fac685
- mothur_homova was updated to 9a215084d776
- mothur_lefse was updated to c98e47f7b233
- mothur_list_seqs was updated to 37a896516dc3
- mothur_make_biom was updated to 143cd841de28
- mothur_make_fastq was updated to 25b9449a5f3d
- mothur_make_fastq was updated to ecbc8745f135
- mothur_make_lookup was updated to 4dd1404ee026
- mothur_merge_files was updated to 80e3857bf744
- mothur_merge_sfffiles was updated to e7d03df2fc00
- mothur_merge_taxsummary was updated to a2dda99b6d79
- mothur_mimarks_attributes was updated to 247d1bacbefe
- mothur_nmds was updated to 5b3e10ccf581
- mothur_normalize_shared was updated to ad80d646ed1c
- mothur_otu_association was updated to 0fb08aeb215e
- mothur_otu_hierarchy was updated to 7590f83a6419
- mothur_phylo_diversity was updated to 3868f54b097e
- mothur_phylotype was updated to 249cdeb3cdb1
- mothur_phylotype was updated to e18d25fb125e
- mothur_pre_cluster was updated to fbbe2b081299
- mothur_remove_dists was updated to 0ec8be51451b
- mothur_remove_otus was updated to 8a1fbb8e703c
- mothur_remove_rare was updated to 196b1583580a
- mothur_remove_seqs was updated to 2fa446f85b18
- mothur_reverse_seqs was updated to c7cde36b331a
- mothur_sens_spec was updated to ddda05cfccb4
- mothur_sffinfo was updated to 5d52096c0a9c
- mothur_shhh_seqs was updated to c7e60f5aadcb
- mothur_sort_seqs was updated to 2f6a9498447e
- mothur_split_abund was updated to d850b4b9659d
- mothur_sub_sample was updated to e866e31f6da3
- mothur_summary_tax was updated to 5eb0f670aa35
- mothur_unifrac_unweighted was updated to 46ba42ec466b
Mapping
- bowtie2 was updated to a9d4f71dbfb0
- lastz_paired_reads was updated to ecc974513241
- rgrnastar was updated to bc685d13b637
Join, Subtract and Group
- collection_column_join was updated to 9c8536c7ed42
Graph/Display Data
- gmaj was updated to 2cd5ee197ec7
- bandage was updated to ebe4463404b4
- ggplot2_violin was updated to 637cf21db396
- jbrowse was updated to 9de82b4963e6
- jbrowse was updated to fa30df9b79c2
Statistics
- best_regression_subsets was updated to 4f33ec73e445
- count_gff_features was updated to fabda887a71f
- mine was updated to 5e2c89443c44
- seq_composition was updated to c0eb0e5792f3
SAM Tools
- bam_to_sam was updated to f57df915aa10
- pileup_parser was updated to 85bedbea8a12
- sam_pileup was updated to 95612c159681
- sam_to_bam was updated to b77f7b516b17
- sam_to_bam was updated to f7a0d41036c7
- samtool_filter2 was updated to 886b73f04847
- samtools_bedcov was updated to 9149ad20699a
- samtools_flagstat was updated to 13c4ad597626
- samtools_flagstat was updated to 4e404acfafa6
- samtools_idxstats was updated to 88b8c2916784
- samtools_phase was updated to 6166013090c0
- samtools_phase was updated to cba1944e3ed0
- samtools_stats was updated to 24c5d43cb545
- ngsutils_bam_filter was updated to 2e957d4c4b95
- ngsutils_bam_filter was updated to 49bf71fbc574
HiCExplorer
- hicexplorer_hicaggregatecontacts was updated to a48457358aa8
- hicexplorer_hicmergematrixbins was updated to 90645548f8cc
- hicexplorer_hicpca was updated to d5a86de86846
- hicexplorer_hicplotdistvscounts was updated to 6abd5817e0cd
- hicexplorer_hicplotmatrix was updated to a9050bffb50c
- hicexplorer_hicplotviewpoint was updated to 67bd57e960a3
- hicexplorer_hicsummatrices was updated to 6d1526527417
RNA Analysis
- salmon was updated to 5a60f347f566
- cufflinks was updated to e04dbae2abe0
- cummerbund_to_tabular was updated to 0761bbc0a4e7
- tophat_fusion_post was updated to f83394a2c2da
- dexseq was updated to f1c406f9554c
- featurecounts was updated to a37612abf7f9
- pizzly was updated to f7556cfa4047
- stringtie was updated to dd4df992d93d
- mirdeep2_mapper was updated to ab8cd78709e1
- rnabob was updated to cd00b4fe6552
Annotation
- antismash was updated to 5db064bbb3be
- nucleosome_prediction was updated to 2c42bb973ac3
- dgidb_annotator was updated to c5bb987015c5
- annotatemyids was updated to 38eedf3cc3c9
- annotatemyids was updated to b467a89be0c6
- goseq was updated to 8b3e3657034e
- goseq was updated to ae39895af5fe
- transtermhp was updated to 9a90656a1af9
- tmhmm_and_signalp was updated to 7de64c8b258d
- miranda was updated to bf6976462251
Single-cell
- anndata_manipulate was updated to 19592ec717ef
- scanpy_remove_confounders was updated to 9ca360dde8e3
- scater_normalize was updated to 87757f7b9974
- scater_plot_dist_scatter was updated to 4887c4c69847
HCA-Single Cell
- gtf2gene_list was updated to e255c0e5dfca
Epigenetics
- bwameth was updated to 95219305823a
Operate on Genomic Intervals
- cluster was updated to 765ceb06c3e2
- concat was updated to d491589307e7
- bedtools was updated to 4f7a5ccd2ae9
- bedtools was updated to b28e0cfa7ba1
- bedtools was updated to b8348686a0b9
- bedtools was updated to dde39ba9c031
- bedtools was updated to e19bebe96cd2
- translate_bed_sequences was updated to d328db400280
Filter and Sort
- gffcompare was updated to f99d7825a501
Peak Calling
- diffbind was updated to 69138bfd8644
- macs was updated to f6319b0b4391
- macs2 was updated to bfe57d6e0c4c
Motif Tools
- meme_fimo was updated to fd522a964017
FASTA/FASTQ manipulation
- fasta_compute_length was updated to de2db1bdfbf8
- fastq_filter was updated to b957f55f3955
- fastq_paired_end_joiner was updated to 6a7f5da7c76d
- short_reads_figure_score was updated to b52b9c7aabd9
- fasta_merge_files_and_filter_unique_sequences was updated to 9ad0d336e5ed
- sickle was updated to edaa8572219d
- umi_tools_count was updated to 8db56d2f8b72
Data Managers
- data_manager_qiime_database_downloader was updated to cbe065fbd038
ChemicalToolBox
- autodock_vina_prepare_box was updated to 908880455b2d
- autodock_vina_prepare_receptor was updated to d15e5a2a7558
- confab was updated to 039ef13e3676
- ctb_rdkit_descriptors was updated to 617d4555d8d3
- openbabel was updated to 125da3a296ca
- openbabel_addh was updated to 0691e5e97cd5
- openbabel_addh was updated to bfb8555f0003
- openbabel_filter was updated to 72d13f75b67c
- openbabel_genprop was updated to ebe0654a8b85
- openbabel_obgrep was updated to 1c418abdafd9
- openbabel_remduplicates was updated to 39895aff0dd7
- openbabel_remduplicates was updated to d751e92477ea
- openbabel_remove_protonation_state was updated to 0bf5331f62ef
- openbabel_subsearch was updated to 202e3a64859b
- opsin was updated to cda22c799d0a
- osra was updated to 0916781bc971
- rdock_rbdock was updated to bad150d12198
- sucos_clustering was updated to f80cfac80c53
- bio3d_dccm was updated to 386b4f4b6a85
- gmx_em was updated to c1e98d48b8b4
- gmx_merge_topology_files was updated to f2faba46d680
- gmx_solvate was updated to 77aaf9a68166
- md_converter was updated to acce5039ece7
- mdanalysis_angle was updated to fc7293c6cb6a
- mdanalysis_cosine_analysis was updated to d18e7db42633
- mdanalysis_dihedral was updated to d8178fe9aaff
- mdanalysis_ramachandran_plot was updated to ce0728b92289
- mdanalysis_rdf was updated to 9bb57bd1fdc8
- packmol was updated to 539fb45630e6
Text Manipulation
- coverage was updated to bc9c66c1e9c9
- get_flanks was updated to 4cd116158aef
- subtract was updated to 7a2a604ae9c8
Metagenomic analyses
- poisson2test was updated to 5ff18ec88181
- khmer_abundance_distribution was updated to 5a97c5bbd51e
- khmer_abundance_distribution_single was updated to 792d520ba676
- khmer_filter_abundance was updated to a4970dfc331c
- vegan_diversity was updated to db56c8e79b1e
- vegan_fisher_alpha was updated to d6b92ca3a9a1
- vegan_rarefaction was updated to b0d5976540e3
- vsearch was updated to 576963db5f1b
Convert Formats
- gffread was updated to 0232f19d300f
- gtftobed12 was updated to 75a14cc16d4d
- intermine_galaxy_exchange was updated to c24014d80001
- resize_coordinate_window was updated to 08b6255afde7
Proteomics
- peptideshaker was updated to 78fad25eff17
Regional Variation
- compute_motifs_frequency was updated to 1f8ee7f9701b
deepTools
- deeptools_bam_coverage was updated to 5d11599b8a7d
- deeptools_plot_coverage was updated to 7e361d147872
- deeptools_plot_heatmap was updated to 512155688d98
- deeptools_plot_pca was updated to 38e3f226248b
Variant Calling
- naive_variant_caller was updated to cfc86c3fc5c8
- bamleftalign was updated to e65540a91b87
- vcf2tsv was updated to e92b3c0f9224
- vcfaddinfo was updated to 196ed76d2619
- vcfallelicprimitives was updated to 0a69cff7946e
- vcfbedintersect was updated to 31a86dbe17c0
- vcfbedintersect was updated to 9edfe5145ba8
- vcfcheck was updated to 40a339e4692e
- vcfcombine was updated to da419f5ed589
- vcfcommonsamples was updated to f27d6187d808
- vcffilter was updated to 9442e22779ca
- vcffixup was updated to 9d7e64e4b9fc
- vcffixup was updated to a03f346b6aae
- vcfgenotypes was updated to f5653ed90dfd
- vcfhethom was updated to c9bb9f126282
- vcfleftalign was updated to 8e02d116b0f9
- vcfrandomsample was updated to c035d96c5cbe
- vcfselectsamples was updated to 43cecdfe7107
- vcfsort was updated to a8c5440d69e3
- vcftools_annotate was updated to 57a6550df582
- vcftools_compare was updated to ad50c257e758
- vcftools_isec was updated to 026d0f104183
- vcftools_merge was updated to 71e19ddf52f5
- vcfvcfintersect was updated to 6f6bf10618d7
- bcftools_call was updated to 0fba2c15b40d
- bcftools_call was updated to a531317a3527
- bcftools_cnv was updated to 635532ff1ac9
- bcftools_csq was updated to 33df4e68959b
- bcftools_plugin_color_chrs was updated to 47ee1925fe9e
- snpeff was updated to 268d162b9c49
- snpeff was updated to e8adfc4c0a6b
- snpsift was updated to 2b3e65a4252f
- snpsift_dbnsfp was updated to 563d1bdb7b80
- snpsift_genesets was updated to 9e6fa49c1077
- vt_variant_tools was updated to 6e073fc99d9c
NCBI Blast
- taxonomy_krona_chart was updated to 020b3087d0b7
- kraken was updated to 658d47fd33e3
- kraken_report was updated to a3a7440fc618
- ncbi_blast_plus was updated to 2889433c7ae1
- ncbi_blast_plus was updated to 393a7a35383c
- kraken_taxonomy_report was updated to b11b3ac48bb9
RAD-seq
- stacks_assembleperead was updated to fea78fd36a05
- stacks_cstacks was updated to dab92afa0c98
- stacks_denovomap was updated to eb1e95f88e96
- stacks_populations was updated to d504d945a655
- stacks_procrad was updated to 5d12647ff71f
- stacks_procrad was updated to 8fe258d72ff3
- stacks_pstacks was updated to 7ebc7d229deb
- stacks_refmap was updated to 7c42e6768c41
- stacks_rxstacks was updated to 2360d8cf42f7
- stacks_sstacks was updated to e880ddd2d8fa