UseGalaxy.eu Tool Updates for 2019-10-19

October 19, 2019

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