UseGalaxy.eu Tool Updates for 2019-04-06

April 6, 2019

On 2019-04-06, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #85

Gemini Tools

gemini_actionable_mutations was updated to 3630a6e624d4
gemini_amend was updated to 4bd4870ecd33
gemini_annotate was updated to 8da05bf2b1d1
gemini_burden was updated to fd6052cdc2c3
gemini_db_info was updated to 124c5faef773
gemini_db_info was updated to f3cc64057b4e
gemini_dump was updated to 187b57debbba
gemini_fusions was updated to 37f9901b674d
gemini_fusions was updated to 5ff5586b4681
gemini_gene_wise was updated to 99d6e7b1b7f1
gemini_gene_wise was updated to bc66ebfd4159
gemini_interactions was updated to 4234e3248f4d
gemini_interactions was updated to 527c8e4a356f
gemini_load was updated to 269c40fdcccb
gemini_load was updated to 993ccb45326b
gemini_load was updated to b2c25142267e
gemini_lof_sieve was updated to 9511c648d044
gemini_lof_sieve was updated to be7ac09bc2fa
gemini_mendel_errors was updated to dd963f00f297
gemini_pathways was updated to 42d3c5077378
gemini_pathways was updated to 66bc68095012
gemini_pathways was updated to 69b5327a1f88
gemini_qc was updated to 9872131c2377
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 69ec574f6f41
gemini_region was updated to bb4a5f979906
gemini_roh was updated to 91b4db3e6df4
gemini_roh was updated to 932a57d22888
gemini_set_somatic was updated to 230c975e7759
gemini_set_somatic was updated to ef9991a4a9a7
gemini_stats was updated to 4de57a28e609
gemini_stats was updated to ac761838cdaf
gemini_windower was updated to 8f04952b8882
gemini_windower was updated to 9aad9ef0502c

Statistics

scipy_sparse was updated to 102c8bae2e9c
sklearn_build_pipeline was updated to 9ddacd0b8c8b
sklearn_clf_metrics was updated to 5621f2be9fbc
sklearn_data_preprocess was updated to 4fc54bac4254
sklearn_discriminant_classifier was updated to 1d2bcebc8678
sklearn_ensemble was updated to f4d8a82e167c
sklearn_generalized_linear was updated to 6cf4b82c72bc
sklearn_model_validation was updated to 60b8a683ba99
sklearn_nn_classifier was updated to 23fb598a09d7
sklearn_numeric_clustering was updated to ff955d4fc5b1
sklearn_pairwise_metrics was updated to bd9481c0af38
sklearn_regression_metrics was updated to 64c87ceb6766
sklearn_sample_generator was updated to 0ba38603a0d6
sklearn_searchcv was updated to 907bb0418c9f
sklearn_suite was updated to 66c3d026fc62
sklearn_suite was updated to ed957fdd670d
sklearn_svm_classifier was updated to 295c383c3282
heatmap was updated to db1d80e89156
transformation was updated to d9e05021553c
iwtomics_loadandplot was updated to 0027f3287b34
iwtomics_loadandplot was updated to 8eb7dded0d52
iwtomics_loadandplot was updated to ee7dd07a530e
iwtomics_plotwithscale was updated to 25030f0d1154
iwtomics_plotwithscale was updated to 4bd560127b68
iwtomics_testandplot was updated to 800c7e974e3b
iwtomics_testandplot was updated to 926cdd3158ae

Picard

picard was updated to 6f9c0884a3e7
picard was updated to f6ced08779c4

Phylogenetics

gstf_preparation was updated to f4acbfe8d6fe

Get Data

ebi_metagenomics_run_downloader was updated to a1ef6c88ee37
sra_tools was updated to 5534eb46de20

Multiple Alignments

cdhit was updated to 93f25d52cfa5
mummer_mummer was updated to 48badcd29c5d

Quality Control

trim_galore was updated to 2c1f0fe810f7
trim_galore was updated to f1e71aeaa923
fastqc was updated to 0b201de108b9
fastqc was updated to 9337dd1fbc66
trimmomatic was updated to 415a165d92bb

Genome editing

suite_mageck was updated to 004e44994149
suite_mageck was updated to 125a82d47d22
suite_mageck was updated to 3269047c7d2e
suite_mageck was updated to 5146f144e7d4
suite_mageck was updated to b090e112e23b
suite_mageck was updated to e17f44672822

Metabolomics

transformation was updated to d9e05021553c
hmdb_ms_search was updated to 505956db90c5
xcms_group was updated to 9e45e1c404a4
xcms_merge was updated to 47f9b1fd5ce6
xcms_summary was updated to 27e7da5f6848

Collection Operations

split_file_to_collection was updated to 750c1684d47c
collection_element_identifiers was updated to d3c07d270a50

Assembly

nanopolish_eventalign was updated to 5c360c46eac7
nanopolish_eventalign was updated to bee42f615f28
racon was updated to aa39b19ca11e
disco was updated to 6d447ebb2bf4
shovill was updated to 57d5928f456e
unicycler was updated to 23300b42ca18
metaspades was updated to 01a241476407

GraphClust

graphclust_postprocessing was updated to e080ebe95476

Mothur

mothur_align_check was updated to dd533a49feed
mothur_align_seqs was updated to 5d134e0b31fd
mothur_amova was updated to 5aa5d26efeea
mothur_anosim was updated to 652d2803062c
mothur_bin_seqs was updated to 3fc101a0498f
mothur_chimera_bellerophon was updated to ad0df6ad0499
mothur_chimera_ccode was updated to 79255ca0b19a
mothur_chimera_check was updated to 35c91da65b75
mothur_chimera_perseus was updated to 128cbea05aeb
mothur_chimera_pintail was updated to cc3eef74fe31
mothur_chimera_slayer was updated to a899cc1416bc
mothur_chimera_uchime was updated to 4e3780d096af
mothur_chop_seqs was updated to 6e1047fa1a51
mothur_classify_otu was updated to 29882f4a1ef3
mothur_classify_seqs was updated to 65b370206748
mothur_classify_tree was updated to 931e9b25e81d
mothur_clearcut was updated to 20e764494303
mothur_cluster was updated to 3bb756df109c
mothur_cluster_classic was updated to 6ba59950d95c
mothur_cluster_fragments was updated to 881f9a4013a9
mothur_cluster_split was updated to 2c02989afecb
mothur_collect_shared was updated to 9c78c5ffa049
mothur_collect_single was updated to 7f212a2a4a3b
mothur_consensus_seqs was updated to e432f17722c8
mothur_cooccurrence was updated to 57fe046c8fbe
mothur_corr_axes was updated to 0968daa9b52f
mothur_count_groups was updated to dc02f3831a1a
mothur_count_seqs was updated to f00841c6fc14
mothur_create_database was updated to 34669a26ea47
mothur_degap_seqs was updated to a7fced14ce99
mothur_deunique_seqs was updated to 0369aff1be76
mothur_deunique_tree was updated to 98083c5a4338
mothur_dist_seqs was updated to 57eb5df69242
mothur_dist_shared was updated to 5d6d9f0d0652
mothur_fastq_info was updated to f02f3ca6dfd1
mothur_filter_seqs was updated to a0ce9fb3f260
mothur_filter_shared was updated to e44c38a17c7a
mothur_get_communitytype was updated to beb4e0832f3b
mothur_get_coremicrobiome was updated to ae1411cffbee
mothur_get_coremicrobiome was updated to c0b8bcf733cf
mothur_get_dists was updated to 6936b18e2a9e
mothur_get_group was updated to f2b626fe7082
mothur_get_groups was updated to b1c35f71607f
mothur_get_label was updated to bb8b69e90604
mothur_get_lineage was updated to b2b145255ece
mothur_get_mimarkspackage was updated to 6c54b38dd0da
mothur_get_otulabels was updated to 630ad54722c6
mothur_get_otulist was updated to 2478fb777d97
mothur_get_oturep was updated to 648b3da84b07
mothur_get_otus was updated to 278a9f09614c
mothur_get_rabund was updated to 398973de93ab
mothur_get_relabund was updated to 7756edb68ddc
mothur_get_sabund was updated to c79ecbd31c44
mothur_get_seqs was updated to f31e3b8f2336
mothur_get_sharedseqs was updated to 75b80a4fa86d
mothur_heatmap_bin was updated to 5e6fddbd1366
mothur_heatmap_sim was updated to 0674bdcb3019
mothur_homova was updated to 68005ede9e6e
mothur_indicator was updated to 0232e2fe594c
mothur_lefse was updated to 772e6a5b7358
mothur_libshuff was updated to eefbe872fd04
mothur_list_otulabels was updated to 0c9eb32683bf
mothur_list_seqs was updated to ea1a32c7927e
mothur_make_biom was updated to 143cd841de28
mothur_make_contigs was updated to 4b72b6c43327
mothur_make_design was updated to 5280cc8135eb
mothur_make_fastq was updated to 25b9449a5f3d
mothur_make_fastq was updated to e9b12c5ad27f
mothur_make_group was updated to 63a75db03ecc
mothur_make_group was updated to afc13b55ead3
mothur_make_lefse was updated to 678c90b43e17
mothur_make_lookup was updated to 4dd1404ee026
mothur_make_lookup was updated to d56e5a7a9cef
mothur_make_shared was updated to b5f98810181e
mothur_make_sra was updated to 33a3f68dc34b
mothur_mantel was updated to 17b471efdc40
mothur_merge_files was updated to 12b1bd17d614
mothur_merge_groups was updated to 052bc33e134e
mothur_merge_sfffiles was updated to ec717c8dce9b
mothur_merge_taxsummary was updated to 80bd73567a2c
mothur_metastats was updated to 10866c1f8e06
mothur_mimarks_attributes was updated to 247d1bacbefe
mothur_nmds was updated to 98f1cc2bc428
mothur_normalize_shared was updated to ad80d646ed1c
mothur_otu_association was updated to 0fb08aeb215e
mothur_otu_hierarchy was updated to 7590f83a6419
mothur_pairwise_seqs was updated to c05906ab8c41
mothur_parse_list was updated to 3b803b7f3388
mothur_parsimony was updated to 65955ae23f29
mothur_parsimony was updated to da7f70ebfb4c
mothur_pca was updated to 7474b222205d
mothur_pcoa was updated to c9fc98593dec
mothur_pcr_seqs was updated to 2b8dce0751e5
mothur_phylo_diversity was updated to 3868f54b097e
mothur_phylotype was updated to 58f143161d30
mothur_pre_cluster was updated to fbbe2b081299
mothur_primer_design was updated to 6e8cdd7e6825
mothur_rarefaction_shared was updated to 419266a5e29e
mothur_rarefaction_single was updated to 8091da04fbac
mothur_remove_dists was updated to ea7b70e1a61b
mothur_remove_groups was updated to 7c5b7dddd02e
mothur_remove_lineage was updated to 2f633c057c0d
mothur_remove_otulabels was updated to ba9df7320629
mothur_remove_otus was updated to ce3c9cb04314
mothur_remove_rare was updated to 196b1583580a
mothur_remove_seqs was updated to 2fa446f85b18
mothur_remove_seqs was updated to 92eb629218e1
mothur_reverse_seqs was updated to 03450507aa98
mothur_screen_seqs was updated to 94d8dbac60d8
mothur_sens_spec was updated to ddda05cfccb4
mothur_seq_error was updated to a03c9ebf1959
mothur_sffinfo was updated to 12507ed33710
mothur_shhh_flows was updated to 7cca6773bc2a
mothur_shhh_seqs was updated to 6ee54b761c3c
mothur_sort_seqs was updated to cbe644faff63
mothur_split_abund was updated to d850b4b9659d
mothur_split_groups was updated to 68c20caae797
mothur_sub_sample was updated to 34e1fbd32a04
mothur_sub_sample was updated to e866e31f6da3
mothur_summary_qual was updated to d50fdfdc2a0c
mothur_summary_seqs was updated to 411ddfefe041
mothur_summary_shared was updated to 74c8ebee088c
mothur_summary_single was updated to 2857a688a7e9
mothur_summary_tax was updated to 5eb0f670aa35
mothur_tree_shared was updated to 40d8938eaa24
mothur_trim_flows was updated to 4d56c7e82ba6
mothur_trim_seqs was updated to c49a6454726c
mothur_trim_seqs was updated to fc17c9a3c800
mothur_unifrac_unweighted was updated to 3597ca9089a5
mothur_unifrac_weighted was updated to 136cb4f4b996
mothur_unique_seqs was updated to 7c3f9c0850ac
mothur_venn was updated to e4f4c1c0d193
suite_mothur was updated to 739aa9d138d6
suite_mothur was updated to 768c2e48b706
suite_mothur was updated to a5ee03dfb216
suite_mothur was updated to d2fa47f91d9d
suite_mothur was updated to f9d288a66ab3

Qiime

suite_qiime was updated to a3f284fa7215
suite_qiime was updated to b2e54849fd5c
suite_qiime was updated to c5d785da19a7

mothur

suite_mothur was updated to 768c2e48b706

Mapping

bowtie2 was updated to 017aba02828d
bowtie2 was updated to 17062a0decb7
bowtie2 was updated to 42bb952b4e3c
bowtie2 was updated to 8ccbdbe9a695
bowtie2 was updated to 96d2e31a3938
bwa was updated to 48f306c57611
hisat2 was updated to 61ee47027bd3
rgrnastar was updated to 318b2a9d54dd
star_fusion was updated to 04b73d626680

Join, Subtract and Group

collection_column_join was updated to 071084070619

Graph/Display Data

plotly_regression_performance_plots was updated to 0800a1b66bbd
taxonomy_krona_chart was updated to 020b3087d0b7
circos was updated to ae9994cf526f
fasta_nucleotide_color_plot was updated to 0fba45ac3987
ggplot2_heatmap was updated to de002ba2b849
ggplot2_heatmap was updated to fe8d4655ee10
ggplot2_heatmap2 was updated to 76380bf74511
ggplot2_histogram was updated to 1f0242e49a58
ggplot2_histogram was updated to 536078949ae4
ggplot2_histogram was updated to 63a595b451d1
ggplot2_histogram was updated to 9d060114554c
ggplot2_pca was updated to 1b9406a1a769
ggplot2_pca was updated to bb6ec8e5387f
ggplot2_point was updated to 1bff6682e780
ggplot2_point was updated to 46f91106439b
ggplot2_violin was updated to 3a270cee1239
ggplot2_violin was updated to 637cf21db396
ggplot2_violin was updated to a597d59df9ee
intervene was updated to f5fa293605ca
jbrowse was updated to 112eb40ba6cf
jbrowse was updated to 1cfc579079a6
jbrowse was updated to 558d652cd681
jbrowse was updated to 69c5e9c0add0
jbrowse was updated to 8f33c9fbc119
nanoplot was updated to 4c172a4a4c9e
volcanoplot was updated to 6d532d760950

SAM Tools

bam_to_sam was updated to 88eedb4abea0
bamtools_filter was updated to 4fe8a75334c8
samtool_filter2 was updated to b7aa423007bf
ngsutils_bam_filter was updated to 2e957d4c4b95
ngsutils_bam_filter was updated to 49bf71fbc574
tag_pileup_frequency was updated to b7d7ae3963aa

HiCExplorer

suite_hicexplorer was updated to 12aca5abdc48
suite_hicexplorer was updated to 695ad2efeb79
suite_hicexplorer was updated to 714964678346
suite_hicexplorer was updated to aa5d613b707a
suite_hicexplorer was updated to fa64378b04b1

RNA Analysis

salmon was updated to 5a60f347f566
deseq2 was updated to 0696db066a5b
deseq2 was updated to 6f91b8ce6e07
deseq2 was updated to 89d26b11d452
deseq2 was updated to a416957ee305
deseq2 was updated to d9e5cadc7f0b
dexseq was updated to 278b189248cd
dexseq was updated to 9fd8b69e6e68
dexseq was updated to f89c9b25feb4
edger was updated to 555659de7321
edger was updated to fb9b9f0f2f06
heinz was updated to 5f589c91566e
kallisto_pseudo was updated to 2953303df011
limma_voom was updated to 5d903d528193
raceid_clustering was updated to 528a43b1cbcf
raceid_filtnormconf was updated to 56a093c2a3f9
raceid_inspectclusters was updated to 106718959281
raceid_inspecttrajectory was updated to 5156383d3a5d
raceid_trajectory was updated to 87de515af823
suite_trinity was updated to bcb1eff1d726
suite_trinity was updated to d8e02e80b0ad
trinity_run_de_analysis was updated to 2af5fd8210c5

Apollo

suite_apollo was updated to c2fa387439d6

Annotation

annotatemyids was updated to 9ab35a2245ce
annotatemyids was updated to ecc913a7334b
exonerate was updated to 2485637fe656
goseq was updated to ade933eff007
roary was updated to e02e9af2743f
suite_picrust was updated to 9a3fe0bd7481
tbprofiler was updated to 5182e1a99313
transtermhp was updated to 9a90656a1af9
sortmerna was updated to 185effcdfb68

Imaging

binary2labelimage was updated to b97a362ff321
coordinates_of_roi was updated to 0d30ffea8874
coordinates_of_roi was updated to 24d9bd16c953
imagecoordinates_flipaxis was updated to 5a210baa2ff1
landmark_registration was updated to a71239f3543a
points2labelimage was updated to dcc8c1d6af48
visceral_evaluatesegmentation was updated to d098aed00229

Evolution

codeml was updated to 961a712f9743
iqtree was updated to 288db50d1fb9
structure was updated to 0080ad37f8a0

Epigenetics

nanopolish_methylation was updated to 07cf146e8964
nanopolish_methylation was updated to f9dadc362197
suite_deeptools was updated to 197493196075
hifive was updated to 4a978cf8cf92

Operate on Genomic Intervals

concat was updated to 35a89f8cc96e
bedtools was updated to 6bb3cd018203
bedtools was updated to 87ee588b3d45

EMBOSS Tools

emboss_5 was updated to 1b6538ec8b56

Peak Calling

macs2 was updated to 495a4173006f

Motif Tools

meme_fimo was updated to c1a9a297ba8b
meme_psp_gen was updated to a0fa4efeeee3

FASTA/FASTQ manipulation

lighter was updated to 89b453176d05
fasta_filter_by_length was updated to c8cd0a03db49
fastqc was updated to 3e1cdf5406db
fastx_artifacts_filter was updated to 567d5b3c52b1
fastx_barcode_splitter was updated to 4bedca26c133
fastx_renamer was updated to 3599f5451ee2
fastx_trimmer was updated to 547e8d00f11c
je_markdupes was updated to 384b972e43bc
flash was updated to a27654fc4270
suite_bctools was updated to 035a8df3214f
suite_bctools was updated to e8826fd7edc0
suite_umi_tools was updated to 1cc341f20285
suite_umi_tools was updated to 32db578d29b1
suite_umi_tools was updated to 3657b4d9c528
suite_umi_tools was updated to 384598789816
suite_umi_tools was updated to 3de29ae524a0
suite_umi_tools was updated to 8632189ff7be
suite_umi_tools was updated to c2664661e1c5
suite_umi_tools was updated to c8a5934f6a04
suite_umi_tools was updated to ddf98b8748d0
suite_umi_tools was updated to e3313bb98911
trimmomatic was updated to 415a165d92bb

Other Tools

extract_genomic_dna was updated to c8467246b57e

Data Managers

data_manager_qiime_database_downloader was updated to 9e86c09a6cae
data_manager_sortmerna_database_downloader was updated to 30bb49887172

Text Manipulation

tables_arithmetic_operations was updated to 82fa5062d611
gff3_rebase was updated to e54940ea270c
gff3_rebase was updated to ea35a85b941d

Metagenomic analyses

interproscan5 was updated to 82547f0d3a29
suite_humann2 was updated to a6d24a7c473f
suite_humann2 was updated to b6817cd584e1
staramr was updated to 930893c83a1a

Convert Formats

graphicsmagick_image_convert was updated to c01226f0d828
graphicsmagick_image_convert was updated to e88f1111d9e7
uniprot_rest_interface was updated to 48522382b6a4
msconvert was updated to cc5ccfa8ee28
bam_to_scidx was updated to b737f6d83f48
gtftobed12 was updated to 57d45064f114
resize_coordinate_window was updated to 541f300f322d
ucsc_twobittofa was updated to d025a40bbff1

Proteomics

protease_prediction was updated to 8e8c6df5cc64
cardinal_classification was updated to cbc7e53518ce
cardinal_combine was updated to 129cddd02600
cardinal_data_exporter was updated to 28ba52c9548c
cardinal_data_exporter was updated to e30d8b72415f
cardinal_filtering was updated to 0c4579390f73
cardinal_mz_images was updated to 27a4c660bbca
cardinal_mz_images was updated to 773a24b240e1
cardinal_preprocessing was updated to 1b875f0b8024
cardinal_quality_report was updated to d4803c1e5e19
cardinal_segmentations was updated to 034885df9b09
cardinal_spectra_plots was updated to 3642ed221eb2
eggnog_mapper was updated to a37df6f6b869
hardklor was updated to 539f157784e7
msgfplus was updated to ee56530a559f
myrimatch was updated to e26ef51ef341
rawtools was updated to 51e4aa55ea04
suite_openms was updated to 0c22108365d1
megahit_contig2fastg was updated to ed22349139ee
suite_query_tabular was updated to 4712dbb7b00d

OBO Ontology manipulation

suite_onto_toolkit was updated to cbedf28208ae

Test Tools

hifive was updated to 4a978cf8cf92

Variant Calling

nanopolish_variants was updated to 639b3a5bb415
nanopolish_variants was updated to f1cb13497323
vcffilter was updated to 9442e22779ca
bcftools_call was updated to 3296c3680d96
snippy was updated to feb7e635c6af
snpeff was updated to 36dc3690a82c
snpeff was updated to 479c4f2f4826
suite_varscan was updated to 43975c89ccaa
suite_varscan was updated to 4555028c2815
suite_varscan was updated to 9bfb92848131
suite_varscan was updated to c037bdc0f28a
varscan_copynumber was updated to 192bd5b78300
varscan_copynumber was updated to c24910ad5441
varscan_copynumber was updated to e814a042315f
varscan_mpileup was updated to 1e667badbe87
varscan_mpileup was updated to 45288fb1f3f5
varscan_mpileup was updated to 7c5e867820cf
varscan_mpileup was updated to d7e6c347538d
varscan_somatic was updated to 31a38ce7e8ae

NCBI Blast

taxonomy_krona_chart was updated to 020b3087d0b7
kraken_taxonomy_report was updated to b11b3ac48bb9
kraken_taxonomy_report was updated to b97694b21bc3

RAD-seq

stacks_cstacks was updated to 5bd1418f4227
stacks_denovomap was updated to b8827c571fbd