UseGalaxy.eu Tool Updates for 2022-01-14

January 14, 2022

On 2022-01-14, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #304

Graph/Display Data

bandage was updated to b9e31c5c01c7
circos was updated to 290a11559985
ggplot2_heatmap was updated to d3a9e32672ec
ggplot2_histogram was updated to 355a82227003
ggplot2_point was updated to 1acf88921176
ggplot2_violin was updated to e44775efb2dc

RAD-seq

stacks2_denovomap was updated to ad5ab22ffe24
stacks2_gstacks was updated to eb784fa07f80
stacks2_kmerfilter was updated to 1544278c272e
stacks2_populations was updated to 887cf585cafc
stacks2_procrad was updated to e897c74a48bb
stacks2_refmap was updated to 4f65e343ecdf
stacks2_shortreads was updated to c5d7050e4ad7
stacks2_sstacks was updated to cd034465d4a4
stacks2_ustacks was updated to cfb504394ae1

ChemicalToolBox

autodock_vina was updated to 90ea16534012
ctb_rdkit_descriptors was updated to 0993ac4f4a23
ambertools_antechamber was updated to 4fff93efc0f9
ambertools_antechamber was updated to c280abd461a6
gmx_editconf was updated to 79cfd9ead848
gmx_em was updated to 59c662ca4211
gmx_em was updated to 715cd0e87781
gmx_energy was updated to 58c3e6711e94
gmx_energy was updated to fdf2cc80adb5
gmx_makendx was updated to 358747bce4fd
gmx_merge_topology_files was updated to 3cf3b3b305ea
gmx_restraints was updated to 14a7bf3e03df
gmx_restraints was updated to 9dde06738154
gmx_rg was updated to f360f62ac4c4
gmx_setup was updated to 1d4dd4f908d4
gmx_setup was updated to ed736e6eee39
gmx_sim was updated to d1f803b5943c
gmx_solvate was updated to 7568ae18908a
gmx_trj was updated to 16fad30d566a
gmx_trj was updated to 240834a8b602
mmpbsa_mmgbsa was updated to 12caa50c0d5f
traj_selections_and_merge was updated to a26c4750c7c7

RNA Analysis

chira_collapse was updated to 05996586c8b3
chira_extract was updated to 73d2b7a8d94b
chira_map was updated to 7925dd016f53
chira_merge was updated to 9930af9d17f8
chira_quantify was updated to 38d2b1f38992
dexseq was updated to 2872c633f07e
edger was updated to df0c8d0a5992
edger was updated to f2843df56434
genomic_super_signature was updated to d0cbe6cc1f04
limma_voom was updated to 32511f586472
limma_voom was updated to e827f9aae031
seurat was updated to bb9732cfcdbe
trinity was updated to d2bc35f3d1c5
trinity_abundance_estimates_to_matrix was updated to 2e21a7c28b38
trinity_abundance_estimates_to_matrix was updated to bcc5f03f1900
trinity_align_and_estimate_abundance was updated to 00719b8004c9
trinity_align_and_estimate_abundance was updated to c2b82a94493e
trinity_contig_exn50_statistic was updated to 34840e9c79b0
trinity_contig_exn50_statistic was updated to be3f26533209
trinity_filter_low_expr_transcripts was updated to 1007cdb58d91
trinity_filter_low_expr_transcripts was updated to 1fdb25a8384d
trinity_run_de_analysis was updated to 3bff7c3cf63c
trinity_run_de_analysis was updated to eafea3083352
trinity_super_transcripts was updated to 18a069ea4b96
trinity_super_transcripts was updated to bdede464821e
trinotate was updated to 2b093007fab9

Epigenetics

bwameth was updated to 62f5fab76dfb

Proteomics

maxquant_mqpar was updated to 2d67fb758956
maxquant_mqpar was updated to 9cb7dcc07dae
metaquantome_sample was updated to c1343e3389ca
openms_openpepxl was updated to 40cc19c0dbd6
openms_openpepxl was updated to a2a842b00f9c
openms_openpepxl was updated to fc36cfd19834
openms_percolatoradapter was updated to 0fc9ae55bcfc
openms_percolatoradapter was updated to e7881a82b56d
openms_xfdr was updated to 4fdeb75928ea
openms_xfdr was updated to 81402a5e4173
openms_xfdr was updated to 9a6e3bb0f358
pepquery was updated to 962599ac5406
peptideshaker was updated to a6ff76e057fd
proteinortho was updated to 9b99159b2b23
proteinortho_grab_proteins was updated to 6eec1c6410fe
proteinortho_grab_proteins was updated to d5e4450964f8
proteinortho_summary was updated to 1883d2bffd14

Assembly

abyss was updated to 890b794c997d
minia was updated to 734cd5f1c1b2
novoplasty was updated to 15200570e926
quast was updated to 7594365c546b
raven was updated to f11b994b7eb2
trycycler_cluster was updated to 189e837009c9
trycycler_cluster was updated to 505a9833ab5d
trycycler_consensus was updated to 43af166bc01e
trycycler_consensus was updated to 9ded6109434a
trycycler_partition was updated to b23249f81bc4
trycycler_reconcile_msa was updated to 59bd28f6265d
trycycler_subsample was updated to 05bd7504fdb2

hca_sc_scanpy_tools

anndata_ops was updated to 890fb06a2893

Imaging

points_association_nn was updated to fd4293bee0dc
spot_detection_2d was updated to d78372040976
idr_download_by_ids was updated to 4aed70472589

Metagenomic Analysis

data_manager_build_bracken_database was updated to 3c7d2c84cb09
data_manager_build_bracken_database was updated to fd5830f88314
last was updated to 19c265784f35
megan_blast2lca was updated to a80281b0172e
megan_blast2rma was updated to d326b943f5e2
megan_sam2rma was updated to 4f0a8e401e2e

Annotation

repeatmodeler was updated to 41bfbaf3c959
funannotate_annotate was updated to 14f588312c56
funannotate_clean was updated to a230ea445788
funannotate_compare was updated to 563a19373357
funannotate_predict was updated to 2bba2ff070d9
funannotate_sort was updated to b3cf4684e9c7
gff_to_prot was updated to 07d7991bf205
gff_to_prot was updated to 79261884facd
homer_annotatepeaks was updated to 35dc2f57d755
homer_findmotifsgenome was updated to a8f207b43f64
homer_gtf_to_annotations was updated to 396cf2c12173
homer_scanmotifgenomewide was updated to db456c398880
orthofinder_onlygroups was updated to 3b974afde673
progressivemauve was updated to ce795616bd9c
transit_gumbel was updated to 8fc50fe60127
transit_resampling was updated to 885459e1c83b
transit_tn5gaps was updated to 3f5fc4b09496

Nanopore

flair_collapse was updated to 1fdcbfcca71c

Single-cell

raceid_clustering was updated to c4f39bf4a068
raceid_clustering was updated to f911a64454fb
raceid_filtnormconf was updated to c891d8b33ede
raceid_filtnormconf was updated to d45f092caf24
raceid_inspectclusters was updated to 2b0d3e2f402a
raceid_inspectclusters was updated to be4646256624
raceid_inspecttrajectory was updated to 3478133d0f6f
raceid_inspecttrajectory was updated to df8e4e54d367
raceid_trajectory was updated to c92d0f9338c5
raceid_trajectory was updated to e93b008c637a

Variant Calling

freebayes was updated to 04fa42777df9
freebayes was updated to 57def2d7c093
vcfcheck was updated to 2968c6916579
vcfcheck was updated to aa8e8c96ca06
artic_guppyplex was updated to 5ceeb5a5d70f
artic_guppyplex was updated to 7a82006f7c05
artic_minion was updated to 7a7d7f30ddfc
artic_minion was updated to f212134e204c
bbtools_callvariants was updated to b955346ef41e
delly_call was updated to 6f383714149d
delly_classify was updated to d31211a43b19
delly_cnv was updated to 56781a718729
delly_filter was updated to d2590fe6793f
delly_lr was updated to d30785dbe6b7
delly_merge was updated to 1efb2b927957
plink was updated to 16d22eee0fe3
plink was updated to 272aca44b3dd
seqwish was updated to 36dc42da5687
varscan_copynumber was updated to 0bc56f894766
varscan_copynumber was updated to 9f8dbbbc0267
varscan_mpileup was updated to 45288fb1f3f5
varscan_somatic was updated to a57606054bd7
varscan_somatic was updated to cf8ffc79db67
vcfanno was updated to cdcaa40e5e45

Evolution

codeml was updated to f9cb3a4339c2
iqtree was updated to 563c3aa769f2
iqtree was updated to 9b892d7f82cc

Convert Formats

crossmap_bam was updated to e13f565068d6
genebed_maf_to_fasta was updated to 020c78e91cc5
genebed_maf_to_fasta was updated to e25ee6bac872

FASTA/FASTQ

fastx_clipper was updated to b8658f852bc7
fastx_clipper was updated to cb1e251cac37
fasta_stats was updated to 16f1f3e2de42
fasta_stats was updated to cd0874854f51
cutadapt was updated to c053d4cad713

Motif Tools

meme_chip was updated to 091a9d638d78
meme_chip was updated to cc100e0f61f4

Multiple Alignments

mummer_delta_filter was updated to fbca557a4847
mummer_dnadiff was updated to c9685bc0407c
mummer_nucmer was updated to e18267f90096

Mapping

bbtools_bbmap was updated to e0ca2ec4f5d9
bioext_bealign was updated to 09dbbf5d3201
bioext_bealign was updated to a07a2d9ddd42
bwa_mem2 was updated to 88bcfaea2fb6
bwa_mem2 was updated to b4a22d90cce9
kma was updated to 95ab864b281a
minimap2 was updated to 11a0d50a54e6

Peak Calling

ccat was updated to 1a6979fbd544

SAM/BAM

bamtools was updated to befc9dad4ca8
bamtools_filter was updated to 1dfd95ee241e
samtools_calmd was updated to 92ec40abcdcf
samtools_mpileup was updated to 111f83918fe6
samtools_mpileup was updated to 329deb17a9f7
samtools_mpileup was updated to 9da0311ab1dd
bamtools_split_mapped was updated to 2ed961caae0a
bamtools_split_paired was updated to 75104ddce35f
bamtools_split_ref was updated to 09470ab960f1
bamtools_split_tag was updated to c9fbbe6f5fc8
samtools_coverage was updated to 90f2dd176d80
samtools_markdup was updated to 8c440c3002bc
samtools_merge was updated to b40e2d865d52
samtools_view was updated to 0dbf49c414ae

HiCExplorer

hicexplorer_hicfindrestrictionsites was updated to 8823a9d45ed0
hicexplorer_hicfindrestrictionsites was updated to 9369e9b11b8d

Phylogenetics

hyphy_absrel was updated to 3f59ebfbfe3d
hyphy_annotate was updated to 0cd45491b297
hyphy_annotate was updated to fa913c2975da
hyphy_busted was updated to d09dd951d0c4
hyphy_cfel was updated to 0990351232c6
hyphy_cfel was updated to fcabcc150d21
hyphy_fel was updated to 09afc9104fc8
hyphy_fel was updated to fc50c4bac0a3
hyphy_slac was updated to 0c6724c345d9
hyphy_slac was updated to 54a5bb259ba2
hyphy_strike_ambigs was updated to 4bf743518e41
hyphy_strike_ambigs was updated to dc8875a13914
nextalign was updated to 1c785a6b4d90
nextalign was updated to 4771f8bc8fa4
nextclade was updated to 51f5e7505c4b
nextclade was updated to d34df92e598f
pangolin was updated to 36912871ccdc
pangolin was updated to ca0d8cf80567
usher was updated to 524cb8f7a69a
usher was updated to 8f6c7638eab2
usher_matutils was updated to 52fd1d491417

None

data_manager_genomic_super_signature_ravmodels was updated to b5bca6d58e4c
data_manager_humann_database_downloader was updated to 87febc68b45b

Apollo

apollo_create_account was updated to 0929c15c3d70
apollo_create_or_update was updated to 9e7b8c7185ad
apollo_delete_features was updated to 02404029ae4c
apollo_delete_organism was updated to 3b4fe78bbe83
apollo_export was updated to c3251541cf2b
apollo_feat_from_gff3 was updated to 12ebb583b8a3
apollo_fetch_jbrowse was updated to 654af4ba76bc
apollo_iframe was updated to 29159d9ce6f0
apollo_list_organism was updated to 78abc724d792