I need software to be installed

usegalaxy.eu support
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1

Hello, I am trying to use the following workflow

But I am lacking several software (

Please review the following issues, possibly resulting from tool upgrades or changes.
Step 10: galaxy-ntnu.bioinfo.no/toolshed_nels/repos/nuc/snpfinder/snpfinder/0.1.0

    • Tool is not installed
  • Step 11: galaxy-ntnu.bioinfo.no/toolshed_nels/repos/nuc/resistome_analyzer/resistome_analyzer/0.1.0
      • Tool is not installed
  • Step 12: galaxy-ntnu.bioinfo.no/toolshed_nels/repos/nuc/rarefaction_analyzer/rarefaction_analyzer/0.1.0
      • Tool is not installed

There is also an additional issue with bowtie that I need to fix.
Anyway, Im trying to use this workflow in a course, and would need these wrappers. Is it possible?

  • Step 6: Bowtie2
      • parameter ‘index’: an invalid option (‘susScr3’) was selected (valid options: Oryza_sativa_ssp._indica_9311_BGF_2005,Solanum_lycopersicum_ITAG_2.3,Elaeis_guineensis_EG5.1,Nelumbo_nucifera_LOTUS-DB_v1.1,Spirodela_polyrhiza_JGI_v2.0,hg19chrM,Arabidopsis_lyrata_JGI_v1.0,Oryza_brachyantha_Ensembl_Plants_v1.4b,Brassica_rapa_JGI_FPsc1.3,hg19,Arabidopsis_lyrata_JGI_v2.1,Carica_papaya_Hawaii_Agriculture_Research_Center,Corchorus_olitorius_GenBank_v1.0,Musa_acuminata_Genescope-Cirad,apiMel3,Hordeum_vulgare_Ensembl_Genomes_ASM32608v1,Musa_acuminata_Banana_Genome_v2.0,mm10_ERCC,Marchantia_polymorpha_JGI_v3.1,Medicago_truncatula_JGI_Mt4.0v1,Eucalyptus_grandis_JGI_v2.0,Zostera_marina_JGI_v2.2,mm9_ERCC,Oryza_sativa_ssp._indica_MBKBASE_v1.0,Ostreococcus_lucimarinus_JGI_v2.0_assembly_and_annotation,Arabidopsis_thaliana_COL-0_Araport11,Cicer_arietinum_LIS_v1.0,Brassica_rapa_Annotation_v1.2_on_assembly_v1.1_Phytozome_9.1,Solanum_lycopersicum_Sol_Genomics_itag2.4,Oropetium_thomaeum_JGI_v1.0,mm10,Oryza_sativa_ssp._japonica_JGI_v7.0,Micromonas_commoda_JGI_v3.0,Petunia_axillaris_Sol_Genomics_v1.6.2,mm9,Populus_trichocarpa_JGI_v3.1,equCab3,Beta_vulgaris_RefBeet_v1.2,GCF_016700215.2,Erythranthe_guttata_JGI_v2.0,Sorghum_bicolor_JGI_v3.1,sacCer3,Carica_papaya_JGI_ASGPB0.4,AaloF1,bosTau9,colLiv2.1,Solanum_tuberosum_ITAG_001,rn6,hg38,CHM13_T2T_v2.0,dm3,Selaginella_moellendorffii_JGI_v1.0,xenLae9.2,Phalaenopsis_equestris_Genomics_v1.0,Brachypodium_distachyon_JGI_v3.1,Beta_vulgaris_RefBeet_1.1,galGal6,GCF_019279795.1,Thellungiella_parvula_TpV84,Brassica_oleracea_Ensembl_Genomes_v2.1,Chlamydomonas_reinhardtii_JGI_v5.5,Malus_domestica_IASMA,GCF_001704415.2,rn5,Vigna_radiata_var._radiata_LIS_v6,Citrus_sinensis_JGI_v1_assembly_and_v1.0_annotation,Arachis_ipaensis_Peanut_Base_v1.0,Populus_trichocarpa_JGI_assembly_release_v3.0_annotation_v3.0,Pyrus_bretschneideri_Pear_Genome_Project_v1.0,Fragaria_vesca_JGI_v1.1,mm39,pp1.2b,Actinidia_chinensis_FEI_Lab_v1.0,Ricinus_communis_JCVI_1.0,Manihot_esculenta_JGI_v6.1,Brachypodium_distachyon_MIPS_1.2,Elaeis_guineensis_NCBI_Genome_v1.0,Medicago_truncatula_JCVI_4.0,Coffea_canephora_Coffee_Genome_Hub_v1,anoGam3,canFam6,Zea_mays_B73_AGP_v4.0,Solanum_tuberosum_JGI_v4.03,Zea_mays_PH207_v1.0,dm6,Citrus_clementina_JGI_v1.0,Phyllostachys_edulis_NCGR_v1.0,Vitis_vinifera_JGI_12xMarch2010,Glycine_max_JGI_Glyma1.1_annotation_of_the_chromosome-based_Glyma1_assembly,danRer11_wo_alt,danRer7,xenTro9.1,hg18,Capsella_rubella_JGI_annotation_v1.0_on_assembly_v1,Saccharum_spontaneum_v20190103,Sorghum_bicolor_JGI_1.4,Trifolium_pratense_JGI_v2,Schrenkiella_parvula_Thellungiella_v2.0_TpV84,Ostreococcus_lucimarinus_JGI_2.0,h7n7_360722,rn7,hg38full,Lotus_japonicus_Kazusa_2.5,CHM13_T2T_v1.0,Tarenaya_hassleriana_RefSeq_v1,Selaginella_moellendorffii_NCBIr100,od01,Gossypium_raimondii_JGI_annotation_v2.1_on_assembly_v2.0,Citrullus_lanatus_Cucurbit_Genomics_Database_v1.0,oviAri4,Glycine_max_JGI_Wm82.a2.v1,Theobroma_cacao_D._Gilbert_public_gene_set_8_Mar_2012_on_assembly_v1.1,Physcomitrella_patens_JGI_v3.3,NC_045512.2,Manihot_esculenta_Cassava4,Utricularia_gibba_CoGe_v4,Cajanus_cajan_Penguin_Genomics_v5.0,TAIR10,Theobroma_cacao_RefSeq_v1.1,ce11,Arabidopsis_thaliana_COL-0_TAIR10,susScr11,canFam3,Asparagus_officinalis_v1.1,Physcomitrella_patens_JGI_assembly_release_v1.1_and_COSMOSS_annotation_v1.6,Daucus_carota_JGI_v2.0,danRer11,Hevea_brasiliensis_NCBI_Genomes_v1,Chlamydomonas_reinhardtii_JGI_v5.0_assembly_annot_v5.3.1_based_on_Augustus_u11.6,hg38canon,Ananas_comosus_JGI_v3.0,SL4.0,danRer10,bosTau8,eschColi_K12,Gossypium_raimondii_JGI_v2.1,Capsella_rubella_JGI_v1.0,Setaria_italica_JGI_v2.2,Musa_acuminata_Banana_Genome_v1.0,Cucumis_melo_Melonomics_v3.5,Citrullus_lanatus_Cucurbit_Genomics_Database) Using default: ‘apiMel3’.
  • Step 10: galaxy-ntnu.bioinfo.no/toolshed_nels/repos/nuc/snpfinder/snpfinder/0.1.0
      • Tool is not installed
  • Step 11: galaxy-ntnu.bioinfo.no/toolshed_nels/repos/nuc/resistome_analyzer/resistome_analyzer/0.1.0
      • Tool is not installed
  • Step 12: galaxy-ntnu.bioinfo.no/toolshed_nels/repos/nuc/rarefaction_analyzer/rarefaction_analyzer/0.1.0
      • Tool is not installed
2

Hi @allarena

Was the workflow developed at a private server and now you want to publish it to work at a public server?

It looks like the missing tools are hosted at a private ToolShed, not where all tools are sourced for public Galaxy servers: https://toolshed.g2.bx.psu.edu/. Getting the tools in the public ToolShed seems like the first thing to do. Are you having trouble at that step?

Please describe with more details if those guesses are wrong. At least these two seem relevant for scope reasons:

  1. Where was the workflow sourced if from public workflow repository, or ??
  2. What is the target server to run this at? UseGalaxy.eu, or ??

Thanks!

3

Thank you for helping!
Ive never tried to put tools in public toolshed as they were available to me at usegalaxy.no. But I could try to do so.
Target server is usegalaxy.eu, and workflow sourced from usegalaxy.no

best regards,

AK

4

Ok, thanks for explaining. The resources (including tools) are distinct between public Galaxy servers. The usegalaxy.org, usegalaxy.eu, and usegalaxy.org.au servers will generally have the same resources. Others may be specialized, or at least for now.

Write into the administrators of the server you are working to develop the workflow UseGalaxy.no - Galaxy Community Hub and explain what you are trying to do. You can even include a link to this topic for reference. They can work with other server admins to sort out potential solutions. Only admins of a server can install tools, and not all tools are “ready” to be hosted at the larger servers (can be for technical or other reasons).

For now, working at the server where the workflow was developed is likely the best advice we can offer at this forum.