Request: install multiple tools for a MAGs WF to ORG

[SantaMcCloud]

Hello i got ask to open this request to install multiple tools at ORG.

We need the followed tools install here:

• SemiBin: https://toolshed.g2.bx.psu.edu/view/iuc/semibin/b5a7583b8db0
• CONCOCT Tools:
  • https://toolshed.g2.bx.psu.edu/view/iuc/concoct/eae7ee167917
  • https://toolshed.g2.bx.psu.edu/view/iuc/concoct_coverage_table/fd31cd168efc
  • https://toolshed.g2.bx.psu.edu/view/iuc/concoct_cut_up_fasta/4d8bc5dd9e95
  • https://toolshed.g2.bx.psu.edu/view/iuc/concoct_extract_fasta_bins/8b1b09fcd8b7
  • https://toolshed.g2.bx.psu.edu/view/iuc/concoct_merge_cut_up_clustering/20ccec4a2c38
• convert genoms bins in fasta format: https://toolshed.g2.bx.psu.edu/view/iuc/fasta_to_contig2bin/fb2bed0eb02f
• Binette: https://toolshed.g2.bx.psu.edu/view/iuc/binette/1d97ddbc3464
• dRep dereplicate: https://toolshed.g2.bx.psu.edu/view/iuc/drep_dereplicate/d730086e1432
• coverM genome: https://toolshed.g2.bx.psu.edu/view/iuc/coverm_genome/73b667038f46

If hope this are all informations which should be needed to add them to ORG!

[mvdbeek]

If you have the workflow that would be a lot quicker for us.

[SantaMcCloud]

https://usegalaxy.eu/u/paulzierep/w/imported-mags-individual-workflow-v20 should be this WF @paulzierep should double check if this is the correct one.

[paulzierep]

@SantaMcCloud can you make a PR to add the tools, I think all tools should fit here: usegalaxy.org/metagenomic_analysis.yml

[mvdbeek]

This is not necessary, tools for merged workflows are automatically installed after the merge. But also I can do this based on the workflow (that's why I asked).

[mvdbeek]

#959 -- you can run a script to do that, python scripts/get_iwc_tools.py -w /tmp/workflows -s usegalaxy.org -u uncategorized.yml, where /tmp/workflows is some folder with workflows for which you need tools.

[paulzierep]

Ah cool, good to know !