Question: Why can't I get gi2taxonomy to work as expected? -- Deprecated tool Fetch taxonomic representation (Galaxy Version 1.1.0)
gravatar for rleach
8 months ago by
rleach10 wrote:


We have "Fetch taxonomic representation (Galaxy Version 1.1.0)" installed on our galaxy installation. A user tried to use it to get taxonomic information on gis in a tab delimited file, but it produces an empty file with no errors. So I created a test file containing the GI shown in the tool's example output to test it out. It also produced an empty output file.

I ended up downloading the ncbi taxonomy database and wrote a few perl one-liners to compile the user's results for him. Turns out, every GI in his file is in fact in the taxonomy database, along with lineage.

So why doesn't the galaxy tool produce this output?

Here's the example I tried in my test:

1L_EYKX4VC01BXWX1_265   9606

The GIs column was set to 2 and the name column to 1. The output file was empty.

I could not find that GI in the tax database I downloaded, but one of the GIs from the user's file that was there was 504863860. The example file for that I made is:

90002   504863860

The expected output for that GI would be:

90002   504863860   root    Bacteria                Firmicutes          Clostridia          Thermoanaerobacterales          Thermoanaerobacteraceae             Thermacetogenium        Thermacetogenium phaeum

However, the tool produces an empty file for that as well...

ADD COMMENTlink modified 8 months ago by Jennifer Hillman Jackson25k • written 8 months ago by rleach10
gravatar for Jennifer Hillman Jackson
8 months ago by
United States
Jennifer Hillman Jackson25k wrote:


This tool (and the original Galaxy workflows that used it) have been deprecated in favor of more current tools and methods.

The latest Metagenomics tools are listed in the tool group Metagenomic Analysis at for review before installing locally. Try Kraken - the Main Tool Shed has the primary Kraken tools along with a data manager to build up the indexes:

Galaxy tutorials that cover Metagenomics:

All Galaxy tutorials:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 8 months ago by Jennifer Hillman Jackson25k

Update: Some work was in progress as recently as last December for an upgrade related to this tool's underlying functionality, but there are still some technical issues from what I can tell. If this is still the tool/function your users want to eventually use, you could ask about the most current status from the tool author at this ticket or one of those linked to it. The ticket also has details about the associated data manager/config/new tool name/id.

ADD REPLYlink written 8 months ago by Jennifer Hillman Jackson25k
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