Installation: Tax4Fun2 package are not found and github repository is not maintained anymore

Question

[Elsa]

Hi everyone!

I have tried to find the R package Tax4Fun2 from the paper (https://pubmed.ncbi.nlm.nih.gov/33902725/) . This R package lets analizes the microbiome in an easy way to predict functional profiles from metagenomic 16S rRNA data.

However, I have not found the package in R CRAN packages, neither in the github refered in the original paper (https://github.com/bwemheu/Tax4Fun2) or the Tax4Fun page (http://tax4fun.gobics.de/).

I am looking for Tax4Fun2 because gives higher accuracies than PICRUSt and Tax4Fun.

Any help will be grateful!

Best,

E

[andres.firrincieli]

Tax4Fun2 because gives higher accuracies than PICRUSt

They tested Tax4Fun2 (2020) against PICRUSTt version 1, which is very old (2013). In this paper on the other hand, Tax4Fun2 actually performs worse than PICRUSt2

[safeassli]

Hello , I also have the same problem. Did you find repositories for installing T4F2 and T4F please ? if not what did you use as an alternative and are you satisfied with the results of the alternative tool ? please answer !!

[Mai Abdelmonem]

please I am trying to install and use Tax4fun2. but do you have the SILVA_132_SSURef_NR90.fasta file? I attempted to locate it in the Silva Database, but I couldn't find it.

https://www.arb-silva.de/no_cache/download/archive/release_132/ARB_files/

Tax4Fun2 requires the SILVA_132_SSURef_NR90.fasta file specifically... Thank you so much

[Mensur Dlakic]

You just need to look through other directories. This file is the closest to what you want:

https://www.arb-silva.de/fileadmin/silva_databases/release_132/Exports/SILVA_132_SSURef_Nr99_tax_silva.fasta.gz

After unpacking, you can either rename the file to SILVA_132_SSURef_NR90.fasta or change the code to use the file you have.

[Mai Abdelmonem]

Thank you so much. I downloaded it and renamed it, now I need to download and install prodigal_v2.6.3

Thank so much

[Mai Abdelmonem]

I have downloaded it from here: https://mirrors.opensource.is/ubuntu/pool/universe/p/prodigal/

prodigal_2.6.3.orig.tar.gz

but there is no file named: prodigal.macos

[Mai Abdelmonem]

assignFunction(genome_file = "OneProkaryoticGenome.fasta", 
               file_extension = "fasta", 
               path_to_reference_data = "Tax4Fun2_ReferenceData_v2", 
               num_of_threads = 1, fast = TRUE)

chmod: Tax4Fun2_ReferenceData_v2/TOOLS/prodigal_v2.6.3/prodigal.macos: No such file or directory
chmod: Tax4Fun2_ReferenceData_v2/TOOLS/diamond_v0.9.24/diamond.macos: No such file or directory

Error in system(command = paste(path_to_diamond, "help"), intern = T,  : 
  error in running command

what should i do? I have Tax4Fun2_ReferenceData_v2/TOOLS/prodigal_v2.6.3/prodigal.macos (renamed it prodigal), Tax4Fun2_ReferenceData_v2/TOOLS/diamond_v0.9.24/diamond.macos (renamed it: diamond)

[GenoMax]

Mai Abdelmonem : Stop posting errors and comments as new answers. Submit answer is only for new answers to the original question.

[Mai Abdelmonem]

Okay, I see. Sorry for that

Answer 1

[Mensur Dlakic]

I searched GitHub for Tax4Fun2 and found this:

https://github.com/ZihaoShu/Tax4Fun2

[djeppschmidt]

This is a repository for a project that uses tax4fun2, not the repository that documents T4F and provides it for download/installation. All repositories for installing T4F2 and T4F seem to have been removed from the internet in the last few months.

[safeassli]

Hello , I also have the same problem. Did you find repositories for installing T4F2 and T4F please ? if not what did you use as an alternative and are you satisfied with the results of the alternative tool ? please answer !!

[zx8754]

https://github.com/ZihaoShu/Tax4Fun2 has tar file Tax4Fun2_1.1.5.tar.gz, download and install from source.

install.packages("Tax4Fun2_1.1.5.tar.gz", repos = NULL, type = "source")

Answer 2

[Viviane]

Hello! I was confused as well.

When installing Tax4Fun2, Follow this: https://github.com/songweizhi/Tax4Fun2_short_tutorial?search=1