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Perl version control #25
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Hi @pooser Thank you for reporting! Quick question were bactopia and fastq-dl installed into the same Conda environment? Haha I also might need to look at the dependencies again, because its a little funny that Perl is causing issues with two mostly Python based tools! EDIT fastq-dl --- sra-tools brings in Perl |
Greetings @rpetit3 ! As per the no docker/singularity install instructions for Bactopia (yeah, yeah, I know...I'm a glutton for punishment, ha!) one should install Miniforge3 and then leverage its conda environment to then install Bactopia. I did exactly that and then realized I needed your nifty tool to download thousands of sequence data sets. To manage this environment, I utilized module files and my default was to have Miniforge3, Bactopia, and fastq-dl loaded simultaneously. Using fastq-dl to fetch the SRA data went fine however, once I pointed bactopia to the data, it crashed with With all three modules loaded I find Ergo, I concur that fasq-dl brings in perl while bactopia does not. This is not a big issue of course its just that as a total bactopia newb, I though others may have run into this as well. |
Ah, I see now haha you are a glutton for punishment. A few options here.
here are some links: https://bactopia.github.io/latest/tutorial/#multiple-samples Let me know if this helps, if not, please don't hesistate to let me know! haha we'll get this figured out |
Does bactopia have a built in mechanism to both search and retrieve the data whilst not executing the analysis? I am open to any suggestions you might have here. FWIW I am not a biologist/bioinformatician and am instead simply treating this an advanced data processing problem. |
Oh, this is very interesting. There isn't a mechanism to directly do this, but I imagine you could indirectly do it by setting |
The current version of Perl associated with fastq-dl is 5.22.0 which conflicts with the current version of Bactopia's (v3.0.0) Perl version which is 5.26.0. I ran into this conflict when loading Bactopia and fasq-dl as module files. Food for thought. TIA!
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