tradis_merge_plots cannot find tradisfind

[cerebis]

When using the Docker image within Singularity, invoking tradis_merge_plots produces the error:

sh: 1: tradisfind: not found

This is not surprising as I cannot find an instance of tradisfind within the Bio-Tradis repository.

Is it possible that this tool was mistakenly left behind within your dev/execution environment?

[cerebis]

Looking further, it appears these scripts are also relying on LSF calls (bsub)-- so I suspect not really intended for public consumption.

[lbarquist]

Yeah, this wasn't part of the original distribution and looks like it's been added for internal use at Sanger where sequencing might be split up across multiple lanes/runs. If you need this functionality, the script looks like it could be modified pretty easily -- or cat-ing together the fastq files would probably work just as well. This script isn't really needed to just run a TraDIS analysis.

[cerebis]

Ok thanks for the info. I did end up merging the separate plot files in pandas through summmation at each coordinate. I suspect I could have done this at an earlier stage and avoided a bit of scripting. Regards Matt DeMaere

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On Sun, 27 Aug 2023 at 5:31 am, lbarquist ***@***.***> wrote: Yeah, this wasn't part of the original distribution and looks like it's been added for internal use at Sanger where sequencing might be split up across multiple lanes/runs. If you need this functionality, the script looks like it could be modified pretty easily -- or cat-ing together the fastq files would probably work just as well. This script isn't really needed to just run a TraDIS analysis. — Reply to this email directly, view it on GitHub <#133 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABN2PCY4RH4ESSAOJ5PCVRTXXJFJBANCNFSM6AAAAAA35YK6V4> . You are receiving this because you authored the thread.Message ID: ***@***.***>