custom_gtf: unbound variable error

[danielrebib]

Hello,

Thank you for such a great publication/tool. I am attempting to run the riboseq pipeline, and am encountering issues stemming from the check_annotation() function in the general_functions.sh script. It does seem that indeed custom_gtf isn't created anywhere before or in the config file. Is there something I am doing incorrectly?

Apologies if my question is a bit silly, I do not have vast coding experience! Thank you.

[damhof]

Hi,

Thanks! Apologies for the oversight, this is still a remnant of an older version - I'll fix this soon. In the meantime, locally you could try changing the following lines in the general_functions.sh script:

# Check to see whether custom GTF / Rannot was provided
    if [[ -f ${custom_gtf} ]]; then
        export gtf=${custom_gtf}
    else
        export gtf=${reference_gtf}
    fi

to export gtf=${reference_gtf}

Let me know if this works for you.

[danielrebib]

Thank you! This works well. For what it's worth, I've run into a few other bugs that prevented me for running. In the future, I'll push my branch with the changes I’ll encounter (still working on getting it to run) to be more organized. The bugs were:

In general_functions.sh, line 48 should be for r1_filename in "${r1_filenames[@]}"; do

Additionally, I think the script expects filenames to be in the format you received them from sequencing “ID_R1_001.fastq.gz”, but when I publicly access your data the IDs are in SRR# format. This was easily fixed, though, with a symbolic link.

Again, thank you for publishing your work and code!