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smithlabcode / falco

A C++ drop-in replacement of FastQC to assess the quality of sequence read data
https://falco.readthedocs.io
GNU General Public License v3.0
98 stars 11 forks source link

Package adapters and other default files with bioconda #31

Closed schorlton closed 2 years ago

schorlton commented 2 years ago

Hi, thanks for the great tool!

Is it still the case that the adapter_list.txt and potentially the other default configuration files are not shipped with the bioconda package? https://github.com/smithlabcode/falco/issues/16 and https://github.com/smithlabcode/falco/releases/tag/v0.3.0

I could not find them when I tried a simple find. Is there a reason for this? If not, perhaps they should be shipped with bioconda and falco should default to using them, similar to how FastQC functions? Thanks for your consideration!

guilhermesena1 commented 2 years ago

Hey.

Thank you for reaching out about this. The fix I found for this problem was not really a fix. What we did is to have the default information of the files built into the program and ship it to conda without them. We will be drafting a new release in the coming weeks given the recent issues that arose, and I will tyr to find the proper syntax in autotools so the program knows where it is installed on Conda and knows the absolute path for these files at compile time.

In the meantime, the super dirty solution would be as follows:

(1) under the bin directory on conda, rename falco to falco-tmp (2) place your default adapters/contaminants/limits files anywhere on conda (3) under the conda bin directory, create a file called falco with the following:

/path/to/conda/bin/falco-tmp -c /path/to/your/contaminant_list.txt -l /path/to/your/limits.txt -a /path/to/your/adapter_list.txt $*;

(4) make this file executable with chmod +x /path/to/conda/bin/falco

now you can run falco any-file.fastq and add any other user flags you might need :)

Again I'm sorry for proposing this trick, it shouldn't be on the user to have to sort these things out. We'll find a more elegant solution on the next release.

schorlton commented 2 years ago

Thanks for your response! I think I'll wait for the next release so I can use falco as a drop-in replacement for FastQC...thanks!

guilhermesena1 commented 2 years ago

Better (very) late than never, I just created a falco-1.2.0 release, and when updating Conda I replicated FastQC's approach of adding the default files to opt/falco-1.2.0/Configuration, so now you can use them as a template to run falco :)

schorlton commented 2 years ago

Thank you!! :tada: