Error starting the FLAMES pipeline

[vasikara17]

Hello, thank you for the nice tool!! I would like to ask you if I am missing something for the starting of the pipeline. I have minimap2 tool in my miniconda folder installed and there is also the K8 but I think that FLAMES cannot find the path. Is there a way to give the absolute path to the function? Best regards, Vasiliki

**10:02:51 AM Wed Jun 12 2024 minimap2_alignError in if (file_test("-f", file.path(minimap2_dir, "k8")) && file_test("-f", :

missing value where TRUE/FALSE needed

In addition: Warning messages:

1: In base::system2(command = "command", args = c("-v", "minimap2")) :

error in running command

2: In base::system2(command = "command", args = c("-v", "minimap2")) :

error in running command

3: In base::system2(command = "command", args = c("-v", "samtools")) :

error in running command**

[vasikara17]

Thank you very much I found out the issue!!

[rb520826]

Hi Vasiliki, how did you solve the issue please? Thanks!

[vasikara17]

Hello, I actually solve it partially! the minimap2 path is now ok however I have the same error coming after with samtools! Best, Vasiliki

In base::system2(command = "command", args = c("-v", "samtools")) : error in running command**

[ChangqingW]

I added the minimap2 and k8 arguments to sc_long_pipeline the user can provide the paths to them if it is not available in $PATH. Should probably do it for samtools as well -- I thought I had it use Rsamtools when samtools is not available, apparently that did not work.

[vasikara17]

Hello, I have still the samtools error. I have tried to give the path for samtools like for minimap2 but it did not work. Is there any temporary solution to this?

Thanks in advance!

[vasikara17]

Hello, any updates on the issue?

[ChangqingW]

I'll add another argument for samtools path. You should be able to get around this by adding samtools to your $PATH environment variable though

[ChangqingW]

Let me know if it still errors after https://github.com/mritchielab/FLAMES/commit/d4727af4138ccc014d0a13f5b9ea91d1083016db