cannot get this to work

[herber4]

Hello,

I have been unable to successfully download and run vcfkit and have exhausted all options. I have tried the various install methods and even tried changing the primer3.py script to include the path to the primer3_config but I keep getting the same result: Cannot find thermo path '/primer3_config/

Neither vcfkit nor primer3 is being installed with a primer3_config that is unless I just clone the entire repositories. which still didn't solve the : Cannot find thermo path '/primer3_config/ issue.

Any help?

[SilenWang]

Hello,

I have been unable to successfully download and run vcfkit and have exhausted all options. I have tried the various install methods and even tried changing the primer3.py script to include the path to the primer3_config but I keep getting the same result: Cannot find thermo path '/primer3_config/

Neither vcfkit nor primer3 is being installed with a primer3_config that is unless I just clone the entire repositories. which still didn't solve the : Cannot find thermo path '/primer3_config/ issue.

Any help?

My vcfkit was installed using conda, and I create the following folder to solve the same issue: /PATH/TO/CONDA/ENV/lib/python3.7/site-packages/vcfkit/static/primer3_config/

However, after solve this, I still can't get right primer result. The script can run without error, but I got noting in the output.

[hans-vg]

Same problem. I installed primer3 through brew, ran vcfkit as the following: vk primer sanger --ref=genome.fa test.vcf.gz

I get no error and no output too.

[danielecook]

Hello @hans-vg @SilenWang @herber4

Have you tried to run VCF-kit using docker?

docker run -it andersenlab/vcf-kit vk primer

Unfortunately I am not always able to keep up with the changing dependencies that can break installation, but the docker image is static and should work for you.

Please try to use the Docker image and let me know if you run into any problems.

[ddenney1]

Hello @danielecook

I have had the same problem as the others and fixed it using the same steps they outlined. The conda environment is still running VCF-kit 0.2.6 whereas the newest version is 0.2.9. Perhaps that could be part of the issue with conda?

I tried running the docker environment as you mentioned but it seems there's an issue with the image and its dependencies. With each option following vk, it threw an error that the modules could not be found (docopt, etc.) I tried installing each of these in the Docker environment but then was met with an error that it could not find the vcfkit module.

[Rohit-Satyam]

The following command worked for me:

mamba create -n vcf-kit   danielecook::vcf-kit=0.2.6   bwa==0.7.17   samtools==1.10   bcftools==1.10   blast==2.2.31   muscle==3.8.31   primer3==2.5.0