Installation with and without Docker: A Nightmarish Experience

[Sandyyy123]

Issues with echolocatoR Installation and Dependencies

I was initially impressed by the numerous packages offered here, aimed at making life easier for bioinformaticians. However, the utility of these packages diminishes when the Docker image cannot function properly.

Wasted whole day trying to install.

Description:
I have encountered numerous challenges while trying to install and use the echolocatoR package. Despite following the installation instructions, I've faced continuous dependency issues, particularly with PolyFun and PANTOR. Below are the steps I've taken and the errors encountered:
Installation Steps:

Initial Installation:

remotes::install_github("RajLabMSSM/echolocatoR")
library(echolocatoR)

Dependency Issues:

During the installation process, I was prompted for multiple dependencies in both R and my Linux environment.

Attempted Functionality:

I tried to run echolocatoR::finemap_loci without PolyFun and PANTOR but received the following error:

Explicit format: 'vcf'
Querying VCF tabix file.
Querying VCF file using: VariantAnnotation
Checking query chromosome style is correct.
Chromosome format: 1
Filtering query to 503 samples and returning ScanVcfParam object.
Retrieving data.
[E::bgzf_read_block] Invalid BGZF header at offset 249638006

Docker Installation:

I decided to try the Docker approach, hoping for a more controlled environment. Unfortunately, I encountered the same dependency issues and package updates, ultimately leading to the following error:

[E::hts_itr_next] Failed to seek to offset 16825466131484: Illegal seek

Feedback:

Package Management: Clearer documentation on dependencies and any known installation issues would be beneficial.

Error Handling: More informative error messages or checks for data integrity could help users diagnose problems more efficiently.

Docker Image: If the Docker container is intended to provide an isolated environment, thorough testing is essential to ensure that all necessary dependencies are included.

Conclusion:

I appreciate the effort that has gone into developing echolocatoR, but the current installation experience has been quite challenging. I hope my feedback can help improve the package for future users.