entrez-direct and sra tools

[qabbalah]

May I ask what would be the reason to install entrez-driect and sra tools outside of the mamba env instead of installing it inside the env? Since both package are available through the bioconda channel. If I was to install it inside the env, would it have any appreciable difference?

[ialbert]

Neither tool is updated sufficiently frequently in bioconda, so you would end up with grossly outdated versions. I have tried myself to maintain these tools in bioconda but when the tool authors don't consider bioconda a priority it is much more difficult to do so. Since the tools have binary versions I went on the route of separate installs outside the env.

[qabbalah]

Thank you for letting me know. It seemed like entrez-direct and sra-tools are both recently updated last month on bioconda. The only other thing is that when i use mamba to install SRA-tools it would remove aria2. would not having aria2 impact how we fetch things from online

[ialbert]

I had a lot of back and forth with sra developers and I recall them flat out refusing to support deploying via bioconda - but it is possible that the policy changed.

with entrez-direct it does indeed look like the latest version is now available via bioconda - but as you can see with the bioconda search entrez-direct command most versions never made it into bioconda,

that being said it is great that it looks like both software are more up-to-date than before.

I'll keep watching the developments and as far as I am concerned I would be happy to be able to rely on bioconda, the installation would be much simpler