How can I update fastq-dump to 3.0.0?

Question

[gallardodiazmiriam]

Hello!

I'm trying to install the latest version of fastq dump, but all I could achieve is to install the 2.8.0, even though I used the code that is written on the Sra tools website (https://anaconda.org/bioconda/sra-tools). I want to install at least the 3.0.0 version. What can I do?

[barslmn]

Have you tried updating?

conda update sra-tools

[gallardodiazmiriam]

This worked! Thank you so much!

Answer 1

[Istvan Albert]

Get the official prebuilt binary version for your platform:

https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/

Unfortunately, in my experience, the conda versions often have various weird problems.

It is a catch-22 problem.

The sra-tools developers refuse to support conda and expect that the bioconda folks package the binaries.

The bioconda folks refuse to package binaries and want to compile from the source, but the code only compiles for bioconda if various shims and tiny code corrections are added. Alas, these latter can fail in various subtle ways leading to very hard-to-debug errors.

After a couple of years of installing with conda only to be fighting these errors, I found that it is much simpler to install the official binaries. No errors since.

Download the version you need, and put it in the $PATH.

Answer 2

[ATpoint]

I would make a fresh environment and try installing in that. This works for me:

mamba create --name sra-env
mamba activate sra-env
mamba install -c bioconda sra-tools=3.0.0