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SRA Tools
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vdb-config failed #579

Closed mlathara closed 2 years ago

mlathara commented 2 years ago

I'm trying to follow the basic guide here to install the SRA toolkit. I'm trying to install on a headless Centos 7 server (maybe that's the problem...? Though I've tried to x2go as well without success)

I tried both the yum install route and the tarball and with both options, I get hung up when trying to run vdb-config

$ vdb-config -i -vvvvvv
failed

Any pointers? A quick perusal of the issues/wiki seems to suggest that there is no way to non-interactively configure. I should also mention that running vdb-config with no options does spit out some sort of xml config.

mlathara commented 2 years ago

I had an older version of the toolkit installed on a different Centos server in my cluster (sratoolkit.2.9.6-1), and that seemed to still work.

I went back to that, not really sure why more recent version isn't working 🤷 I'll leave it to the repository maintainers if they want to close the issue or not.

durbrow commented 2 years ago

vdb-config -i needs a tty that supports a multiline display and ANSI formatting code. Your headless system probably does not.

One way to get around this is, you run vdb-config somewhere else and copy the file it creates. This file is ${HOME}/.ncbi/user-settings.mkfg, and the SRA toolkit expects to find this file by that name/path on whatever system it is currently running on.