Snakemake/directsketch not able to find the global variable NCBI_API_KEY

[ccbaumler]

I have my NCBI_API_KEY in both my bashrc and bash_profile. gbsketch was not able to find the key unless I set it in the command with -a '$NCBI_API_KEY'

Error: please provide an API Key to use n_simultaneous_downloads > 3.

[bluegenes]

@ccbaumler I noticed this on farm as well - it doesn't always seem to get set properly. Can you run echo $NCBI_API_KEY when you run into this issue to see if it's actually set?

If it's not set properly (as happened for me), it's a farm issue and not a directsketch issue

[ccbaumler]

Echo returns the API key with the correct information.

I ran the command in both command line and snakemake. Both needed the -a flag to register the API key. Is that a farm thing?

[bluegenes]

hmm. I can't replicate this -- when I run, it is able to detect and use $NCBI_API_KEY automatically. @ctb is the variable detection working for you?

[ctb]

@ccbaumler what specific commands are you using in your bashrc? In particular do you have 'export' in front?

[ctb]

see https://superuser.com/questions/153371/what-does-export-do-in-bash - I did not actually know this, FWIW :)