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SRA tool kit

hi everybody; I installed SRA toolkit last day but when I want to use prefetch this message appears:

This SRA tool kit installation has not been configured what's the problem??

rna-seq next-gen prefetch
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updated by GenoMax GenoMax • written by mo.ghasemi717 • mo.ghasemi717

Can you change this to a question?

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written by Medhat Medhat

yeah I only can use prefetch in the SRA tool kit directory. but I want to use it anywhere else. for example in the home directory. last day I put prefetch in the path by this command: cp prefetch /usr/local /bin but I can't use it from other directories and when I want to use it this message appears: SRA tool kit installation has not been configured.

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written by mo.ghasemi717 • mo.ghasemi717

1 answer

See the section on Configuring the toolkit on this page.

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written by GenoMax GenoMax

I saw it before but I can't understand it, could you please help me?

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written by mo.ghasemi717 • mo.ghasemi717

If you install it with conda you won't have to configure anything

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written by jordi.planells jordi.planells

You need to set a temp directory where prefetch can download/store data. Directions are clear on the page I linked. You need to run ./vdb-config -i from within the bin directory. You should then see the text GUI. Change between different options using tab key. Minimally you should just need to run the config program, tab over to Exit button (pressing 7 may do the same) and then save when you exit.

If you find this complicated then install a new copy of sratoolkit using conda as noted by @jordi.

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written by GenoMax GenoMax

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