Question

SRA tool kit

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5.3 years ago

mo.ghasemi717 ▴ 10

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 • 2.3k views

ADD COMMENT • link updated 5.3 years ago by GenoMax 154k • written 5.3 years ago by mo.ghasemi717 ▴ 10

score 3 · Accepted Answer · 2020-07-15

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5.3 years ago

GenoMax 154k

See the section on Configuring the toolkit on this page.

ADD COMMENT • link 5.3 years ago by GenoMax 154k

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

ADD REPLY • link 5.3 years ago by mo.ghasemi717 ▴ 10

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

ADD REPLY • link 5.3 years ago by jordi.planells ▴ 480

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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.

ADD REPLY • link 5.3 years ago by GenoMax 154k