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Old 08-22-2019, 11:58 AM   #1
fznajar
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Default esearch stuck

Hi,
I am using esearch (part of the edirect tools) and it seems that it gets stuck without feedback. I am using version 12.0
Any suggestions?
Thank you all
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Old 08-22-2019, 01:11 PM   #2
GenoMax
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Break your search into smaller chunks. Make sure you are signed-up for and are using NCBI_API_KEY.
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Old 08-22-2019, 01:25 PM   #3
fznajar
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I did not realize edirect needs a key at command line. As an example, I am using this command:
$ esearch -db pubmed -query "Roe B" | efetch -format docum

On different note, While setting up edirect on cygwin, the setup.sh complained about "too many arguments on line 85" before declaring "installation was successful".
I am not sure this is linked to my problem.

Thanks
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Old 08-22-2019, 01:34 PM   #4
GenoMax
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Do you get something back with just first part? An API key is only needed if you are going to run multiple entrezdirect commands over a period of time.

Code:
esearch -db pubmed -query "Roe B"
Second part has a typo. Option should be "docsum`.
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Old 08-22-2019, 01:40 PM   #5
fznajar
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I get nothing back. It just keeps running until I interrupt it.
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Old 08-22-2019, 01:43 PM   #6
GenoMax
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You likely have a broken install then. Is entrezdirect supported on cygwin? If you have Windows 10 then you should use WSL instead.
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Old 08-22-2019, 02:12 PM   #7
fznajar
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They mentioned to download "cygwin" for windows users. I am trying to find what other emulators I can use.
Thank you for your time Genomax
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