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  • fznajar
    Member
    • Jan 2012
    • 35

    #1

    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
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142

    #2
    Break your search into smaller chunks. Make sure you are signed-up for and are using NCBI_API_KEY.

    Comment

    • fznajar
      Member
      • Jan 2012
      • 35

      #3
      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

      Comment

      • GenoMax
        Senior Member
        • Feb 2008
        • 7142

        #4
        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`.

        Comment

        • fznajar
          Member
          • Jan 2012
          • 35

          #5
          I get nothing back. It just keeps running until I interrupt it.

          Comment

          • GenoMax
            Senior Member
            • Feb 2008
            • 7142

            #6
            You likely have a broken install then. Is entrezdirect supported on cygwin? If you have Windows 10 then you should use WSL instead.

            Comment

            • fznajar
              Member
              • Jan 2012
              • 35

              #7
              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

              Comment

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