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  • problems with installation FastQC

    when I finished installation of FastQC, then applied fastqc --help, it worked well.
    but when run it, it was said "can't exec "java".
    I'm using my university's super comperter, so I think java is already installed.
    what can I do next?

  • #2
    Can you post the exact error message?

    And the output of

    Code:
    $ which java
    $ java -version

    Comment


    • #3
      Originally posted by GenoMax View Post
      Can you post the exact error message?

      And the output of

      Code:
      $ which java
      $ java -version
      $ fastqc -v
      Can't exec "java": No such file or directory at /N/u/daih/Karst/FastQC/fastqc line 266.

      then the output:
      $ which java
      /usr/bin/which: no java in (/N/soft/rhel6/perl/5.16.2/bin:/N/soft/rhel6/python/2.7.3/bin:/opt/moab/bin:/N/soft/rhel6/gcc/4.9.2/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/N/u/daih/Karst/FastQC/:/N/soft/rhel6/perl/5.16.2/bin:/N/soft/rhel6/python/2.7.3/bin:/opt/moab/bin:/N/soft/rhel6/gcc/4.9.2/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/N/u/daih/Karst/tophat-2.0.14.Linux_x86_64/:/N/u/daih/Karst/bin)

      $ java -v
      -bash: java: command not found

      Comment


      • #4
        You have no system-wide java installed. Looks like a RHEL 6 server so you should be able to get the java from java.com: https://www.java.com/en/download/hel...64_install.xml Look for the non-root install instructions to install in a directory you have write access to.

        Comment

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