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Old 05-04-2015, 01:56 PM   #1
shirley47162928
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Default 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?
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Old 05-04-2015, 04:12 PM   #2
GenoMax
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Can you post the exact error message?

And the output of

Code:
$ which java
$ java -version
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Old 05-04-2015, 04:57 PM   #3
shirley47162928
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Quote:
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
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Old 05-04-2015, 05:57 PM   #4
GenoMax
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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.
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