STAR-fusion cannot execute STAR

[Daphne Guo]

Hello,

I recently submitted a test run of STAR-fusion, but found that the program, which I installed separately from STAR, apparently could not execute STAR and did not run at all. This line stood out to me:

Can't exec "STAR": No such file or directory at /home/dguo/local/STAR-Fusion_V0.7.0/PerlLib/Pipeliner.pm line 71.

This is confusing to me since I wouldn't necessarily expect STAR to be called in a perl module, and when I glanced over Pipeliner.pm briefly I did not see any obvious mention of calling STAR. Is there a way I can set the directory for STAR in a STAR-fusion PBS scripts, or is there something else I am missing?

Thanks!

[Brian Haas]

Hi,

You just need to have the latest version of STAR installed, and it must be available via your PATH setting. 

 eg.   

    which STAR

should return the full path to STAR

best,

~brian

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[Daphne Guo]

Thank you! I added the full path to STAR in the script, and it should work now.

Best,

Daphne

[huang...@gmail.com]

I met the same problem when running STAR-fusion (V1.4.0) with error report "cannot locate STAR program in the PATH setting at ./STAR-Fusion line 374". But It can be solved by using the "--STAR_PATH " to add STAR path. It is annoying to add the PATH every time when running STAR-fusion. How to add the PATH in the STAR fusion script? Thank you very much.

Bo

[Brian Haas]

Hi,

If the STAR software is installed somewhere that's in your PATH setting, then it should find it.  ie.  put STAR in /usr/local/bin

If you can't do that, just update your PATH setting to include where STAR is installed.

ie.

  export PATH = /path/to/dir/containing/STAR/software/bin:${PATH}

and then run STAR-Fusion

best,

~brian

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