Fastqc 0.67 errors while Fastqc 0.64 does not

Question

[rjames]

When I run FastQC version 0.64 on a fastqsanger dataset I get results. However when I run FastQC version0.67 on the same dataset I get the following error:

Fatal error: Exit code 1 () /bin/sh: 1: fastqc: not found Traceback (most recent call last): File "/mnt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/3a458e268066/fastqc/rgFastQC.py", line 166, in <module> fastqc_runner.run_fastqc().

Why?

[GenoMax]

FastQC is currently in v.0.11.5? Where in the future did you get 0.67 from?

I assume this is some other software (in v. 0.67) calling FastQC internally? It seems that FastQC is not in $PATH. This appears to be a galaxy related error.

[rjames]

version 0.67 is the version number that Galaxy supplies. I assume this is up to date in that Galaxay was just installed on my computer 3 weeks ago.

[GenoMax]

Please use ADD REPLY/ADD COMMENT when responding to existing posts.

Do you have FastQC installed on your computer? You could try adding that directory to $PATH and re-starting galaxy.

You may also want to post this question to Galaxy biostars in case this is not enough.

[sasha.atmadjaja]

Just wondering whether you've managed to fix this issue, because I have the exact same problem and I'm stuck. Thanks!

[rjames]

I was no ever to fix the problem and so I just use the earlier version 0.67