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Question: Galaxy in Ubuntu14 can't find directory
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gravatar for sundaochun
3.3 years ago by
sundaochun • 0
United States
sundaochun • 0 wrote:

I just intall the Galaxy on my Ubuntu 14 and install tools from tool sheds successfully.  However, when I try to excute any analysis, the Galaxy always report error like below. I think probably the PATH configuration is not correct. Can anyone help me on this? Thanks!

Fatal error: Exit code 1 ()
Can't exec "java": No such file or directory at /home/sdcwin/galaxy/dependency_dir/FastQC/0.11.2/devteam/package_fastqc_0_11_2/4b65f6e39cb0/fastqc line 257.

 

Fatal error: Exit code 2 ()
python: can't open file '/home/sdcwin/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/2d094334f61e/fastqc/rgFastQC.py': [Errno 2] No such file or directory

 

/home/sdcwin/galaxy/database/job_working_directory/000/16/galaxy_16.sh: 21: /home/sdcwin/galaxy/database/job_working_directory/000/16/galaxy_16.sh: fastq_quality_boxplot_graph.sh: not found
galaxy • 1.1k views
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modified 3.3 years ago by wrf • 0 • written 3.3 years ago by sundaochun • 0
0
gravatar for wrf
3.3 years ago by
wrf • 0
Germany
wrf • 0 wrote:

for Galaxy all processes are called/run as user "galaxy", so perhaps that user needs to be added to the group "users" or whoever is the owner of the programs.
ADD COMMENT • link written 3.3 years ago by wrf • 0

Thank you for your reply.  I figured out and it is because java environment is not set up well on my Ubuntu. I have to install it manually on Ubuntu 14.03.

 

ADD REPLY • link written 3.3 years ago by sundaochun • 0
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