Dear all, I'm trying to run the JBrowse tool within Galaxy. The installation was fine (I think), but when I run the tool, I get this error: Fatal error: Exit code 1 () Traceback (most recent call last): File "/d15/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/d022577ff9cf/jbrowse/jbrowse.py", line 11, in <module> from Bio.Data import CodonTable ImportError: No module named Does this mean I'm missing something? In the history, if I click the "(i)" icon for the incomplete job (in red), everything looks fine, except that it says: Tool Version: python: can't open file 'jbrowse.py': [Errno 2] No such file or directory However, "jbrowse.py" does exist in the path above. Any idea what could be wrong? Thank you! Ray
Hi Ray, Sorry I missed this mail. On 23. juni 2016 10:27, Raymond Wan wrote:
Dear all,
I'm trying to run the JBrowse tool within Galaxy. The installation was fine (I think), but when I run the tool, I get this error:
Fatal error: Exit code 1 () Traceback (most recent call last): File "/d15/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/d022577ff9cf/jbrowse/jbrowse.py", line 11, in <module> from Bio.Data import CodonTable ImportError: No module named This sounds like it means you're missing the biopython dependency.
You should check if it installed correctly in the admin interface.
Does this mean I'm missing something?
In the history, if I click the "(i)" icon for the incomplete job (in red), everything looks fine, except that it says:
Tool Version: python: can't open file 'jbrowse.py': [Errno 2] No such file or directory
The version command is misbehaving, safe to ignore.
However, "jbrowse.py" does exist in the path above. Any idea what could be wrong?
Thank you!
Ray ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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-- Eric Rasche Programmer II Center for Phage Technology Rm 312A, Biochemistry & Biophysics Texas A&M University College Station, TX 77843 esr@tamu.edu <mailto:esr@tamu.edu>
Hi Eric, On Wed, Aug 17, 2016 at 4:31 AM, Eric Rasche <esr@tamu.edu> wrote:
Hi Ray,
Sorry I missed this mail.
No problem! Thanks for getting back to me!
On 23. juni 2016 10:27, Raymond Wan wrote: I'm trying to run the JBrowse tool within Galaxy. The installation was fine (I think), but when I run the tool, I get this error:
Fatal error: Exit code 1 () Traceback (most recent call last): File "/d15/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/d022577ff9cf/jbrowse/jbrowse.py", line 11, in <module> from Bio.Data import CodonTable ImportError: No module named
This sounds like it means you're missing the biopython dependency.
You should check if it installed correctly in the admin interface.
I managed to solve this problem over the last few weeks. It seems soon after I sent my message (June 23rd), there was an update of the JBrowse tool (around late June)? So, after some persistence, it finally worked. I guess what I was wondering was whether asking the system administrator of the server to install biopython, etc. would solve my problem(s). But I guess not -- JBrowse and the rest of Galaxy seems to use a self-contained Python/biopython. Actually, several other tools got updated around that time and many of my problems (i.e., I had problems with other tools, including an earlier message I sent to the list about cummeRbund) all got solved. I'm sure everyone was busy late June (I didn't realize there was some kind of release scheduled for that?). Thank you again for getting back to me! Ray
participants (2)
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Eric Rasche -
Raymond Wan