Installation error

[Yinping]

Hi,

I think I already installed PBJelly as described. But when I tried to run ./bin/Jelly.py, I got an error message like this:

Traceback (most recent call last):
File "./Jelly.py", line 15, in <module>
from pbsuite.jelly import Stages
ImportError: No module named pbsuite.jelly

Any suggestions? Thanks!

[Adam English]

Can you make sure that the SWEETPATH environment variable is set?

Also, be sure that you are sourcing the setup.sh before trying to run jelly, otherwise the correct paths won't be in your environment.

[Michael.W]

Hi,

I've just installed PBJelly 14.1.14 and I've got the same error
Traceback (most recent call last):
File "Jelly.py", line 15, in <module>
from pbsuite.jelly import Stages
ImportError: No module named pbsuite.jelly
The SWEETPATH is setup.sh was corrected for my folder where Jelly is and in home folder I have .bash_profile file with line:

source /home/michal/Documents/programs/Jelly_14.1.14/setup.sh

Any advice?

[Laura H.]

I'm having the same problem with 14.1.15. My SWEETPATH variable is correct, and both fakeQuals.py and sumAssembly.py run just fine, but when I run

Jelly.py setup JellyProtocol.xml

I get

Traceback (most recent call last):
File "/global/software/pbsuite/PBSuite_14.1.15/bin/Jelly.py", line 15, in <module>
from pbsuite.jelly import Stages
ImportError: No module named pbsuite.jelly

[jeff]

Any updates on this? echo'ing the env properly yields the PBsuite installation path. Do we need to point to the bin subdirectory, or the pbjelly subdirectory specifically within pbsuite? thanks

[jeff]

Figured it out. PYTHONPATH was not being sourced properly while SWEETPATH was fine. Adding a tip to the install/run instructions to source setup.sh or add PYTHONPATH to the list of env variables could help with people running into the same problem.

[Adam English]

Hey Jeff, Thanks for figuring this out. I'll be sure to keep the docs/JellyReadme.txt Section III (Installation), Step 2 the same.

[jeff]

Ah indeed, it's very clearly laid out there. Sorry about that. Things running smoothly now.

[Edwin S.]

Here's your solution. go to every file in the bin directory of pbsuite and change the header from #!/usr/bin/evn python to #!<the directory="" of="" your="" python="" install="">

I was getting the same errors and then realized it had nothing to do with my python install but with the pbsuite binary she bang header. let me know if this works for you also

[Hério Sousa]

I've got the same error, Edwin's solution didn't work, and I didn't understand Jeff's one. In my .bashrc file I have:

source /home/heriosousa/PBSuite_15.8.24/setup.sh

Additionaly, my SWEETPATH value is:

/home/heriosousa/PBSuite_15.8.24/bin

I can not figure out what is wrong.