Comments (15)
Dear Bastian,
It seems that you were not in the mitozEnv
environment, since the Perl was not from the mitozEnv
environment.
https://github.com/linzhi2013/MitoZ/blob/master/version_2.4-alpha/INSTALL.md
Did you run source activate mitozEnv
before run MitoZ?
from mitoz.
Dear Guanling,
I did yes. Can I somehow re-direct to the specific Perl version used within the MitoZ environment?
Cheers Bastian
from mitoz.
Hi Bastian,
I am not sure about the way you said about.
Can you check which Perl you are using by running which perl
in your console (in the mitozEnv
environment)?
Cheers,
Guanliang
from mitoz.
Sorry,
was a bit confusing my comment/question. Here is the output from $ which perl:
~/miniconda2/envs/mitoz/bin/perl
from mitoz.
That's weird. I cannot figure it out why you ran into this problem.
After googling a bit, someone had such similar problem, e.g. https://stackoverflow.com/questions/30626245/undefined-symbol-perl-xs-apiversion-bootcheck.
You may google "undefined symbol: Perl_xs_apiversion_bootcheck" and maybe can find a solution (though I haven't seen a definite one)
from mitoz.
I already did this,
and could not find a solution. I may try to reinstall the whole thing again. I tried to change the first line in draw_circos_for_mitogenome_auto_depth.pl from #!/usr/bin/perl to #!/usr/bin/env perl, but without any luck. It still shows the same error as before.
Cheers Bastian
from mitoz.
I see. Maybe re-install the whole is a solution, or use Docker or Singularity version? I found many people have problems with solving the dependencies.
Cheers,
Guanliang
from mitoz.
I don't have root privileges on the cluster I'm using though docker and singularity cannot be used, right?
Cheers Bastian
from mitoz.
I could install MitoZ locally on my PC, but then I'm limited in the usage of threads to use. But I may have to do it this way then.
from mitoz.
I could install MitoZ locally on my PC, but then I'm limited in the usage of threads to use. But I may have to do it this way then.
yes, the visualization step won't take much memory.
from mitoz.
Hi,
docker did the trick. Nice programm --- Congrats. I will close this issue now.
Cheers and have a good weekend,
Bastian
from mitoz.
Hi,
I've encountered another problem once I'm typing
$ ./MitoZ.simg --help
/app/anaconda/bin/python3: can't open file '/app/release_MitoZ_v2.4-alpha/MitoZ.py': [Errno 2] No such file or directory
I simply downloaded the container, though what am I doing wrong here? Is the download link broken?
Cheers Bastian
from mitoz.
Hi,
I've encountered another problem once I'm typing
$ ./MitoZ.simg --help /app/anaconda/bin/python3: can't open file '/app/release_MitoZ_v2.4-alpha/MitoZ.py': [Errno 2] No such file or directory
I simply downloaded the container, though what am I doing wrong here? Is the download link broken?
Cheers Bastian
Hi Bastian,
Maybe the Singularity image was not built successfully for version 2.4. Please consider the version 2.3 for now. I will check what happened to the version 2.4 Singularity images.
Thank you for reporting the issue.
Cheers,
guanliang
from mitoz.
Hi,
any news whether the image of version 2.4 is broken or not?
Cheers Bastian
from mitoz.
or
it is broken. Now we use conda
for MitoZ 3.0.
from mitoz.
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from mitoz.