Open af8 opened 3 years ago
Hi,
conda installation for FusionCatcher does not work. It needs to be updated. If someone would jump here and help would be great!
Cheers, Daniel
Ok thanks. I will then try to build from GitHub. By the way, the patch I mentioned above does not work. I got 'symbol lookup error' so this is not a good idea.
Cheers, Anthony
@ndaniel
I am also getting the same error with docker.
/usr/local/bin/bowtie-align-s: error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory
Used fusioncatcher.py 1.33
, executed with docker run quay.io/biocontainers/fusioncatcher:1.33--hdfd78af_0 fusioncatcher
Any thoughts how to proceed further?
@praveenraj2018 It looks like libtbb is not installed. Probably this would help on Ubuntu:
sudo apt-get -y install libtbb-dev libtbb2
It is not clear why conda does not install the dependencies like libtbb-dev and libtbb2 for bowtie.
libtbb2 was broken on conda for while - attempting to fix the recipe in this PR here https://github.com/bioconda/bioconda-recipes/pull/32012
Hello,
I just installed fusioncatcher through conda:
After installation, it fails to run because bowtie can not found
libtbb.so.2
:Nonetheless, I can see that in the lib folder of the conda env
libtbb.so.12.1
is present.This issue relates to a few previous issues where it is advised to install tbb system wide with
apt-get
or such. I would like to avoid that to keep things in the conda env properly.As a patch, I have done :
Now obviously the lib is found and bowtie prints the version correctly:
But I am not sure whether this is really clean. In others words if
libtbb.so.12.1
is compatible withlibtbb.so.2
and that both can be switched as I just did for bowtie ?Or anything else you would advised to solve this situation ?
Many thanks, Anthony