Closed jvollme closed 7 years ago
Oh, wait, I now did find "libhts.so.1", but it is in my anaconda path (because I use virtual environments from conda). Maybe I'll have to recompile setting the htslib flag for setup.py? But still i wonder if not the bundled version should have been installed if BamM is using the systems library paths instead of the currently active conda environment's?
For instance, the BamM python libraries were installed in /usr/local/lib/python2.7/dist-packages
instead of my currently active environments specific python installation (which should be the only one listed in PYTHON_PATH). Can/should I set the exact preferred python-path for setup.py similar to the htslib paths? However, this does not seem to matter so much, because as i mentioned above bamm make
works just fine as it is (only bamm parse
seems to be giving me trouble).
Hi there,
I'm a little confused about how you installed bamm, but I can say that where parse
uses the C part (and hence htslib). make
is pure python. So that is probably why you are seeing a difference.
You could try specifying --with-libhts-lib
and --with-libhts-inc
to setup.py
, as you suggest.
Good luck.
Actually, before trying recompiling I just now tried explicitely adding the conda-environments htslib path i found to LD_LIBRARY_PATH, and now it seems to work, so that seems to be fine for me.
Concerning the way I installed BamM was by just cloning the BamM git and then running "setup.py" using sudo. Now I realize that I must have used sudo without the "-E" argument, so it would not have my conda environments PYTHON_PATH, explaining why it was installed in my systems general Python_path. Simple mistake, sorry for posting prematurely...
Hi, I installed BamM 1.7.3. I used the included
setup.py
.Using
bamm make
to map against a reference worked fine. But when I tried to extract coverage or linkage information usingbamm parse
(bamm parse -b *.bam -c testcov.tab -m opmean -t 8
), i get several error messages, mostly mentioning that "libhts.so.1" was not found (complete error message below, but it is quite long).Indeed, I can't find this file on my machine, but shouldn't the hts library have come bundled with BamM (at least it says so in the manual)? What am I doing wrong?
The exact Error-message: