Error: pysam is not installed for about speedseq HOT 8 OPEN

This issue has actually been seen before (#29) but I don't know the exact cause.

What is the result of which python2.7?

If you take the path to python2.7 and substitute it for $PYTHON in the following, what is the result?

$PYTHON -c "import imp; imp.find_module('pysam')"

from speedseq.

Hi Chiang,
the result of "which python2.7" tell the path to python, and the command: (absolute path to python2.7) -c "import imp; imp.find_module('pysam')" reports noting, no matter I used pysam 0.7.4 or pysam 0.8.3.
I have read the issue 29 which have the same error report, after re-install new version pysam, the problem is fixed. while I re-installed pysam 0.8.3 then re-installed speed-seq 0.1.0, speedseq sv still reported that pysam is not installed, it is really confusing.

from speedseq.

what about running the following?

/path/to/python2.7
import pysam

i'm trying to determine whether this is an issue with the pysam installation or the "-c" syntax

from speedseq.

Pysam can be imported in python, I do not know why it does not work in speedseq.
Both sv and realign commands would use "check_python_modules" function, but when I use realign commands, speedseq reported no error.

from speedseq.

Ok, well if Python and all the required modules are indeed installed, I suppose you can just comment out the lines for check_python_modules from speedseq. There was a previous issue with the "-c" flag not working on an anaconda python build, so this may be the problem (arq5x/lumpy-sv#88)

from speedseq.

Well, actually, I have commented out the check_python_modules function below sv function, and it works now, thx.

from speedseq.

ok, in that case this is a bug, and I'll get it fixed. sorry about that.

from speedseq.

Same issue here.

Modules are there and the test commands from speedseq work when running them separately in the shell - but not when calling speedseq sv (doesn't find numpy).

from speedseq.