miso installed but no executables available
I've problems with MISO, I've installed it on a cluster following the site instructions
pip install misopy
after that, I tested the "import modules" in python and everything is ok! But after that, no executable files are available in the binary path.
So, when I run the
python -m unittest discover misopy
it fails:
.Testing conversion of SAM to BAM...
[...]
sh: sam_to_bam: command not found
[...]
sh: index_gff: command not found
[...] sh: miso: command not found .
[...]
FAILED
(failures=1)
How can i solve this problem?
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Are the executables in this directory (What does this show
ls -lh ~/.local/bin)?nope...
I've root access to the machine, and the executables aren't present anywhere! :(
Can you try again with
python -m pip install misopyto make sure the correct python and correct pip are used?yes, I made it and the command output tells that all the requirements are already satisfied. Also the paths of each requirement is right!
I'm going mad... ^^'
If you are doing this as root perhaps the program is going to the home directory for root. Have you done a "find / -name misopy"?
yes, the command returns only the misopy source directories and the site-packages directories! (obviously I "greped" the output of find command)
So, no misopy binaries found... :(
Now we are grasping for straws but what OS are you running? Perhaps there is some incompatibility with your default python (do you have both 2 and 3) and MISO.
I'm on a cluster running Rocks OS (v 6.2), based on CentOS (6.6). I've already upgraded the python version from 2.6 to 2.7. Indeed, it works with other software.
I checked the misopy installation package, and it is installed in the right site-packages position. (inside the python 2.7 folder)
Anyway, it is the first time that I install a python software with pip. Most of times, I compiled and installed python software manually. But this time I preferred to use pip, cause the developers suggested to do in this way!
Since that does not appear to be working I suggest you go back to your trusted way. This being a cluster makes things different as well.