Question: miso installed but no executables available
0
gravatar for inzirio
2.5 years ago by
inzirio0
inzirio0 wrote:

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?

rna-seq miso • 1.1k views
ADD COMMENTlink written 2.5 years ago by inzirio0

Are the executables in this directory (What does this show ls -lh ~/.local/bin)?

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by genomax74k

nope...

I've root access to the machine, and the executables aren't present anywhere! :(

ADD REPLYlink written 2.5 years ago by inzirio0

Can you try again with python -m pip install misopy to make sure the correct python and correct pip are used?

ADD REPLYlink written 2.5 years ago by WouterDeCoster42k

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... ^^'

ADD REPLYlink written 2.5 years ago by inzirio0

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"?

ADD REPLYlink written 2.5 years ago by genomax74k

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... :(

ADD REPLYlink written 2.5 years ago by inzirio0

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.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by genomax74k

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!

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by inzirio0

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.

ADD REPLYlink written 2.5 years ago by genomax74k
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