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philippdre / omniCLIP

omniCLIP is a CLIP-Seq peak caller
GNU General Public License v3.0
15 stars 9 forks source link

installation failure #26

Open stasaki opened 3 years ago

stasaki commented 3 years ago

I ran the following command but it returned an error.

(omniEnv) root@c0560292e992:/var/omniCLIP# python3 setup.py usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...] or: setup.py --help [cmd1 cmd2 ...] or: setup.py --help-commands or: setup.py cmd --help

error: no commands supplied

I modified the command as follows but I still got an error with running the main script. Thank you for your assistance.

(omniEnv) root@c0560292e992:/var/omniCLIP# python3 setup.py install

(omniEnv) root@c0560292e992:/var/omniCLIP# python3 omniCLIP/omniCLIP.py Traceback (most recent call last): File "omniCLIP/omniCLIP.py", line 33, in from omniCLIP.data_parsing import CreateGeneAnnotDB File "/var/omniCLIP/omniCLIP/omniCLIP.py", line 33, in from omniCLIP.data_parsing import CreateGeneAnnotDB ModuleNotFoundError: No module named 'omniCLIP.data_parsing'; 'omniCLIP' is not a package

adomingues commented 3 years ago

Hi @stasaki, have you solved this problem? I am running into the same issue.

adomingues commented 3 years ago

Nevermind. Following your instructions the package is installed system wide, so this will work:

omniCLIP generateDB --help
adomingues commented 3 years ago

Also to add that omniCLIP will only run if invoked from inside folder containing the cloned repo which is not super practical.

@philippdre @simojoe would it be possible to make omniCLIP available as conda package? That would make the program much more used.