Open kellogg76 opened 5 years ago
the permissions on your install are messed up. I would re-install from scratch.
Or maybe you can try sudo chown -R $USER:$USER //usr/local/share/gemini/
the permissions on your install are messed up. I would re-install from scratch. Or maybe you can try
sudo chown -R $USER:$USER //usr/local/share/gemini/
Thanks, but reinstalling from scratch with
python gemini_install.py /usr/local /usr/local/share/gemini
Gives another error.
/usr/local/share/gemini/anaconda/bin/gemini --annotation-dir /usr/local/share/gemini/gemini_data update --dataonly --tooldir /usr/local
Upgrading associated tools...
Traceback (most recent call last):
File "/usr/local/share/gemini/anaconda/bin/gemini", line 7, in <module>
gemini_main.main()
File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1249, in main
args.func(parser, args)
File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1085, in update_fn
gemini_update.release(parser, args)
File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/gemini_update.py", line 34, in release
config = gemini.config.read_gemini_config(args=args, allow_missing=True)
File "/usr/local/share/gemini/anaconda/lib/python2.7/site-packages/gemini/config.py", line 65, in read_gemini_config
config["annotation_dir"] = args.annotation_dir
TypeError: 'NoneType' object does not support item assignment
Traceback (most recent call last):
File "gemini_install.py", line 191, in <module>
main(parser.parse_args())
File "gemini_install.py", line 84, in main
install_rest(gemini, args)
File "gemini_install.py", line 149, in install_rest
subprocess.check_call(cmd)
File "/usr/lib/python2.7/subprocess.py", line 541, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/usr/local/share/gemini/anaconda/bin/gemini', '--annotation-dir', '/usr/local/share/gemini/gemini_data', 'update', '--dataonly', '--tooldir', '/usr/local']' returned non-zero exit status 1
I've restinstalled Anaconda but didn't make any difference. Do you have any other suggestions on what I can try?
It looks like that's the same error, you don't have permissions in /usr/local/share
It looks like that's the same error, you don't have permissions in /usr/local/share
I wondered that but my permissions for /usr/local/share are rwxrwxrwx, and I get the same error no matter where I try installing even though my account is Admin.
same problem here
I'm having an issue running gemini commands that worked just a few weeks ago.
running :-
gemini load -v ~/FEVR/hg19.snpEff.vcf -t snpEff --cores 8 ~/FEVR/hg19.db
gives the following error
If I try to run gemini update, I get :-
gemini --v show's i'm running 0.30.1
Any help is appreciated.