search

AnantharamanLab / METABOLIC

A scalable high-throughput metabolic and biogeochemical functional trait profiler
165 stars 42 forks source link

problem in installation - step 8 #103

Open ariasamin opened 1 year ago

ariasamin commented 1 year ago

Hello, I got a problem in installation I have a problem with "bash run_to_setup.sh", it stoped in: ............. Motif/sox_genes/06.test_soxB_motif.pl Motif/sox_genes/07.find_soxC_motif.pl Motif/sox_genes/08.test_soxC_motif.pl

### Then I tried to install from ".sh file" and I got an error in last command:

(metabolic) [narges@node1910 METABOLIC]$ gdown --quiet https://drive.google.com/uc?id=1JQJpw_elM4IyGo_BIfioy8XnmqgoN-Iw Traceback (most recent call last): File "/home/narges/.conda/envs/metabolic/bin/gdown", line 10, in sys.exit(main()) File "/home/narges/.conda/envs/metabolic/lib/python3.8/site-packages/gdown/cli.py", line 99, in main download( File "/home/narges/.conda/envs/metabolic/lib/python3.8/site-packages/gdown/download.py", line 110, in download res = sess.get(url, stream=True) File "/home/narges/.conda/envs/metabolic/lib/python3.8/site-packages/requests/sessions.py", line 555, in get return self.request('GET', url, kwargs) File "/home/narges/.conda/envs/metabolic/lib/python3.8/site-packages/requests/sessions.py", line 528, in request prep = self.prepare_request(req) File "/home/narges/.conda/envs/metabolic/lib/python3.8/site-packages/requests/sessions.py", line 456, in prepare_request p.prepare( File "/home/narges/.conda/envs/metabolic/lib/python3.8/site-packages/requests/models.py", line 316, in prepare self.prepare_url(url, params) File "/home/narges/.conda/envs/metabolic/lib/python3.8/site-packages/requests/models.py", line 390, in prepare_url raise MissingSchema(error) requests.exceptions.MissingSchema: Invalid URL '': No schema supplied. Perhaps you meant http://?**

Thank you for your help,

ChaoLab commented 1 year ago

It seems that you have something wrong with using gdown. There is an alternative to directly download the test tgz file from "https://drive.google.com/uc?id=1JQJpw_elM4IyGo_BIfioy8XnmqgoN-Iw" and decompress it manually. This will be much easier than solving the potential environment set-up issues

ariasamin commented 1 year ago

Thank you so much for your reply, You were right. The problem was with "gdown", as new links also didn't work. As I found "gdown" shows different behavior in different linux environment, I installed "gdown" locally and it worked!!