KwatMDPhD
commented
5 years ago I don't think this old analysis can run anymore because some of the data (not hosted by us) has been moved. Sorry.
Closed bpmunson closed 5 years ago
KwatMDPhD
commented
5 years ago I don't think this old analysis can run anymore because some of the data (not hosted by us) has been moved. Sorry.
Hi,
Using SPro to download the necessary data, I'm running to an HTTP error when attempting to grab CCLE data. I get the same error in a browser when trying to access the url which gives the error:"https://portals.broadinstitute.org/ccle_legacy/downloadFile/DefaultSystemRoot/exp_10/ds_30/CCLE_MUT_EXPR_RPPA_OncoGPS.zip?downloadff=true&fileId=27325"
Thanks!
Traceback:
(onco_gps_paper_analysis) [ onco_gps_paper_analysis ] spro download spro version 0.7.2 - see https://spro.io to learn more about shareable project.
Checking if entered project environment ... Downloading project.json's downloads... Downloading ftp://caftpd.nci.nih.gov/pub/OCG-DCC/CTD2/Broad/CTRPv2.2_2015_pub_CancerDisc_5_1210/CTRPv2.2_2015_pub_CancerDisc_5_1210.zip =(into)=> /data/cellardata/users/bpmunson/projects/pfizer_cdk/dual_crispr/oncogps/spro/onco_gps_paper_analysis/data/CTRPv2.2_2015_pub_CancerDisc_5_1210.zip ... Downloading https://portals.broadinstitute.org/ccle_legacy/downloadFile/DefaultSystemRoot/exp_10/ds_30/CCLE_MUT_EXPR_RPPA_OncoGPS.zip?downloadff=true&fileId=27325 =(into)=> /data/cellardata/users/bpmunson/projects/pfizer_cdk/dual_crispr/oncogps/spro/onco_gps_paper_analysis/data/CCLE_MUT_EXPR_RPPA_OncoGPS.zip ... Traceback (most recent call last): File "/data/cellardata/users/bpmunson/projects/pfizer_cdk/dual_crispr/oncogps/spro/onco_gps_paperanalysis/environment/bin/spro", line 6, in
from spro import spro
File "/cellar/users/bpmunson/Software/conda/miniconda3/envs/oncogps/lib/python3.7/site-packages/spro.py", line 45, in
spro_()
File "/cellar/users/bpmunson/Software/conda/miniconda3/envs/oncogps/lib/python3.7/site-packages/click/core.py", line 764, in call
return self.main(args, kwargs)
File "/cellar/users/bpmunson/Software/conda/miniconda3/envs/oncogps/lib/python3.7/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/cellar/users/bpmunson/Software/conda/miniconda3/envs/oncogps/lib/python3.7/site-packages/click/core.py", line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/cellar/users/bpmunson/Software/conda/miniconda3/envs/oncogps/lib/python3.7/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, ctx.params)
File "/cellar/users/bpmunson/Software/conda/miniconda3/envs/oncogps/lib/python3.7/site-packages/click/core.py", line 555, in invoke
return callback(args, *kwargs)
File "/cellar/users/bpmunson/Software/conda/miniconda3/envs/oncogps/lib/python3.7/site-packages/spro/download.py", line 30, in download
join(project_root_directory_path, directory_path))
File "/cellar/users/bpmunson/Software/conda/miniconda3/envs/oncogps/lib/python3.7/site-packages/spro/support/support/network.py", line 23, in download
urlretrieve(url, file_path)
File "/cellar/users/bpmunson/Software/conda/miniconda3/envs/oncogps/lib/python3.7/urllib/request.py", line 247, in urlretrieve
with contextlib.closing(urlopen(url, data)) as fp:
File "/cellar/users/bpmunson/Software/conda/miniconda3/envs/oncogps/lib/python3.7/urllib/request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "/cellar/users/bpmunson/Software/conda/miniconda3/envs/oncogps/lib/python3.7/urllib/request.py", line 531, in open
response = meth(req, response)
File "/cellar/users/bpmunson/Software/conda/miniconda3/envs/oncogps/lib/python3.7/urllib/request.py", line 641, in http_response
'http', request, response, code, msg, hdrs)
File "/cellar/users/bpmunson/Software/conda/miniconda3/envs/oncogps/lib/python3.7/urllib/request.py", line 569, in error
return self._call_chain(args)
File "/cellar/users/bpmunson/Software/conda/miniconda3/envs/oncogps/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/cellar/users/bpmunson/Software/conda/miniconda3/envs/oncogps/lib/python3.7/urllib/request.py", line 649, in http_error_default
raise HTTPError(req.full_url, code, msg, hdrs, fp)
urllib.error.HTTPError: HTTP Error 502: Proxy Error
(onco_gps_paper_analysis) [ onco_gps_paper_analysis ]