Hi Team,
I have been trying to install package_snpEff_3_5 from the Galaxy main tool shed and package_snpEff_3_6 from the Galaxy test tool shed and have the same issue. Once the installer completes it
shows that the dependency snpEff.x.x was not installed. When I try to install the dependency it reports that the directory /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/tmp/tmp-toolshed-mtdi48tQV/snpEff does not exist. I have checked to confirm
that this is true and discovered that rather then a directory I find a null file named "snpEff and the snpEff_v3.x_core.zip file. I checked my shedtool dependencies folder and the directory for these tools are empty. I have since uninstalled the package.
I just tried again to install the snpEff tool and am getting the followig error message:
Internal Server Error
Galaxy was unable to successfully complete your request
URL:
http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413
Module
galaxy.web.framework.middleware.error:
149 in
__call__
>>
app_iter = self.application(environ,
sr_checker)
Module
paste.recursive:
84 in
__call__
>>
return self.application(environ,
start_response)
Module
paste.httpexceptions:
633 in
__call__
>>
return self.application(environ,
start_response)
Module
galaxy.web.framework.base:
132 in
__call__
>>
return self.handle_request(
environ, start_response
)
Module
galaxy.web.framework.base:
190 in
handle_request
>>
body = method(
trans, **kwargs
)
Module
galaxy.web.framework:
377 in
decorator
>>
return func(
self, trans,
*args, **kwargs
)
Module
galaxy.webapps.galaxy.controllers.admin_toolshed:
1035 in
prepare_for_install
>>
raw_text = common_util.tool_shed_get(
trans.app,
tool_shed_url, url
)
Module
tool_shed.util.common_util:
310 in
tool_shed_get
>>
response = urlopener.open(
uri )
Module
urllib2:
395 in
open
>>
response = meth(req,
response)
Module
urllib2:
508 in
http_response
>>
'http', request,
response, code,
msg, hdrs)
Module
urllib2:
427 in
error
>>
result = self._call_chain(*args)
Module
urllib2:
367 in
_call_chain
>>
result = func(*args)
Module
urllib2:
603 in
http_error_302
>>
return self.parent.open(new)
Module
urllib2:
395 in
open
>>
response = meth(req,
response)
Module
urllib2:
508 in
http_response
>>
'http', request,
response, code,
msg, hdrs)
Module
urllib2:
433 in
error
>>
return self._call_chain(*args)
Module
urllib2:
367 in
_call_chain
>>
result = func(*args)
Module
urllib2:
516 in
http_error_default
>>
raise HTTPError(req.get_full_url(),
code, msg,
hdrs, fp)
HTTPError: HTTP Error 500: Internal Server Error
extra data
This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.
I appreciate any possible assistance,
Regards,
__________________________________
Iry T. Witham
Scientific Applications Administrator
Scientific Computing Group
Computational Sciences Dept.
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609
Phone: 207-288-6744
email: iry.witham@jax.org
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