Entering edit mode
6.4 years ago
joselu
▴
110
Hello. I am new in Biostar, and I am learnig bioinformatics. I am trying to install VARSIMLAB to create aritificial fastq files for DNA resequencing. When I try to install the program I get the next error: Somebody can help me please. Thank you.
*jose@jose-M61PME-S2P:~/Descargas/hg19$ sudo ./run.sh
[sudo] password for jose:
varsimlab
varsimlab
Performing system checks...
VarSimLab 1.0: reading manifest.json ..
Unhandled exception in thread started by <function wrapper at 0x7f6c790bfcf8>
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/django/utils/autoreload.py", line 226, in wrapper
fn(*args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/django/core/management/commands/runserver.py", line 116, in inner_run
self.check(display_num_errors=True)
File "/usr/local/lib/python2.7/dist-packages/django/core/management/base.py", line 426, in check
include_deployment_checks=include_deployment_checks,
File "/usr/local/lib/python2.7/dist-packages/django/core/checks/registry.py", line 75, in run_checks
new_errors = check(app_configs=app_configs)
File "/usr/local/lib/python2.7/dist-packages/django/core/checks/urls.py", line 13, in check_url_config
return check_resolver(resolver)
File "/usr/local/lib/python2.7/dist-packages/django/core/checks/urls.py", line 23, in check_resolver
for pattern in resolver.url_patterns:
File "/usr/local/lib/python2.7/dist-packages/django/utils/functional.py", line 33, in __get__
res = instance.__dict__[self.name] = self.func(instance)
File "/usr/local/lib/python2.7/dist-packages/django/core/urlresolvers.py", line 417, in url_patterns
patterns = getattr(self.urlconf_module, "urlpatterns", self.urlconf_module)
File "/usr/local/lib/python2.7/dist-packages/django/utils/functional.py", line 33, in __get__
res = instance.__dict__[self.name] = self.func(instance)
File "/usr/local/lib/python2.7/dist-packages/django/core/urlresolvers.py", line 410, in urlconf_module
return import_module(self.urlconf_name)
File "/usr/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
File "/easyscnvsim/easyscnvsim/urls.py", line 20, in <module>
url(r'^', include('webapp.urls')),
File "/usr/local/lib/python2.7/dist-packages/django/conf/urls/__init__.py", line 52, in include
urlconf_module = import_module(urlconf_module)
File "/usr/lib/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
File "/easyscnvsim/webapp/urls.py", line 14, in <module>
check_reference_ready()
File "/easyscnvsim/webapp/scnvsim.py", line 27, in check_reference_ready
data = json.load(manifest)
File "/usr/lib/python2.7/json/__init__.py", line 290, in load
**kw)
File "/usr/lib/python2.7/json/__init__.py", line 338, in loads
return _default_decoder.decode(s)
File "/usr/lib/python2.7/json/decoder.py", line 366, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/usr/lib/python2.7/json/decoder.py", line 384, in raw_decode
raise ValueError("No JSON object could be decoded")
ValueError: No JSON object could be decoded*
VarSimLab https://github.com/NabaviLab/VarSimLab
Prepare The Reference Genome http://varsimlab.readthedocs.io/en/latest/user-guide.html#installing-docker , show us the location and the content of
manifest.json
I have downloaded and decompressed the reference genome. I have 4 files: "hg19.fa", hg19-targets.bed", "manifest.json" and "run.sh". The manifest.json file is:
}
I ejecute "sudo ./run.sh" into the folder and I get the error above.
why 'sudo' ?
If I don't write sudo i get the next message:
jose@jose-M61PME-S2P:~/Descargas/hg19$ ./run.sh Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post http://%2Fvar%2Frun%2Fdocker.sock/v1.37/containers/varsimlab/stop: dial unix /var/run/docker.sock: connect: permission denied Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Delete http://%2Fvar%2Frun%2Fdocker.sock/v1.37/containers/varsimlab: dial unix /var/run/docker.sock: connect: permission denied docker: Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post http://%2Fvar%2Frun%2Fdocker.sock/v1.37/containers/create?name=varsimlab: dial unix /var/run/docker.sock: connect: permission denied. See 'docker run --help'.