error to install varsimlab
0
0
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*
SNP • 1.6k views
ADD COMMENT
0
Entering edit mode
ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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:

{
"reference": “hg19.fa",
"targets": “hg19-targets.bed"

}

ADD REPLY
0
Entering edit mode

I ejecute "sudo ./run.sh" into the folder and I get the error above.

ADD REPLY
0
Entering edit mode

why 'sudo' ?

ADD REPLY
0
Entering edit mode

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'.

ADD REPLY

Login before adding your answer.

Traffic: 1804 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6