Question: error to install varsimlab
0
gravatar for joselu
6 months ago by
joselu60
joselu60 wrote:

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 • 263 views
ADD COMMENTlink modified 6 months ago by Pierre Lindenbaum115k • written 6 months ago by joselu60

VarSimLab https://github.com/NabaviLab/VarSimLab

ADD REPLYlink written 6 months ago by Pierre Lindenbaum115k

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 REPLYlink written 6 months ago by Pierre Lindenbaum115k

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 REPLYlink modified 6 months ago • written 6 months ago by joselu60

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

ADD REPLYlink written 6 months ago by joselu60

why 'sudo' ?

ADD REPLYlink written 6 months ago by Pierre Lindenbaum115k

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 REPLYlink written 6 months ago by joselu60
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