minotour/minotour_archive

Real time data analysis tools for the minION sequencing platform.

minoTour - this is now deprecated users should go to https://github.com/LooseLab/minotourapp

minoTour

PLEASE NOTE: This is an experimental release of minoTour posted on 18 November 2015. This brings some significant improvements to minoTour including some speed ups to deal with the new levels of data generated by the minION device.

Real time data analysis tools for the minION sequencing platform.

The simplest way to use minoTour is to register for an account on our server in Nottingham. To do so, visit http://minotour.nottingham.ac.uk/register_new.php and create an account. Then contact Matt Loose ([email protected]) to activate your account for data upload. You must include your user name with that email.

The next easiest method would be to set up your own Amazon instance of minoTour using our preconfigured installation. Details of this will be provided here shortly.

The most complex method is to configure your own server. Full details for this are provided in the accompanying PDF document and also at http://minotour.github.io/minoTour/ .

To just download these files ensure that you have GIT configured on your target server. Create a directory and type: git clone https://github.com/minoTour/minoTour.git

To set up a repository that you can pull updates in to, create a new folder and initialise it for git use and set this repository as your origin. You then pull down the files and set your branch to the master version. Unless you know what you are doing you should not use the develop branch at this time.

git init

git remote add origin https://github.com/minoTour/minoTour.git

git pull

git checkout master

Subsequent updates can be retrieved by simply repulling the repository down.

A development version will be made available shortly which will provide additional features that are in development and may break existing areas of the site. Bug fixes for the current version will be provided via the master branch. Users are advised that the development branch is exactly that - in development - and should be treated with extreme caution!

This work is supported by the BBSRC.

minotour_archive's Issues

Corrupted HD5 files

Some of our runs will not import and crash with the following error:

2015-10-27 17:58:32 CACHED: 25087 PROCESSED: 24090
HDF5-DIAG: Error detected in HDF5 (1.8.11) thread 140532754958080:
#000: ../../../src/H5O.c line 242 in H5Oopen(): no name
major: Invalid arguments to routine
minor: Bad value
Exception in thread Thread-1:
Traceback (most recent call last):
File "/usr/lib/python2.7/threading.py", line 810, in *bootstrap_inner
self.run()
File "/usr/lib/python2.7/threading.py", line 763, in run
self.__target(_self.__args, _self.__kwargs)
File "minup.py", line 2234, in processfiles
process_fast5(fast5file, self.hdf, self.db_name, cursor)
File "minup.py", line 561, in process_fast5
configdata=hdf[basecalldirconfig]
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/tmp/pip_build_root/h5py/h5py/_objects.c:2467)
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/tmp/pip_build_root/h5py/h5py/_objects.c:2424)
File "/usr/local/lib/python2.7/dist-packages/h5py/_hl/group.py", line 164, in __getitem
oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/tmp/pip_build_root/h5py/h5py/_objects.c:2467)
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/tmp/pip_build_root/h5py/h5py/_objects.c:2424)
File "h5py/h5o.pyx", line 190, in h5py.h5o.open (/tmp/pip_build_root/h5py/h5py/h5o.c:3516)
ValueError: No name (No name)

stopping monitor.
setting run12 to an inactive run
finished.

HDF5: infinite loop closing library
D,G,A,S,T,F,FD,P,FD,P,FD,P,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E,E

I guess something is wrong with the fast5 files. We base-called everything again but the error persists.

Any ideas?

Any updates on the preconfigured install on AWS?

The README.md file says

The next easiest method would be to set up your own Amazon instance of minoTour using our preconfigured installation. Details of this will be provided here shortly.

Is that still on the roadmap? I am looking into setting up my own instance and would love to benefit from a . preconfigured AWS image / installation ;-)

Thanks a lot!
Thomas

Docker?

Any chance you have plans to release on a docker container?