linnarsson-lab / cytograph-dev Goto Github PK

Apparently Ubuntu has dropped a package that is a dependency for graphviz (and made it tricky to install since libgraphviz4 might break a preinstalled package libcdt5).

See more here:
http://askubuntu.com/questions/418054/how-do-i-install-latest-graphviz

and this claims that it is solvable but it does not work for me:
http://stackoverflow.com/questions/29630434/graphviz-installation-ubuntu-14-04

Any idea how to overcome this?

I open this issue here since might related to both adolescent-mouse and development-mouse pipelines.

Many of luigi.Tasks accept as main parameter --tissue, I propose to change the name with the more general --pool, since what it is reading is the Pool column of the pooling_sepcification.tab filem and tissue is confusing for the context we use it in development.

Following instructions on cytograph main page:

$ git clone https://github.com/linnarsson-lab/cytograph.git
Klonar till "cytograph"
...
$ cd cytograph/bhtsne
$ g++ sptree.cpp tsne.cpp -o bh_tsne -O2
$ cd ..
$ python setup.py install
......
Installed /home/peter/anaconda3/lib/python3.6/site-packages/cytograph-0.6.1-py3.6.egg
Processing dependencies for cytograph==0.6.1
Searching for numpy-groupies
Downloading http://github.com/linnarsson-lab/numpy-groupies/tarball/master#egg=numpy_groupies
error: Can't download http://github.com/linnarsson-lab/numpy-groupies/tarball/master#egg=numpy_groupies: 404 Not Found

We are producing many pool cytograph .loom files. They are created in different build folder but once copied elsewhere there is not way to track when the file was generated and to wich build it belongs. Therefore I suggest we should store the build id in the loom file as a column or file attribute.

cytograph is heavily underdocumented. This has recently been problem for both @kasiletti trying to get started with the library and me trying to come back to the code I wrote after a while.

There is no easy way to visualize the tasks tree (and no, the built in graph viewer is not an option, it is only meant to work for running tasks). Docstrings are short and not very descriptive. Documentation of the options that one can pass to the command line interface and on which task they have effect would be really needed.

With this issue I suggest that we join efforts to make an effort to document cytograph a bit while we work with it over the next months. It does not have to be something production-ready, but a documentation layer that spares us the work of going and read the source over and over again! Me and @kasiletti could add new docs/dosctrings while we modify/read the code. @slinnarsson, since you understand the luigi internals better, maybe you could help with some ideas on how to build a tasks tree inspector/visualizer.

Regarding how to build the docs, I did not find any sphinx integration or automatic documentation tools for luigi (i.e. nothing like this) , it looks like we will have to do the CLI api of the docs manually. The api of each task can be automatically estracted, and it is probably the best place to document what each task is doing. I suggest that we get started directly with reStructuredText format, allowing to build a neater html documentation with spinx later on.