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Aurélien Béliard
@aurelBZH
@egafni yes it works.
Erik
@egafni
@aurelBZH okay i'll change it.
Erik
@egafni
@aurelBZH okay can you pull/merge the develop branch? You'll have to make a new sqlite database or re-create your tables, but Task.drm_jobID is not a string
see LPM-HMS/COSMOS2@1e588b3
Aurélien Béliard
@aurelBZH
@egafni why did you comment " from .core.cmd_fxn.io import find, out_dir, forward" in the api script ? are those functionalities deprecated?
Aurélien Béliard
@aurelBZH
sorry i wasn't working with the last update of the framework so i have lots of things to change in my pipeline what is the aim of this update
Erik
@egafni
@aurelBZH yeah, they are deprecated. The api changed at version 2.0; find/out_dir/forward are no longer a thing and inputs/outputs are specified explicitly now. We found this type code to be much easier to write and understand. There's also a new Dependency primitive that's useful. Check out the examples, the api is much simpler now. If you don't want to switch, just cherry pick that commit I pasted above into your version and you'll have str drm_jobIDs
footnote: there's no further plans to change the api, we're pretty happy with the way it is now
there's some release notes here: https://github.com/LPM-HMS/COSMOS2/releases
Aurélien Béliard
@aurelBZH
@egafni Have you planned to change for python3 ? if not why ?
Aurélien Béliard
@aurelBZH
@egafni Is there a way to stop a workflow if something happened? In my example I want to stop a workflow if there isn't variant detected.
Erik
@egafni
@aurelBZH I started adding python3 support using 2to3, but it was kind of a hassle. I'd love to just switch to python3 but Invitae is still stuck on python2
@aurelBZH sure, you could try using a signal
Erik
@egafni
let me know if it works (or if it's broken)
Erik
@egafni
I don't have much motivation to add 2to3 support, but you are more than welcome to do it and PR :D
Aurélien Béliard
@aurelBZH
I have modified and used your code and it work! Few weeks ago I have tried something like that but wasn't able to make it works.
Erik
@egafni
@aurelBZH cool, the doc had failed to update, im pretty sure you dont need to send a kill signal http://cosmos.hms.harvard.edu/COSMOS2/workflows/advanced.html
Martin Owens
@doctormo
Happy New Year COSMOS2
Ketan Bhatt
@ketanbhatt
Hey guys, I am right now looking at all the major workflow libraries out there, and getting inspiration for one that we are going to build ourselves.
If there is anything else I could take a look at so that I understand the design decisions taken while building it, I will be more than glad to have a look at it.
I have already gone through the docs, and will now be looking at the code.
ajayk1931
@ajayk1931
Can the link for COSMOS2 documentation be updated please?
Erik
@egafni
@ajayk1931 which link?
the one in the repo works fine..
Erik
@egafni
@ajayk1931 Found some broken links on the website, fixed them. Thanks for pointing it out
Erik
@egafni
Anyone using Cosmos for research/industry please let me know so that I can add you to the "Users of Cosmos" section on the README @ https://github.com/LPM-HMS/COSMOS2
@aurelBZH ^
Erik
@egafni
Just a heads up, I just added python3 support
Oscar Westesson
@breadbaron
I just cloned a fresh version of cosmos2 and the examples are failing with this error, any ideas? ready_tasks = [task for task, degree in list(task_queue.in_degree()) if TypeError: 'Task' object is not iterable
Oops, error lines not rendered nicely above. Let me know if you want me to send the full trace, other info, etc...
Oscar Westesson
@breadbaron
The above error is fixed by changing line 544 in Workflow.py to this:
ready_tasks = [task for task, degree in task_queue.in_degree().items() if degree == 0 and task.status == TaskStatus.no_attempt]
previously task_queue.in_degree() was cast to list - not sure why this didn't cause errors for other folks
Erik
@egafni
@breadbaron thanks for the heads up and sorry for the delay in response.. what version of python are you in? networkx seems to return a different type in python3 than python2, although i'm not sure why our tests aren't catching this since we test both versions. If you could let me know your networkx version as well, that'd be great
Oscar Westesson
@breadbaron
Hey - I'm on python Python 2.7.13 and networkx 1.11. Thanks for looking into it!
Erik
@egafni
@breadbaron why networkx 1.11? 2.0 is out
that's definitely the issue
the networkx api has changed
Erik
@egafni

@breadbaron just checked out your profile - if you are interested applications of machine learning and probabilistic modeling to early detection of cancer using next gen sequencing of cell free DNA, that's what we're doing at Freenome and we're hiring. We've raised 70 million and are only at 40 people (hiring carefully) and have/are generating pretty incredible datasets. We're based in south san francisco inside the verily building (all the google perks).

Side note, this very interesting paper came out recently which may peak your interest: https://www.nature.com/articles/nbt.3300

Ilya Kolpakov
@ilya-kolpakov
Hi there. I am having a problem running examples and the test suite (LPM-HMS/COSMOS2#80). Would appreciate if someone could point me to the possible issues coausing the problem. Thanks a lot.
Ilya Kolpakov
@ilya-kolpakov
The old networkx seems to be the problem indeed. It would be nice to fix the setup.py
Erik
@egafni
@ilya-kolpakov thanks for the PR :D
man4ish
@man4ish
After installing Genomekey using comand pip install . , I am getting following error Traceback (most recent call last):
File "bin/genomekey", line 6, in <module>
from cosmos import session
ImportError: cannot import name session. I have no clue what is the reason behind.
Erik
@egafni
@man4ish Genomekey isn't being maintained anymore, sorry
man4ish
@man4ish
Ok but i have one simple query regarding the above issue. Do i need to install Cosmos first so that i can avoid cosmos import error. Please help me. Thanks
man4ish
@man4ish

I am going through following documentation for installing and configuring cosmos.

https://github.com/LPM-HMS/GenomeKey/wiki/test-new-docs#id14

but after installation cosmos 2.0, configuration give me following errors.

usage: cosmos [-h] <command> ...
cosmos: error: too few arguments

Even though i have created default config file still i get same error.

rafaelfang
@rafaelfang
Hello May I ask a question regarding installing GenomeKey using Cosmos2? I installed both software on my local mac. However, when I execute the "../bin/genomekey json -n fastq.json ." the system gives error and it seems that the session package is not in the cosmos.Traceback (most recent call last):
File "../bin/genomekey", line 6, in <module>
from cosmos import session
ImportError: cannot import name session
Any suggestions are welcome. Thank you.
Erik
@egafni
@rafaelfang are you using genomekey2? https://github.com/LPM-HMS/GenomeKey2