Binary release of HINGE

[HuangYukun]

Hi, The software seems really interesting and I want to try it on my own datasets. Due to unsuccessful trials of compiling the software, may I ask for a binary release to run directly? Thanks.

Jimmy

[ilanshom]

Hi Jimmy, we currently don't have a binary that works across all linux distributions, but we will try to generate one. I'll let you know when this is done.

[HuangYukun]

@ilanshom Thanks for the reply. In fact I am able to compile and run HINGE now. Will come to you for help if there're any problems.

[HuangYukun]

Hi, I have tried several datasets through the pipeline but some of them stuck in the command

get_draft_path.py <working directory> ecoli ecoli<identifier-of-run>.G2.graphml

with error messages like this

Traceback (most recent call last):
File "../../scripts/get_draft_path.py", line 316, in <module>
RCmap[path_to_vert[path]] = path_to_vert[path_to_search]
KeyError: '66239_0'

Would like to know how to solve similar problems? Thanks

[govinda-kamath]

Hi Jimmy,

Are any of the datasets where HINGE fails public? This error seems to be some read not being in the database (I may be mistaken though.)

[HuangYukun]

Hi @govinda-kamath, I don't know if I understand you correctly but the datasets are from ourselves and they can pass all previous steps until get_draft_path.py

[govinda-kamath]

Hi Jimmy,

We do not seem to be able to pinpoint the cause of the error here. Would it be possible for you to send us the *.G2.graphml that creates the error for us to debug that? The graphml file doesn't contain the sequence information, so you wouldn't be sharing any data (in case that's a concern for you).

Thanks, Govinda.

[HuangYukun]

@govinda-kamath Thanks for the kind reply. I am glad to send you the *.G2.graphml. How can we start?

[HuangYukun]

I may also provide the data source however it would take some time. Thanks again.

[govinda-kamath]

Thanks Jimmy.

Can you send the *.G2.graphml to gkamath@stanford.edu and ilan.shomorony@berkeley.edu?

Thanks again for helping us improve the software, Govinda.

[HuangYukun]

The dataset is sent to your email. Thanks.

Best, Jimmy

[govinda-kamath]

Thanks a ton.

Govinda.

[govinda-kamath]

Seems to work with the latest HINGE release.