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cannot clone submodules of Proovread program

Hello everyone:

I got problem when I was trying to git clone some submodules, even though I used --recursive. The thing is I can git clone the repository successfully. The command I used was:

git clone --recursive git://github.com/BioInf-Wuerzburg/proovread

I got log like this:

Cloning into 'proovread'...

remote: Counting objects: 2034, done.

remote: Total 2034 (delta 0), reused 0 (delta 0), pack-reused 2034

Receiving objects: 100% (2034/2034), 9.20 MiB | 4.58 MiB/s, done.

Resolving deltas: 100% (1276/1276), done.

Checking connectivity... done.

Checking out files: 100% (57/57), done.

Submodule 'util/SeqChunker' (https://github.com/BioInf-Wuerzburg/SeqChunker.git) registered for path 'util/SeqChunker'

Submodule 'util/SeqFilter' (https://github.com/BioInf-Wuerzburg/SeqFilter.git) registered for path 'util/SeqFilter'

Submodule 'util/bwa' (https://github.com/BioInf-Wuerzburg/bwa.git) registered for path 'util/bwa'

Cloning into 'util/SeqChunker'...

fatal: unable to access 'https://github.com/BioInf-Wuerzburg/SeqChunker.git/': SSL connection timeout

Clone of 'https://github.com/BioInf-Wuerzburg/SeqChunker.git' into submodule path 'util/SeqChunker' failed

However, it'll work if I clone each submodules seperately, e.g.: git clone git://github.com/BioInf-Wuerzburg/SeqChunker.git .(it won't if I use git clone https://github.com/BioInf-Wuerzburg/SeqChunker.git)

Any help is highly appreciated. Thanks.

software error next-gen
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written by xiachongjing • xiachongjing

This was either a transitory error or something specific to your local conditions. The cloning is working for me.

• 1 views • link
written by GenoMax GenoMax

Thanks. Then do you have any ideas to solve this, assuming there is a transitory error or my local conditions ? Thanks.

• 1 views • link
written by xiachongjing • xiachongjing

Is it still not working for you?

• 1 views • link
written by GenoMax GenoMax

No, still not working. I guess there is something wrong with the submodule part. I can clone each submodule successfuly with code:

git clone git://github.com/BioInf-Wuerzburg/SeqChunker.git

So now I am thinking probably I can try to turn https: into git: for each submodule when doing <git clone="" --recursive="">. Something like this:http://stackoverflow.com/questions/4891527/git-protocol-blocked-by-company-how-can-i-get-around-that

So what's your idea? Thanks

• 1 views • link
written by xiachongjing • xiachongjing

1 answer

Finally, I got this issue solved. Basically, for some reason in my system the <git clone=""> cannot clone repository from https://, but it can clone repository from git://. So my solution is to tell <git clone=""> to change https:// to git://. And it works for me. The code I used for program Proovread v2.13.13 was:

git config --global url."git://github".insteadOf https://github

git clone --recursive git://github.com/BioInf-Wuerzburg/proovread

I got the idea from this http://stackoverflow.com/questions/4891527/git-protocol-blocked-by-company-how-can-i-get-around-that

• 1 views • link
written by xiachongjing • xiachongjing

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