The whole process should just as like your 1st post (ideally)
git clone gitosis.git.ambermd.org:/amber.git <amber install directory>
git pull
git submodule update --init
> What's your git version? if it's old, I recommend to update it and retry.
You have not replied about the git version yet.
btw, I don't have access to amber git now so will check tonight.
Hai
On Mon, Jun 12, 2017 at 12:33 PM, David Cerutti <dscerutti.gmail.com> wrote:
> I've also tried
>
> git submodule foreach git pull
>
> It's complaining
>
> Entering 'AmberTools/src/ambertools-binary-build'
> You are not currently on a branch. Please specify which
> branch you want to merge with. See git-pull(1) for details.
>
> git pull <remote> <branch>
>
> Stopping at 'AmberTools/src/ambertools-binary-build'; script returned
> non-zero status.
>
> I can do git pull, again seeing that I'm already up-to-date, and git
> checkout master, to see that I'm already on master. I can also go into
> AmberTools/src/ambertools-binary-build/ and do
>
> git clone https://github.com/Amber-MD/ambertools-binary-build.git
>
> to see if that helps. Still no luck. That gets me:
>
> Permission denied (publickey).
> fatal: Could not read from remote repository.
>
> Please make sure you have the correct access rights
> and the repository exists.
> Unable to fetch in submodule path 'AmberTools/src/build-bot/
> ambertools-test'
>
> which is a familiar error.
>
> So, I suppose what I should be trying to do at this point is make a fresh
> clone and get its submodules initialized, but I need a protocol for doing
> that. What I'm trying to do at the moment is:
>
> git clone gitosis.git.ambermd.org:/amber.git <new amber repo>
> cd <new amber repo>/AmberTools/src/build-bot/
> git clone https://github.com/Amber-MD/ambertools-ci.git
> cd <new amber repo>/AmberTools/src/ambertools-binary-build/
> git clone https://github.com/Amber-MD/ambertools-binary-build.git
> cd <new amber repo>
> git pull
> git submodule update --init
>
> But, this is not working for various errors shown above.
>
> Dave
>
>
> On Mon, Jun 12, 2017 at 11:55 AM, David Cerutti <dscerutti.gmail.com>
> wrote:
>
> > Aha you were pointing me to github. I can clone that repo directly:
> >
> > git clone https://github.com/Amber-MD/ambertools-ci.git
> >
> > If I do that within AmberTools/src/build-bot/, I also get a directory
> > ambertools-test/ with only a .git file for its contents. Then, if I go
> > back to ${AMBERHOME} and do git pull (already up to date), git submodule
> > update --init I get:
> >
> > fatal: Needed a single revision
> > Unable to find current revision in submodule path
> > 'AmberTools/src/build-bot/ambertools-test'
> >
> >
> >
> >
> > On Mon, Jun 12, 2017 at 11:39 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >
> >> On Mon, Jun 12, 2017 at 11:32 AM, David Cerutti <dscerutti.gmail.com>
> >> wrote:
> >>
> >> > How should I clone just the one directory?
> >>
> >>
> >> I don't know what you meant here.
> >>
> >> What's your git version? if it's old, I recommend to update it and
> retry.
> >>
> >> Hai
> >>
> >>
> >> > I'm warying of doing a sparse
> >> > checkout because all that I see online tends to revolve around
> cloning a
> >> > clean repository with only portions of the original.
> >> >
> >> > On Mon, Jun 12, 2017 at 11:18 AM, Hai Nguyen <nhai.qn.gmail.com>
> wrote:
> >> >
> >> > > I am not sure why, but that ambertools-test repo was renamed to
> >> > > ambertools-ci (https://github.com/Amber-MD/ambertools-ci)
> >> > >
> >> > > Can you try git clone that repo directly to see if you got the
> denial?
> >> > >
> >> > > I will have a look tonight.
> >> > > Meanwhile, you can safely ignore that repo to continue your work.
> >> > >
> >> > > Hai
> >> > >
> >> > > On Mon, Jun 12, 2017 at 11:08 AM, David Cerutti <
> dscerutti.gmail.com>
> >> > > wrote:
> >> > >
> >> > > > Hello devs,
> >> > > >
> >> > > > Has anyone seen this problem? It looks like a git permissions
> >> issue,
> >> > but
> >> > > > that is very odd since I can do a clean
> >> > > >
> >> > > > git clone gitosis.git.ambermd.org:/amber.git <amber install
> >> directory>
> >> > > >
> >> > > > without problems. However, if I then do
> >> > > >
> >> > > > git pull
> >> > > > git submodule update --init
> >> > > >
> >> > > > Submodule 'AmberTools/src/ambertools-binary-build' (
> >> > > > https://github.com/Amber-MD/ambertools-binary-build) registered
> for
> >> > path
> >> > > > 'AmberTools/src/ambertools-binary-build'
> >> > > > Submodule 'AmberTools/src/build-bot/ambertools-test'
> >> > > > (git.github.com:Amber-MD/ambertools-test)
> >> > > > registered for path 'AmberTools/src/build-bot/ambertools-test'
> >> > > > Submodule 'AmberTools/src/build-bot/docker-amber-build-box'
> >> > > > (git.github.com:Amber-MD/docker-amber-build-box)
> >> > > > registered for path 'AmberTools/src/build-bot/dock
> >> er-amber-build-box'
> >> > > > Submodule 'AmberTools/src/cphstats' (git.github.com:/Amber-MD/
> >> > > > cphstats.git)
> >> > > > registered for path 'AmberTools/src/cphstats'
> >> > > > Submodule 'AmberTools/src/cpptraj' (git.github.com:/Amber-MD/
> >> > > cpptraj.git)
> >> > > > registered for path 'AmberTools/src/cpptraj'
> >> > > > Submodule 'AmberTools/src/parmed' (git.github.com:/ParmEd/ParmEd
> >> .git)
> >> > > > registered for path 'AmberTools/src/parmed'
> >> > > > Submodule 'AmberTools/src/pdb4amber' (git.github.com:/Amber-MD/
> >> > > pdb4amber)
> >> > > > registered for path 'AmberTools/src/pdb4amber'
> >> > > > Submodule 'AmberTools/src/pytraj' (git.github.com:/Amber-MD/
> >> > pytraj.git)
> >> > > > registered for path 'AmberTools/src/pytraj'
> >> > > > Cloning into 'AmberTools/src/ambertools-binary-build'...
> >> > > > remote: Counting objects: 1700, done.
> >> > > > remote: Compressing objects: 100% (71/71), done.
> >> > > > remote: Total 1700 (delta 60), reused 65 (delta 32), pack-reused
> >> 1597
> >> > > > Receiving objects: 100% (1700/1700), 246.98 KiB, done.
> >> > > > Resolving deltas: 100% (1012/1012), done.
> >> > > > Submodule path 'AmberTools/src/ambertools-binary-build': checked
> >> out
> >> > > > '18c419831a106b836ed60bf2296c241a44a4714e'
> >> > > > Cloning into 'AmberTools/src/build-bot/ambertools-test'...
> >> > > > Permission denied (publickey).
> >> > > > fatal: Could not read from remote repository.
> >> > > >
> >> > > > Please make sure you have the correct access rights
> >> > > > and the repository exists.
> >> > > > Clone of 'git.github.com:Amber-MD/ambertools-test' into submodule
> >> path
> >> > > > 'AmberTools/src/build-bot/ambertools-test' failed
> >> > > > [cerutti.casegroup1 amber3]$ ls AmberTools/src/build-bot/
> >> > > >
> >> > > > It looks like a permissions issue, but I'm not certain. The
> >> directory
> >> > > > AmberTools/src/build-bot/ certainly exists, and I'm assuming that
> it
> >> > > wants
> >> > > > to clone a new directory ambertools-test/ into that, but at
> present
> >> I
> >> > > don't
> >> > > > see ambertools-test/. I've been trying to clone a new repo
> because
> >> > I've
> >> > > > been having this same problem when I try to update the current
> repo
> >> > I've
> >> > > > been working in. Am I missing something obvious?
> >> > > >
> >> > > > Thanks!
> >> > > >
> >> > > > Dave
> >> > > > _______________________________________________
> >> > > > AMBER-Developers mailing list
> >> > > > AMBER-Developers.ambermd.org
> >> > > > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >> > > >
> >> > > _______________________________________________
> >> > > AMBER-Developers mailing list
> >> > > AMBER-Developers.ambermd.org
> >> > > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >> > >
> >> > _______________________________________________
> >> > AMBER-Developers mailing list
> >> > AMBER-Developers.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >> >
> >> _______________________________________________
> >> AMBER-Developers mailing list
> >> AMBER-Developers.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>
> >
> >
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
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Received on Mon Jun 12 2017 - 10:00:03 PDT
