Re: remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or try a manual "git lfs push --all".

2018-05-30 Thread Ian Jackson
Alexander Wirt writes ("Re: remote: GitLab: LFS objects are missing. Ensure LFS 
is properly set up or try a manual "git lfs push --all"."):
> You are completly right. Thats why I said I will stop answering questions
> here. This will help me to come down.

For my part I think I should apologise, because I think I have
contributed to making you less calm.

I too am impressed by and grateful for your work first on Alioth and
now on Salsa.  I think I let my high expectations get in the way of
expressing that.

Regards,
Ian.

-- 
Ian JacksonThese opinions are my own.

If I emailed you from an address @fyvzl.net or @evade.org.uk, that is
a private address which bypasses my fierce spamfilter.



Re: remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or try a manual "git lfs push --all".

2018-05-30 Thread Alexander Wirt
On Wed, 30 May 2018, Chris Lamb wrote:

Hi, 

> > I am not a kindergarten teacher. I will just stop answering mails here. 
> 
> You must know I have the greatest of respect for the tireless work you
> have done and continue to do so as part of the migration from Alioth
> to salsa.
> 
> You are actually not privy to the number of times I have mentioned
> this both internally and externally to the Project, including to those
> working at GitLab itself. Indeed, it is one of the real delights of
> being the Project Leader to be able to extoll and promote the work
> done by its developers.
> 
> However, I cannot help feel that (at least appearing!) to be little
> more cordial in your communications over the past day or so would be
> more productive and actually reflect your actual personality better.
> 
> I understand that you are only human and thus have finite amount of
> time and energy to exert on what you perceive to be trivial and
> obvious responses. But if you are human too, then so are your fellow
> developers who — like all homo sapiens — ask dumb questions at times,
> rely a little too much on others, tend to skim-read, etc. etc.
> 
> If you would like specific examples (and my associated humbly-offered
> suggestions), I would be very happy to discuss that privately with you
> at your convenience.
You are completly right. Thats why I said I will stop answering questions
here. This will help me to come down.

Alex
 



Re: remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or try a manual "git lfs push --all".

2018-05-30 Thread Chris Lamb
Dear Alexander (et al.),

> I am not a kindergarten teacher. I will just stop answering mails here. 

You must know I have the greatest of respect for the tireless work you
have done and continue to do so as part of the migration from Alioth
to salsa.

You are actually not privy to the number of times I have mentioned
this both internally and externally to the Project, including to those
working at GitLab itself. Indeed, it is one of the real delights of
being the Project Leader to be able to extoll and promote the work
done by its developers.

However, I cannot help feel that (at least appearing!) to be little
more cordial in your communications over the past day or so would be
more productive and actually reflect your actual personality better.

I understand that you are only human and thus have finite amount of
time and energy to exert on what you perceive to be trivial and
obvious responses. But if you are human too, then so are your fellow
developers who — like all homo sapiens — ask dumb questions at times,
rely a little too much on others, tend to skim-read, etc. etc.

If you would like specific examples (and my associated humbly-offered
suggestions), I would be very happy to discuss that privately with you
at your convenience.


Best wishes,

-- 
  ,''`.
 : :'  : Chris Lamb
 `. `'`  la...@debian.org / chris-lamb.co.uk
   `-



Re: remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or try a manual "git lfs push --all".

2018-05-30 Thread Andreas Tille
Hi Alexander,

On Wed, May 30, 2018 at 02:12:38PM +0200, Alexander Wirt wrote:
> 
> > In this particular case, that environment is Salsa.  If course there
> > will always be mistakes and people will overlook things.  But if you
> > find that you are having to explain similar things over and over again
> > then it probably means that your user interfaces or documentation are
> > not sufficiently good.
> He don't read the documentation. Especially the part about "where to find
> support". In fact he knows about it, he just ignores it. 

I was not seeking for Salsa support.  I have originally asked a question
on debian-devel where I get usually some kind answer.  I think it was
sensible to assume that some reader of debian-devel might have had a
similar question and knows the solution.  You picked up the ball as
Salsa admin (which is nice in general, the wording leaves room for
enhancement).  In contrast to your assumption I'm able to find the Salsa
support tracker and I will use it.
 
Kind regards

   Andreas. 

-- 
http://fam-tille.de



Re: remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or try a manual "git lfs push --all".

2018-05-30 Thread Alexander Wirt
On Wed, 30 May 2018, Ian Jackson wrote:

> Alexander Wirt writes ("Re: remote: GitLab: LFS objects are missing. Ensure 
> LFS is properly set up or try a manual "git lfs push --all"."):
> > Alex - fed up with explaining the same things again and again and again
> 
> Debian contributors are not, by and large, stupid or lazy.  If you
> find that many Debian contributors are making similar mistakes then
> probably this is probably because of factors in their environment.
> 
> In this particular case, that environment is Salsa.  If course there
> will always be mistakes and people will overlook things.  But if you
> find that you are having to explain similar things over and over again
> then it probably means that your user interfaces or documentation are
> not sufficiently good.
> 
> A better approach, when someone asks a question you think is answered
> in the docs, is to ask in a friendly way, something like this:
I am not a kindergarten teacher. I will just stop answering mails here. 

Alex
 



Re: remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or try a manual "git lfs push --all".

2018-05-30 Thread Alexander Wirt
On Wed, 30 May 2018, Ian Jackson wrote:

> Alexander Wirt writes ("Re: remote: GitLab: LFS objects are missing. Ensure 
> LFS is properly set up or try a manual "git lfs push --all"."):
> > Alex - fed up with explaining the same things again and again and again
> 
> Debian contributors are not, by and large, stupid or lazy.  If you
> find that many Debian contributors are making similar mistakes then
> probably this is probably because of factors in their environment.
in fact its mostly andreas. 

> In this particular case, that environment is Salsa.  If course there
> will always be mistakes and people will overlook things.  But if you
> find that you are having to explain similar things over and over again
> then it probably means that your user interfaces or documentation are
> not sufficiently good.
He don't read the documentation. Especially the part about "where to find
support". In fact he knows about it, he just ignores it. 

> 
> A better approach, when someone asks a question you think is answered
> in the docs, is to ask in a friendly way, something like this:
Thats the part of again and again. I *KNOW* that andreas knows about the
support channels, he just ignores it. 

> 
>   Can you tell me where you looked for the answer, or where
>   you looked for contact information, before asking your question
>   here on debian-devel ?
> 
>   Your question seems to me to be answered here:
>  https://whatever
>   but perhaps that page wasn't sufficiently discoverable, or maybe
>   it wasn't clear enough ?
> 
>   We want to improve the UI and the documentation so that people
>   more easily find the information they need.  (And of course to
>   reduce our own workload!)  So suggestions for improvement would
>   be very welcome.
> 
> Personally when I make some kind of bug report or support request I
> try to anticipate this kind of question.  The result is often
> suggestions for improvements to docs, or docs visibility.  (Since
> everything we rely on is Free Software, we can always change things to
> make life smoother for users, and less burdensome for service
> operators...)
> 
> Ian.
> 
> -- 
> Ian JacksonThese opinions are my own.
> 
> If I emailed you from an address @fyvzl.net or @evade.org.uk, that is
> a private address which bypasses my fierce spamfilter.
> 



Re: remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or try a manual "git lfs push --all".

2018-05-30 Thread Ian Jackson
Alexander Wirt writes ("Re: remote: GitLab: LFS objects are missing. Ensure LFS 
is properly set up or try a manual "git lfs push --all"."):
> Alex - fed up with explaining the same things again and again and again

Debian contributors are not, by and large, stupid or lazy.  If you
find that many Debian contributors are making similar mistakes then
probably this is probably because of factors in their environment.

In this particular case, that environment is Salsa.  If course there
will always be mistakes and people will overlook things.  But if you
find that you are having to explain similar things over and over again
then it probably means that your user interfaces or documentation are
not sufficiently good.

A better approach, when someone asks a question you think is answered
in the docs, is to ask in a friendly way, something like this:

  Can you tell me where you looked for the answer, or where
  you looked for contact information, before asking your question
  here on debian-devel ?

  Your question seems to me to be answered here:
 https://whatever
  but perhaps that page wasn't sufficiently discoverable, or maybe
  it wasn't clear enough ?

  We want to improve the UI and the documentation so that people
  more easily find the information they need.  (And of course to
  reduce our own workload!)  So suggestions for improvement would
  be very welcome.

Personally when I make some kind of bug report or support request I
try to anticipate this kind of question.  The result is often
suggestions for improvements to docs, or docs visibility.  (Since
everything we rely on is Free Software, we can always change things to
make life smoother for users, and less burdensome for service
operators...)

Ian.

-- 
Ian JacksonThese opinions are my own.

If I emailed you from an address @fyvzl.net or @evade.org.uk, that is
a private address which bypasses my fierce spamfilter.



Re: remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or try a manual "git lfs push --all".

2018-05-30 Thread Alexander Wirt
On Wed, 30 May 2018, Andreas Tille wrote:

> Hi again,
> 
> On Wed, May 30, 2018 at 07:50:01AM +0200, Alexander Wirt wrote:
> > > > Your repo has lfs disabled. You should enable it. 
> > > 
> > > How can I do this?
> > > I've just found[1]:  "Your administrator only need to enable the LFS 
> > > option."
> > *seufz* we enabled it, but as you can guess it needs to get enabled per 
> > repo.
> > 
> > Settings -> Permissions -> Git Large File Storage
> 
> Thanks for the hint.  I would not call "Permissions" the obvious place to
> look for this and my web search did not uncover this, sorry.
> 
> Unfortunately it does not work yet:
> 
> 
> gatk(master) $ git push
> Counting objects: 4599, done.
> Delta compression using up to 4 threads.
> Compressing objects: 100% (4453/4453), done.
> Writing objects: 100% (4599/4599), 64.56 MiB | 462.00 KiB/s, done.
> Total 4599 (delta 811), reused 1 (delta 0)
> remote: Resolving deltas: 100% (811/811), completed with 1 local object.
> remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or try 
> a manual "git lfs push --all".
> To salsa.debian.org:med-team/gatk.git
>  ! [remote rejected] master -> master (pre-receive hook declined)
>  ! [remote rejected] pristine-tar -> pristine-tar (pre-receive hook declined)
>  ! [remote rejected] upstream -> upstream (pre-receive hook declined)
>  ! [remote rejected] upstream/4.0.4.0 -> upstream/4.0.4.0 (pre-receive hook 
> declined)
> error: failed to push some refs to 'g...@salsa.debian.org:med-team/gatk.git'
> gatk(master) $ git lfs push --all
> Specify a remote and a remote branch name (`git lfs push origin master`)
> gatk(master) $ LC_ALL=C git lfs push origin master
> Locking support detected on remote "origin". Consider enabling it with:
>   $ git config 
> lfs.https://salsa.debian.org/med-team/gatk.git/info/lfs.locksverify true
> LFS upload missing objects: (0/246), 0 B | 0 B/s  
>   
>
>   (missing) src/test/resources/large/NA24385.vcf.gz 
> (f3326d552a86197e1d8fbfee2941f6b8684f7b31bfab9730f953401566066e2b)
>   (missing) 
> src/test/resources/large/VQSR/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.sites.20.1M-10M.vcf
>  (48f0bdac467ee4d618e6425c0989a344e5d8523baaf5016e92ef246c4311c58b)
>   (missing) src/test/resources/large/VQSR/g94982_b37_chr20_1m_10m.vcf.gz.tbi 
> (97a7c779a82a4e3aea8de77a4e9bda68909d489e3c0553399c1e9affbba6c0d8)
>   (missing) 
> src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 
> (b916357182a024e126b7754e41d134e67e26d6328538eee8865ac264c981ab04)
>   (missing) src/test/resources/large/mutect/dream_synthetic_bams/tumor_2.bam 
> (9d9ce1ff6c68429befeef11b9626a959af109aa99a637f89d2abf643ab524ffb)
>   (missing) 
> src/test/resources/large/mutect/dream_synthetic_bams/normal_1.bam.bai 
> (369eed4192701e4abd5a9be1e4d308ce46232983812a854a847465ab7a2fc2a5)
>   (missing) 
> src/test/resources/large/mutect/dream_synthetic_bams/tumor_1.bam.bai 
> (566ede9346c4260d7810e112bd4f4892ab1aaa37f5b20ebf4b3ba0fe83db2993)
> Uploading LFS objects:   0% (0/246), 0 B | 0 B/s, done
>   (missing) src/test/resources/large/gvcfs/combined.gatk3.7.g.vcf.gz.tbi 
> (403996681f4a0622236a45c71a63ba8c3594664e379cde16efd10f5f598499ff)
> ...
>   (missing) src/test/resources/large/VQSR/snpRecal.vcf 
> (a9c2535862d234fd09c5978c00a6127caa079989158a93cb13a2356911c561bb)
>   (missing) 
> src/test/resources/large/cnv_germline_workflows_test_files/SM-74P2T_20xy-downsampled.bam
>  (7cfbe031257a12d39c460a775bd22b6713130b9a45f6976df7e7b1c7950a268b)
>   (missing) src/test/resources/large/VQSR/g94982_b37_chr20_1m_10m.vcf.tbi 
> (3540c3ec7d15607a541b5ccf51c8cc60d03d826c5abbd866f4573d2694a86e9f)
>   (missing) 
> src/test/resources/large/funcotator/gencode.v19.chr_patch_hapl_scaff.chr3.gtf 
> (3e935c5ac87020a90689b86f9a6ca5f05c24736528f550ea54a0c84772c6fdd3)
>   (missing) 
> src/test/resources/large/cnv_somatic_workflows_test_files/wes-do-gc.pon.hdf5 
> (b9c1b28743e4569379f987d5eeebc5393467fd2fc981c85475873b219576dfa4)
>   (missing) 
> src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict
>  (604e04600e644864c34e2fce42241febac0f0be062223a66e88499fca1c55147)
>   (missing) 
> src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram.crai
>  (fc99f68bcc0a4fc1ff3a240ad64d62fa8bfd31ecdc11d326107a5e1ec969ccca)
>   (missing) 
> src/test/resources/large/mutect/dream_synthetic_bams/normal_

Re: remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or try a manual "git lfs push --all".

2018-05-30 Thread Alexander Wirt
On Wed, 30 May 2018, Geert Stappers wrote:

> On Wed, May 30, 2018 at 11:19:14AM +0200, Alexander Wirt wrote:
> > On Wed, 30 May 2018, Andreas Tille wrote:
> > > Hi again,
>  
>   :-)
> 
> 
> > > On Wed, May 30, 2018 at 07:50:01AM +0200, Alexander Wirt wrote:
> > > > > > Your repo has lfs disabled. You should enable it. 
> > > > > 
> > > > > How can I do this?
> > > > > I've just found[1]:  "Your administrator only need to enable the LFS 
> > > > > option."
> > > > *seufz* we enabled it, but as you can guess it needs to get enabled per 
> > > > repo.
> > > > 
> > > > Settings -> Permissions -> Git Large File Storage
> > > 
> > > Thanks for the hint.  I would not call "Permissions" the obvious place to
> > > look for this and my web search did not uncover this, sorry.
> > > 
> > > Unfortunately it does not work yet:
> > use the support tracker and I will look after it when I have time.
> 
> Where is that support tracker?
> 
> (It feels strang to report "salsa is broken" at Salsa itself.)
(sorry thats complete nonsense, if the webfrontend would be broken at all.
yes - use IRC. But thats not the case here). 

there are several options to find it: 

1) read my announcements: 
https://lists.debian.org/debian-devel-announce/2018/01/msg4.html
2) press help on salsa: https://salsa.debian.org/help
3) check the wiki https://wiki.debian.org/Salsa/Doc#Support

> 
> > debian-devel is not on the list of salsa supportchannels.
>  
> Even multiple suportchannels for salsa.
> What are the preferred top three?
For all longer taking things of course tickets. 

> In other words
> How cool would it be if the "not here" would have travelled with
>  at URL you find a list of salsa supportchannels
How cool would it be if people would use their heads. I can only tell people
where the door is, but they have to use it on their own. 

Alex - fed up with explaining the same things again and again and again 
 



Re: remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or try a manual "git lfs push --all".

2018-05-30 Thread Emilio Pozuelo Monfort
On 30/05/18 11:40, Geert Stappers wrote:
> On Wed, May 30, 2018 at 11:19:14AM +0200, Alexander Wirt wrote:
>> On Wed, 30 May 2018, Andreas Tille wrote:
>>> Hi again,
>  
>   :-)
> 
> 
>>> On Wed, May 30, 2018 at 07:50:01AM +0200, Alexander Wirt wrote:
>> Your repo has lfs disabled. You should enable it. 
>
> How can I do this?
> I've just found[1]:  "Your administrator only need to enable the LFS 
> option."
 *seufz* we enabled it, but as you can guess it needs to get enabled per 
 repo.

 Settings -> Permissions -> Git Large File Storage
>>>
>>> Thanks for the hint.  I would not call "Permissions" the obvious place to
>>> look for this and my web search did not uncover this, sorry.
>>>
>>> Unfortunately it does not work yet:
>> use the support tracker and I will look after it when I have time.
> 
> Where is that support tracker?
> 
> (It feels strang to report "salsa is broken" at Salsa itself.)

It's not broken. One feature for one package is not working, but the salsa issue
tracker is still working.

BTW you file BTS issues in the BTS. That doesn't feel weird to me.

>> debian-devel is not on the list of salsa supportchannels.
>  
> Even multiple suportchannels for salsa.
> What are the preferred top three?
>
> In other words
> How cool would it be if the "not here" would have travelled with
>  at URL you find a list of salsa supportchannels
> ???

https://salsa.debian.org/help has a "Support" section at the top.

Granted, that page is linked from every salsa page, but the link is not very
discoverable if you are logged in (it's on the top right drop down menu).

Cheers,
Emilio



Re: remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or try a manual "git lfs push --all".

2018-05-30 Thread Geert Stappers
On Wed, May 30, 2018 at 11:19:14AM +0200, Alexander Wirt wrote:
> On Wed, 30 May 2018, Andreas Tille wrote:
> > Hi again,
 
  :-)


> > On Wed, May 30, 2018 at 07:50:01AM +0200, Alexander Wirt wrote:
> > > > > Your repo has lfs disabled. You should enable it. 
> > > > 
> > > > How can I do this?
> > > > I've just found[1]:  "Your administrator only need to enable the LFS 
> > > > option."
> > > *seufz* we enabled it, but as you can guess it needs to get enabled per 
> > > repo.
> > > 
> > > Settings -> Permissions -> Git Large File Storage
> > 
> > Thanks for the hint.  I would not call "Permissions" the obvious place to
> > look for this and my web search did not uncover this, sorry.
> > 
> > Unfortunately it does not work yet:
> use the support tracker and I will look after it when I have time.

Where is that support tracker?

(It feels strang to report "salsa is broken" at Salsa itself.)


> debian-devel is not on the list of salsa supportchannels.
 
Even multiple suportchannels for salsa.
What are the preferred top three?


In other words
How cool would it be if the "not here" would have travelled with
 at URL you find a list of salsa supportchannels
???

 
Groeten
Geert Stappers
-- 
Leven en laten leven



Re: remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or try a manual "git lfs push --all".

2018-05-30 Thread Alexander Wirt
On Wed, 30 May 2018, Andreas Tille wrote:

> Hi again,
> 
> On Wed, May 30, 2018 at 07:50:01AM +0200, Alexander Wirt wrote:
> > > > Your repo has lfs disabled. You should enable it. 
> > > 
> > > How can I do this?
> > > I've just found[1]:  "Your administrator only need to enable the LFS 
> > > option."
> > *seufz* we enabled it, but as you can guess it needs to get enabled per 
> > repo.
> > 
> > Settings -> Permissions -> Git Large File Storage
> 
> Thanks for the hint.  I would not call "Permissions" the obvious place to
> look for this and my web search did not uncover this, sorry.
> 
> Unfortunately it does not work yet:
use the support tracker and I will look after it when I have time.
debian-devel is not on the list of salsa supportchannels.



Re: remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or try a manual "git lfs push --all".

2018-05-29 Thread Andreas Tille
Hi again,

On Wed, May 30, 2018 at 07:50:01AM +0200, Alexander Wirt wrote:
> > > Your repo has lfs disabled. You should enable it. 
> > 
> > How can I do this?
> > I've just found[1]:  "Your administrator only need to enable the LFS 
> > option."
> *seufz* we enabled it, but as you can guess it needs to get enabled per repo.
> 
> Settings -> Permissions -> Git Large File Storage

Thanks for the hint.  I would not call "Permissions" the obvious place to
look for this and my web search did not uncover this, sorry.

Unfortunately it does not work yet:


gatk(master) $ git push
Counting objects: 4599, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (4453/4453), done.
Writing objects: 100% (4599/4599), 64.56 MiB | 462.00 KiB/s, done.
Total 4599 (delta 811), reused 1 (delta 0)
remote: Resolving deltas: 100% (811/811), completed with 1 local object.
remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or try a 
manual "git lfs push --all".
To salsa.debian.org:med-team/gatk.git
 ! [remote rejected] master -> master (pre-receive hook declined)
 ! [remote rejected] pristine-tar -> pristine-tar (pre-receive hook declined)
 ! [remote rejected] upstream -> upstream (pre-receive hook declined)
 ! [remote rejected] upstream/4.0.4.0 -> upstream/4.0.4.0 (pre-receive hook 
declined)
error: failed to push some refs to 'g...@salsa.debian.org:med-team/gatk.git'
gatk(master) $ git lfs push --all
Specify a remote and a remote branch name (`git lfs push origin master`)
gatk(master) $ LC_ALL=C git lfs push origin master
Locking support detected on remote "origin". Consider enabling it with:
  $ git config 
lfs.https://salsa.debian.org/med-team/gatk.git/info/lfs.locksverify true
LFS upload missing objects: (0/246), 0 B | 0 B/s

   
  (missing) src/test/resources/large/NA24385.vcf.gz 
(f3326d552a86197e1d8fbfee2941f6b8684f7b31bfab9730f953401566066e2b)
  (missing) 
src/test/resources/large/VQSR/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.sites.20.1M-10M.vcf
 (48f0bdac467ee4d618e6425c0989a344e5d8523baaf5016e92ef246c4311c58b)
  (missing) src/test/resources/large/VQSR/g94982_b37_chr20_1m_10m.vcf.gz.tbi 
(97a7c779a82a4e3aea8de77a4e9bda68909d489e3c0553399c1e9affbba6c0d8)
  (missing) 
src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 
(b916357182a024e126b7754e41d134e67e26d6328538eee8865ac264c981ab04)
  (missing) src/test/resources/large/mutect/dream_synthetic_bams/tumor_2.bam 
(9d9ce1ff6c68429befeef11b9626a959af109aa99a637f89d2abf643ab524ffb)
  (missing) 
src/test/resources/large/mutect/dream_synthetic_bams/normal_1.bam.bai 
(369eed4192701e4abd5a9be1e4d308ce46232983812a854a847465ab7a2fc2a5)
  (missing) 
src/test/resources/large/mutect/dream_synthetic_bams/tumor_1.bam.bai 
(566ede9346c4260d7810e112bd4f4892ab1aaa37f5b20ebf4b3ba0fe83db2993)
Uploading LFS objects:   0% (0/246), 0 B | 0 B/s, done
  (missing) src/test/resources/large/gvcfs/combined.gatk3.7.g.vcf.gz.tbi 
(403996681f4a0622236a45c71a63ba8c3594664e379cde16efd10f5f598499ff)
...
  (missing) src/test/resources/large/VQSR/snpRecal.vcf 
(a9c2535862d234fd09c5978c00a6127caa079989158a93cb13a2356911c561bb)
  (missing) 
src/test/resources/large/cnv_germline_workflows_test_files/SM-74P2T_20xy-downsampled.bam
 (7cfbe031257a12d39c460a775bd22b6713130b9a45f6976df7e7b1c7950a268b)
  (missing) src/test/resources/large/VQSR/g94982_b37_chr20_1m_10m.vcf.tbi 
(3540c3ec7d15607a541b5ccf51c8cc60d03d826c5abbd866f4573d2694a86e9f)
  (missing) 
src/test/resources/large/funcotator/gencode.v19.chr_patch_hapl_scaff.chr3.gtf 
(3e935c5ac87020a90689b86f9a6ca5f05c24736528f550ea54a0c84772c6fdd3)
  (missing) 
src/test/resources/large/cnv_somatic_workflows_test_files/wes-do-gc.pon.hdf5 
(b9c1b28743e4569379f987d5eeebc5393467fd2fc981c85475873b219576dfa4)
  (missing) 
src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict
 (604e04600e644864c34e2fce42241febac0f0be062223a66e88499fca1c55147)
  (missing) 
src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram.crai
 (fc99f68bcc0a4fc1ff3a240ad64d62fa8bfd31ecdc11d326107a5e1ec969ccca)
  (missing) 
src/test/resources/large/mutect/dream_synthetic_bams/normal_4.bam.bai 
(14620c7d836db17cd2d473658208d44ae3a5c3cec3baf0f6b697dcc87e7075b6)
gatk(master) git lfs push --all
Specify a remote and a remote branch name (`git lfs push origin master`)
gatk(master) $ git push
Counting objects: 4599, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (4453/4453), done.
Writing objects: 100% (4599/4599), 64.56 MiB | 410.00 KiB/s, done.
Total 4599 (delta 810), reused 1 (delta 0)
remote: Resolving deltas: 100% (810/810), complete

Re: remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or try a manual "git lfs push --all".

2018-05-29 Thread Alexander Wirt
On Wed, 30 May 2018, Andreas Tille wrote:

> Hi,
> 
> On Tue, May 29, 2018 at 11:35:00PM +0200, Alexander Wirt wrote:
> > > I intend to push a new version of gatk[1] which contains some large
> > > files.  I imported the new upstream package the usual way.  But if I
> > > want to push I get:
> > > 
> > > (master) $ LC_ALL=C git push
> > > Counting objects: 4599, done.
> > > Delta compression using up to 4 threads.
> > > Compressing objects: 100% (4453/4453), done.
> > > Writing objects: 100% (4599/4599), 64.56 MiB | 1.09 MiB/s, done.
> > > Total 4599 (delta 811), reused 1 (delta 0)
> > > remote: Resolving deltas: 100% (811/811), completed with 1 local object.
> > > remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or 
> > > try a manual "git lfs push --all".
> > > To salsa.debian.org:med-team/gatk.git
> > >  ! [remote rejected] master -> master (pre-receive hook declined)
> > >  ! [remote rejected] pristine-tar -> pristine-tar (pre-receive hook 
> > > declined)
> > >  ! [remote rejected] upstream -> upstream (pre-receive hook declined)
> > >  ! [remote rejected] upstream/4.0.4.0 -> upstream/4.0.4.0 (pre-receive 
> > > hook declined)
> > > error: failed to push some refs to 
> > > 'g...@salsa.debian.org:med-team/gatk.git'
> > > 
> > > 
> > > I installed git-lfs locally and tried the command above but it seems it
> > > is really needed remotely on Salsa.  Am I missing something or is there
> > > some action needed?
> > Your repo has lfs disabled. You should enable it. 
> 
> How can I do this?
> I've just found[1]:  "Your administrator only need to enable the LFS option."
*seufz* we enabled it, but as you can guess it needs to get enabled per repo.

Settings -> Permissions -> Git Large File Storage
 
Alex



Re: remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or try a manual "git lfs push --all".

2018-05-29 Thread Andreas Tille
Hi,

On Tue, May 29, 2018 at 11:35:00PM +0200, Alexander Wirt wrote:
> > I intend to push a new version of gatk[1] which contains some large
> > files.  I imported the new upstream package the usual way.  But if I
> > want to push I get:
> > 
> > (master) $ LC_ALL=C git push
> > Counting objects: 4599, done.
> > Delta compression using up to 4 threads.
> > Compressing objects: 100% (4453/4453), done.
> > Writing objects: 100% (4599/4599), 64.56 MiB | 1.09 MiB/s, done.
> > Total 4599 (delta 811), reused 1 (delta 0)
> > remote: Resolving deltas: 100% (811/811), completed with 1 local object.
> > remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or 
> > try a manual "git lfs push --all".
> > To salsa.debian.org:med-team/gatk.git
> >  ! [remote rejected] master -> master (pre-receive hook declined)
> >  ! [remote rejected] pristine-tar -> pristine-tar (pre-receive hook 
> > declined)
> >  ! [remote rejected] upstream -> upstream (pre-receive hook declined)
> >  ! [remote rejected] upstream/4.0.4.0 -> upstream/4.0.4.0 (pre-receive hook 
> > declined)
> > error: failed to push some refs to 'g...@salsa.debian.org:med-team/gatk.git'
> > 
> > 
> > I installed git-lfs locally and tried the command above but it seems it
> > is really needed remotely on Salsa.  Am I missing something or is there
> > some action needed?
> Your repo has lfs disabled. You should enable it. 

How can I do this?
I've just found[1]:  "Your administrator only need to enable the LFS option."

Thanks for any hint

 Andreas.


[1] https://about.gitlab.com/2017/01/30/getting-started-with-git-lfs-tutorial/

-- 
http://fam-tille.de



Re: remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or try a manual "git lfs push --all".

2018-05-29 Thread Alexander Wirt
On Tue, 29 May 2018, Andreas Tille wrote:

> Hi,
> 
> I intend to push a new version of gatk[1] which contains some large
> files.  I imported the new upstream package the usual way.  But if I
> want to push I get:
> 
> (master) $ LC_ALL=C git push
> Counting objects: 4599, done.
> Delta compression using up to 4 threads.
> Compressing objects: 100% (4453/4453), done.
> Writing objects: 100% (4599/4599), 64.56 MiB | 1.09 MiB/s, done.
> Total 4599 (delta 811), reused 1 (delta 0)
> remote: Resolving deltas: 100% (811/811), completed with 1 local object.
> remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or try 
> a manual "git lfs push --all".
> To salsa.debian.org:med-team/gatk.git
>  ! [remote rejected] master -> master (pre-receive hook declined)
>  ! [remote rejected] pristine-tar -> pristine-tar (pre-receive hook declined)
>  ! [remote rejected] upstream -> upstream (pre-receive hook declined)
>  ! [remote rejected] upstream/4.0.4.0 -> upstream/4.0.4.0 (pre-receive hook 
> declined)
> error: failed to push some refs to 'g...@salsa.debian.org:med-team/gatk.git'
> 
> 
> I installed git-lfs locally and tried the command above but it seems it
> is really needed remotely on Salsa.  Am I missing something or is there
> some action needed?
Your repo has lfs disabled. You should enable it. 

Alex
 



remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or try a manual "git lfs push --all".

2018-05-29 Thread Andreas Tille
Hi,

I intend to push a new version of gatk[1] which contains some large
files.  I imported the new upstream package the usual way.  But if I
want to push I get:

(master) $ LC_ALL=C git push
Counting objects: 4599, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (4453/4453), done.
Writing objects: 100% (4599/4599), 64.56 MiB | 1.09 MiB/s, done.
Total 4599 (delta 811), reused 1 (delta 0)
remote: Resolving deltas: 100% (811/811), completed with 1 local object.
remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or try a 
manual "git lfs push --all".
To salsa.debian.org:med-team/gatk.git
 ! [remote rejected] master -> master (pre-receive hook declined)
 ! [remote rejected] pristine-tar -> pristine-tar (pre-receive hook declined)
 ! [remote rejected] upstream -> upstream (pre-receive hook declined)
 ! [remote rejected] upstream/4.0.4.0 -> upstream/4.0.4.0 (pre-receive hook 
declined)
error: failed to push some refs to 'g...@salsa.debian.org:med-team/gatk.git'


I installed git-lfs locally and tried the command above but it seems it
is really needed remotely on Salsa.  Am I missing something or is there
some action needed?

Kind regards

   Andreas.

[1] https://salsa.debian.org/med-team/gatk

-- 
http://fam-tille.de