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

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 'git@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), 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 'git@salsa.debian.org:med-team/gatk.git'


Seems I'm running circles.  Any hint (besides simply not commiting
pristine-tar which would be an alternative option)?

Kind regards

      Andreas.

  
-- 
http://fam-tille.de
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