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_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 'g...@salsa.debian.org:med-team/gatk.git' Just for the record:
https://salsa.debian.org/formorer/lfs-test/tree/master lfs on salsa works just fine. And you did "git lfs install" on your local machine? Alex
