This commit is contained in:
parent
8fe962dba5
commit
82dfd2d9e7
1 changed files with 52 additions and 0 deletions
|
@ -0,0 +1,52 @@
|
|||
I am trying to use git-annex as part of a datalad install on an Ubuntu 18.04 VirtualBox VM to set up a repository linking to some datasets at a public ftp server. When I use git-annex version 7.20190219 (installed with apt-get install git-annex-standalone from NeuroDebian) to add the links, I get the following error:
|
||||
|
||||
emmet@emmet-VirtualBox:~/conp-dataset/projects/1KGP-22May2019$ git annex addurl ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz –file=1KGP_chr6-vcf.gz
|
||||
addurl ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz Unsupported url scheme ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
|
||||
|
||||
download failed: Unsupported url scheme ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
|
||||
failed
|
||||
git-annex: addurl: 1 failed
|
||||
|
||||
|
||||
|
||||
However when I use git-annex v 6.20180227 (installed from the apt repository that came with Ubuntu 18.04) the link is generated correctly:
|
||||
|
||||
emmet@emmet-VirtualBox:~/conp-dataset/projects/1KGP-22May2019$ git annex addurl ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz --file=1KGP_chr6-vcf.gz
|
||||
addurl ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
|
||||
ALL.chr6.phase3_shapeit2_mvncall_integrated_ 100%[===========================================================================================>] 953.14M 9.81MB/s in 93s
|
||||
2019-05-22 16:10:44 URL: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz [999436830] -> "/home/emmet/conp-dataset/projects/1KGP-22May2019/.git/annex/tmp/URL-s999436830--ftp&c%%ftp.1000genomes.ebi.ac.uk-dda0592051d00d19f6c947a6b3aae6a5" [1]
|
||||
(to 1KGP_chr6-vcf.gz) ok
|
||||
(recording state in git...)
|
||||
|
||||
|
||||
|
||||
Similarly, after publishing the correctly formed links generated with 6.20180227 to github, trying to download them on another Ubuntu VirtualBox VM with git-annex 7.20190219 installed causes the following error:
|
||||
|
||||
emmet@emmet-VirtualBox:~/conp-dataset/projects/1KGP-22May2019$ git annex get 1KGP_chr2-vcf.gz
|
||||
get 1KGP_chr2-vcf.gz (from web...)
|
||||
download failed: Unsupported url scheme ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr2.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
|
||||
|
||||
Unable to access these remotes: web
|
||||
|
||||
Try making some of these repositories available:
|
||||
00000000-0000-0000-0000-000000000001 -- web
|
||||
2cc9a182-813f-4740-8157-c7a560560238 -- emmet@emmet-VirtualBox:~/conp-dataset/projects/1KGP-22May2019
|
||||
|
||||
(Note that these git remotes have annex-ignore set: origin)
|
||||
failed
|
||||
git-annex: get: 1 failed
|
||||
|
||||
|
||||
|
||||
but downloading them on that same VM with git-annex v 6.20180227 installed instead works:
|
||||
|
||||
emmet@emmet-VirtualBox:~/conp-dataset/projects/1KGP-22May2019$ git annex get 1KGP_chr2-vcf.gz
|
||||
get 1KGP_chr2-vcf.gz (from web...)
|
||||
ALL.chr2.phase3_sha 100%[===================>] 1.22G 6.99MB/s in 3m 11s
|
||||
2019-05-22 16:25:44 URL: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr2.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz [1312735578] -> "/home/emmet/conp-dataset/projects/1KGP-22May2019/.git/annex/tmp/MD5E-s1312735578--774370621affaf125e6994089f975ed7.gz" [1]
|
||||
(checksum...) ok
|
||||
(recording state in git...)
|
||||
|
||||
|
||||
Would you know why this is happening? And how I can avoid this failure mode in the more up-to-date version of git-annex?
|
||||
|
Loading…
Add table
Add a link
Reference in a new issue