From 25920832eb5feae9f601afe650ee127c70c5075b Mon Sep 17 00:00:00 2001 From: Geet Duggal Date: Fri, 20 May 2016 14:17:37 -0700 Subject: [PATCH] Increase robustness of unpacking in secure containers By adding the `--no-same-owner` option to the unpacking command, we avoid permission errors like what is below. This can occur in more secure LXC or Docker setups where user ID namespaces that differ from the host. ``` tar: GRCh37/rnaseq-2015-12-01/ref-transcripts.genePred: Cannot change ownership to uid 57074, gid 402011: Invalid argument tar: GRCh37/rnaseq-2015-12-01/tophat/GRCh37_transcriptome.1.bt2: Cannot change ownership to uid 57074, gid 402011: Invalid argument ... ``` --- ggd-recipes/GRCh37/transcripts.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ggd-recipes/GRCh37/transcripts.yaml b/ggd-recipes/GRCh37/transcripts.yaml index 5d4e87fa9..19fb00e19 100644 --- a/ggd-recipes/GRCh37/transcripts.yaml +++ b/ggd-recipes/GRCh37/transcripts.yaml @@ -12,7 +12,7 @@ recipe: - | baseurl=https://s3.amazonaws.com/biodata/annotation/GRCh37-rnaseq-2015-12-01.tar.xz wget -c -N $baseurl - xz -dc *-rnaseq-*.tar.xz | tar -xpf - + xz -dc *-rnaseq-*.tar.xz | tar --no-same-owner -xpf - mv */rnaseq-* rnaseq recipe_outfiles: - rnaseq/kallisto