# Transcript, annotation and indices for RNA-seq analysis
# Prepared from Ensembl transcripts using: 
# https://github.com/chapmanb/cloudbiolinux/blob/master/utils/prepare_tx_gff.py
---
attributes:
  name: transcripts
  version: 2015-12-01
recipe:
  full:
    recipe_type: bash
    recipe_cmds:
      - |
        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 -
        mv */rnaseq-* rnaseq
    recipe_outfiles:
      - rnaseq/kallisto
      - rnaseq/tophat
      - rnaseq/ref-transcripts.bed
      - rnaseq/ref-transcripts.dexseq.gff3
      - rnaseq/ref-transcripts.fa
      - rnaseq/ref-transcripts.genePred
      - rnaseq/ref-transcripts.gtf
      - rnaseq/ref-transcripts.gtf.db
      - rnaseq/ref-transcripts-mask.gtf
      - rnaseq/ref-transcripts.refFlat
      - rnaseq/ref-transcripts-splicesites.txt
      - rnaseq/rRNA.gtf
      - rnaseq/rRNA.gtf.db
      - rnaseq/rRNA.interval_list

# Transcript, annotation and indices for RNA-seq analysis
# Prepared from Ensembl transcripts using: 
# https://github.com/chapmanb/cloudbiolinux/blob/master/utils/prepare_tx_gff.py
---
attributes:
  name: transcripts
  version: 2015-12-01
recipe:
  full:
    recipe_type: bash
    recipe_cmds:
      - |
        baseurl=https://s3.amazonaws.com/biodata/annotation/GRCh37-rnaseq-2015-12-01.tar.xz
        wget -c -N $baseurl
        xz -dc *-rnaseq-*.tar.xz | tar --no-same-owner -xpf -
        mv */rnaseq-* rnaseq
    recipe_outfiles:
      - rnaseq/kallisto
      - rnaseq/tophat
      - rnaseq/ref-transcripts.bed
      - rnaseq/ref-transcripts.dexseq.gff3
      - rnaseq/ref-transcripts.fa
      - rnaseq/ref-transcripts.genePred
      - rnaseq/ref-transcripts.gtf
      - rnaseq/ref-transcripts.gtf.db
      - rnaseq/ref-transcripts-mask.gtf
      - rnaseq/ref-transcripts.refFlat
      - rnaseq/ref-transcripts-splicesites.txt
      - rnaseq/rRNA.gtf
      - rnaseq/rRNA.gtf.db
      - rnaseq/rRNA.interval_list

Increase robustness of unpacking in secure containers
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
...
```