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Reviewing mirbase.org shows that the URLs for downloading have changed (see new locations at CURRENT/genomes) and are no longer compressed.
./ggd-recipes/mm10/mirbase.yaml: wget --random-wait --retry-connrefused -q -c -O hairpin.fa.gz https://www.mirbase.org/ftp/21/hairpin.fa.gz ./ggd-recipes/mm10/mirbase.yaml: wget --random-wait --retry-connrefused -q -c -O mature.fa.gz https://www.mirbase.org/ftp/21/mature.fa.gz ./ggd-recipes/mm10/mirbase.yaml: wget --random-wait --retry-connrefused -q -c -O miRNA.str.gz https://www.mirbase.org/ftp/21/miRNA.str.gz ./ggd-recipes/hg38/mirbase.yaml: wget --random-wait --retry-connrefused -q -c -O hairpin.fa.gz https://www.mirbase.org/ftp/21/hairpin.fa.gz ./ggd-recipes/hg38/mirbase.yaml: wget --random-wait --retry-connrefused -q -c -O mature.fa.gz https://www.mirbase.org/ftp/21/mature.fa.gz ./ggd-recipes/hg38/mirbase.yaml: wget --random-wait --retry-connrefused -q -c -O miRNA.str.gz https://www.mirbase.org/ftp/21/miRNA.str.gz ./ggd-recipes/rn6/mirbase.yaml: wget -q -c -O hairpin.fa.gz ftp://mirbase.org/pub/mirbase/21/hairpin.fa.gz ./ggd-recipes/rn6/mirbase.yaml: wget -q -c -O mature.fa.gz ftp://mirbase.org/pub/mirbase/21/mature.fa.gz ./ggd-recipes/rn6/mirbase.yaml: wget -q -c -O miRNA.str.gz ftp://mirbase.org/pub/mirbase/21/miRNA.str.gz ./ggd-recipes/hg19/mirbase.yaml: wget --random-wait --retry-connrefused -nv -c -O hairpin.fa.gz https://www.mirbase.org/ftp/21/hairpin.fa.gz ./ggd-recipes/hg19/mirbase.yaml: wget --random-wait --retry-connrefused -nv -c -O mature.fa.gz https://www.mirbase.org/ftp/21/mature.fa.gz ./ggd-recipes/hg19/mirbase.yaml: wget --random-wait --retry-connrefused -nv -c -O miRNA.str.gz https://www.mirbase.org/ftp/21/miRNA.str.gz ./ggd-recipes/hg38-noalt/mirbase.yaml: wget --random-wait --retry-connrefused -q -c -O hairpin.fa.gz https://www.mirbase.org/ftp/21/hairpin.fa.gz ./ggd-recipes/hg38-noalt/mirbase.yaml: wget --random-wait --retry-connrefused -q -c -O mature.fa.gz https://www.mirbase.org/ftp/21/mature.fa.gz ./ggd-recipes/hg38-noalt/mirbase.yaml: wget --random-wait --retry-connrefused -q -c -O miRNA.str.gz https://www.mirbase.org/ftp/21/miRNA.str.gz ./ggd-recipes/GRCh37/mirbase.yaml: wget --random-wait --retry-connrefused -nv -c -O hairpin.fa.gz https://www.mirbase.org/ftp/21/hairpin.fa.gz ./ggd-recipes/GRCh37/mirbase.yaml: wget --random-wait --retry-connrefused -nv -c -O mature.fa.gz https://www.mirbase.org/ftp/21/mature.fa.gz ./ggd-recipes/GRCh37/mirbase.yaml: wget --random-wait --retry-connrefused -nv -c -O miRNA.str.gz https://www.mirbase.org/ftp/21/miRNA.str.gz ./ggd-recipes/TAIR10/mirbase.yaml: wget -c -O hairpin.t.fa.gz ftp://mirbase.org/pub/mirbase/21/hairpin.fa.gz && gunzip -f hairpin.t.fa.gz ./ggd-recipes/TAIR10/mirbase.yaml: wget -c -O mature.t.fa.gz ftp://mirbase.org/pub/mirbase/21/mature.fa.gz && gunzip -f mature.t.fa.gz ./ggd-recipes/TAIR10/mirbase.yaml: wget -c -O miRNA.t.str.gz ftp://mirbase.org/pub/mirbase/21/miRNA.str.gz && gunzip -f miRNA.t.str.gz ./ggd-recipes/BDGP6/mirbase.yaml: wget --random-wait --retry-connrefused -nv -c -O hairpin.t.fa.gz ftp://mirbase.org/pub/mirbase/22/hairpin.fa.gz && gunzip -f hairpin.t.fa.gz ./ggd-recipes/BDGP6/mirbase.yaml: wget --random-wait --retry-connrefused -nv -c -O mature.t.fa.gz ftp://mirbase.org/pub/mirbase/22/mature.fa.gz && gunzip -f mature.t.fa.gz ./ggd-recipes/BDGP6/mirbase.yaml: wget --random-wait --retry-connrefused -nv -c -O miRNA.t.str.gz ftp://mirbase.org/pub/mirbase/22/miRNA.str.gz && gunzip -f miRNA.t.str.gz ./ggd-recipes/canFam3/mirbase.yaml: wget --random-wait --retry-connrefused -q -c -O hairpin.fa.gz ftp://mirbase.org/pub/mirbase/21/hairpin.fa.gz ./ggd-recipes/canFam3/mirbase.yaml: wget --random-wait --retry-connrefused -q -c -O mature.fa.gz ftp://mirbase.org/pub/mirbase/21/mature.fa.gz ./ggd-recipes/canFam3/mirbase.yaml: wget --random-wait --retry-connrefused -q -c -O miRNA.str.gz ftp://mirbase.org/pub/mirbase/21/miRNA.str.gz
The text was updated successfully, but these errors were encountered:
Some miRBase downloads no longer require uncompressing. Fixes bcbio/b…
232068a
…cbio-nextgen#3723
Update miRBase download URLs (#413)
cd1b727
* Update mirbase.org URLs fixes bcbio/bcbio-nextgen#3721 fixes bcbio/bcbio-nextgen#3722 * Some miRBase downloads no longer require uncompressing. Fixes bcbio/bcbio-nextgen#3723 --------- Co-authored-by: Rob Chekaluk <rchekaluk@ppolitics.org>
Successfully merging a pull request may close this issue.
Reviewing mirbase.org shows that the URLs for downloading have changed (see new locations at CURRENT/genomes) and are no longer compressed.
The text was updated successfully, but these errors were encountered: