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miRBase download files are not compressed #3723

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rchekaluk opened this issue Nov 1, 2023 · 0 comments · Fixed by chapmanb/cloudbiolinux#413
Closed

miRBase download files are not compressed #3723

rchekaluk opened this issue Nov 1, 2023 · 0 comments · Fixed by chapmanb/cloudbiolinux#413

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@rchekaluk
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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
rchekaluk pushed a commit to rchekaluk/cloudbiolinux that referenced this issue Nov 1, 2023
naumenko-sa pushed a commit to chapmanb/cloudbiolinux that referenced this issue Dec 11, 2023
* 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>
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