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miRBase genomes URLs have changed #3722

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

miRBase genomes URLs have changed #3722

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):

./mm10/mirbase.yaml:        wget --random-wait --retry-connrefused -nv -c -O mirbase.gff3 https://www.mirbase.org/ftp/21/genomes/mmu.gff3
./hg38/mirbase.yaml:        wget --random-wait --retry-connrefused -q -c -O hsa.gff3 https://www.mirbase.org/ftp/21/genomes/hsa.gff3
./hg38/mirbase.yaml:        wget --random-wait --retry-connrefused -q -c -O mirbase.gff3 https://www.mirbase.org/ftp/21/genomes/hsa.gff3
./hg19/mirbase.yaml:        wget --random-wait --retry-connrefused -nv -c -O mirbase.gff3 https://www.mirbase.org/ftp/21/genomes/hsa.gff3
./hg38-noalt/mirbase.yaml:        wget --random-wait --retry-connrefused -q -c -O hsa.gff3 https://www.mirbase.org/ftp/21/genomes/hsa.gff3
./hg38-noalt/mirbase.yaml:        wget --random-wait --retry-connrefused -q -c -O mirbase.gff3 https://www.mirbase.org/ftp/21/genomes/hsa.gff3
./GRCh37/mirbase.yaml:        wget --random-wait --retry-connrefused -nv -c -O mirbase.gff3 https://www.mirbase.org/ftp/21/genomes/hsa.gff3
./BDGP6/mirbase.yaml:        wget --random-wait --retry-connrefused -nv -c -O mirbase.gff3 ftp://mirbase.org/pub/mirbase/22/genomes/dme.gff3
./canFam3/mirbase.yaml:        wget --random-wait --retry-connrefused -q -c -O cfa.gff3 ftp://mirbase.org/pub/mirbase/21/genomes/cfa.gff3
./canFam3/mirbase.yaml:        wget --random-wait --retry-connrefused -q -c -O mirbase.gff3 ftp://mirbase.org/pub/mirbase/21/genomes/cfa.gff3
rchekaluk pushed a commit to rchekaluk/cloudbiolinux that referenced this issue Nov 1, 2023
Update mirbase.org URLs fixes bcbio/bcbio-nextgen#3721 fixes bcbio/bc…
f9c1cc7 
…bio-nextgen#3722
@rchekaluk rchekaluk mentioned this issue Nov 1, 2023
Merged
naumenko-sa pushed a commit to chapmanb/cloudbiolinux that referenced this issue Dec 11, 2023
@rchekaluk
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

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Co-authored-by: Rob Chekaluk <rchekaluk@ppolitics.org>
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Update miRBase download URLs rchekaluk/cloudbiolinux
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@rchekaluk