Update mirbase.org URLs fixes bcbio/bcbio-nextgen#3721 fixes bcbio/bc…

…bio-nextgen#3722

ggd-recipes/BDGP6/mirbase.yaml

@@ -19,7 +19,7 @@ recipe:
         cat mature.t.fa | awk '{if ($0~/>dme/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g'  > mature.fa
         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
         cat miRNA.t.str | awk '{if ($0~/dme/)print $0}' > miRNA.str
-        wget --random-wait --retry-connrefused -nv -c -O mirbase.gff3 ftp://mirbase.org/pub/mirbase/22/genomes/dme.gff3
+        wget --random-wait --retry-connrefused -nv -c -O mirbase.gff3 https://mirbase.org/download/dme.gff3
         wget --no-check-certificate -c -O Rfam_for_miRDeep.fa.gz https://github.com/lpantano/mirdeep2_core/raw/data/Rfam_for_miRDeep.fa.gz && gunzip -f Rfam_for_miRDeep.fa.gz
         # targetscan analysis
         wget  --random-wait --retry-connrefused --no-check-certificate -nv -c -O Summary_Counts.txt.zip http://www.targetscan.org/fly_72/fly_72_data_download/Summary_Counts.all_predictions.txt.zip && unzip Summary_Counts.txt.zip

ggd-recipes/canFam3/mirbase.yaml

@@ -10,7 +10,7 @@ recipe:
       - |
         mkdir -p srnaseq
         cd srnaseq
-        wget --random-wait --retry-connrefused -q -c -O cfa.gff3 ftp://mirbase.org/pub/mirbase/21/genomes/cfa.gff3
+        wget --random-wait --retry-connrefused -q -c -O cfa.gff3 https://mirbase.org/download/cfa.gff3
         awk '$3=="miRNA"' cfa.gff3 | sed 's/=/ /g' > srna-transcripts.gtf
         wget  --random-wait --retry-connrefused -q -c -O rmsk.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/canFam3/database/rmsk.txt.gz
         zcat rmsk.txt.gz | awk '{print $6"\t.\trepeat\t"$7+1"\t"$8+1"\t.\t"$10"\t.\tname "$12";"}' >> srna-transcripts.gtf
@@ -23,7 +23,7 @@ recipe:
         zcat mature.fa.gz |  awk '{if ($0~/>cfa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g'  > mature.fa
         wget  --random-wait --retry-connrefused  -q -c -O miRNA.str.gz ftp://mirbase.org/pub/mirbase/21/miRNA.str.gz
         zcat miRNA.str.gz | awk '{if ($0~/cfa/)print $0}' > miRNA.str
-        wget --random-wait --retry-connrefused -q -c -O mirbase.gff3 ftp://mirbase.org/pub/mirbase/21/genomes/cfa.gff3
+        wget --random-wait --retry-connrefused -q -c -O mirbase.gff3 https://mirbase.org/download/cfa.gff3
         # mintmap
         # mirdeep2
         wget  --random-wait --retry-connrefused --no-check-certificate -q -c -O Rfam_for_miRDeep.fa.gz https://github.com/lpantano/mirdeep2_core/raw/data/Rfam_for_miRDeep.fa.gz && gunzip Rfam_for_miRDeep.fa.gz

ggd-recipes/hg19/mirbase.yaml

@@ -29,7 +29,7 @@ recipe:
         zcat mature.fa.gz |  awk '{if ($0~/>hsa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g'  > mature.fa
         wget  --random-wait --retry-connrefused  -nv -c -O miRNA.str.gz https://www.mirbase.org/ftp/21/miRNA.str.gz
         zcat miRNA.str.gz | awk '{if ($0~/hsa/)print $0}' > miRNA.str
-        wget --random-wait --retry-connrefused -nv -c -O mirbase.gff3 https://www.mirbase.org/ftp/21/genomes/hsa.gff3
+        wget --random-wait --retry-connrefused -nv -c -O mirbase.gff3 https://mirbase.org/download/hsa.gff3
         # tdrmapper
         wget   --random-wait --retry-connrefused  --no-check-certificate -nv -c -O trna_mature_pre.fa https://github.com/sararselitsky/tDRmapper/raw/master/hg19_mature_and_pre.fa
         # mintmap

ggd-recipes/hg38-noalt/mirbase.yaml

@@ -10,7 +10,7 @@ recipe:
       - |
         mkdir -p srnaseq
         cd srnaseq
-        wget --random-wait --retry-connrefused -q -c -O hsa.gff3 https://www.mirbase.org/ftp/21/genomes/hsa.gff3
+        wget --random-wait --retry-connrefused -q -c -O hsa.gff3 https://mirbase.org/download/hsa.gff3
         awk '$3=="miRNA"' hsa.gff3 | sed 's/=/ /g' > srna-transcripts.gtf
         wget  --random-wait --retry-connrefused -q -c -O wgRna.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/wgRna.txt.gz
         zgrep -v 'hsa-' wgRna.txt.gz | awk '{print $2"\t.\tncrna\t"$3"\t"$4"\t.\t"$7"\t.\tname "$5";"}' >> srna-transcripts.gtf
@@ -30,7 +30,7 @@ recipe:
         zcat mature.fa.gz |  awk '{if ($0~/>hsa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g'  > mature.fa
         wget  --random-wait --retry-connrefused  -q -c -O miRNA.str.gz https://www.mirbase.org/ftp/21/miRNA.str.gz
         zcat miRNA.str.gz | awk '{if ($0~/hsa/)print $0}' > miRNA.str
-        wget --random-wait --retry-connrefused -q -c -O mirbase.gff3 https://www.mirbase.org/ftp/21/genomes/hsa.gff3
+        wget --random-wait --retry-connrefused -q -c -O mirbase.gff3 https://mirbase.org/download/hsa.gff3
         #tdrmapper
         wget   --random-wait --retry-connrefused  --no-check-certificate -q -c -O trna_mature_pre.fa https://github.com/sararselitsky/tDRmapper/raw/master/hg19_mature_and_pre.fa
         # mintmap

ggd-recipes/hg38/mirbase.yaml

@@ -10,7 +10,7 @@ recipe:
       - |
         mkdir -p srnaseq
         cd srnaseq
-        wget --random-wait --retry-connrefused -q -c -O hsa.gff3 https://www.mirbase.org/ftp/21/genomes/hsa.gff3
+        wget --random-wait --retry-connrefused -q -c -O hsa.gff3 https://mirbase.org/download/hsa.gff3
         awk '$3=="miRNA"' hsa.gff3 | sed 's/=/ /g' > srna-transcripts.gtf
         wget  --random-wait --retry-connrefused -q -c -O wgRna.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/wgRna.txt.gz
         zgrep -v 'hsa-' wgRna.txt.gz | awk '{print $2"\t.\tncrna\t"$3"\t"$4"\t.\t"$7"\t.\tname "$5";"}' >> srna-transcripts.gtf
@@ -30,7 +30,7 @@ recipe:
         zcat mature.fa.gz |  awk '{if ($0~/>hsa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g'  > mature.fa
         wget  --random-wait --retry-connrefused  -q -c -O miRNA.str.gz https://www.mirbase.org/ftp/21/miRNA.str.gz
         zcat miRNA.str.gz | awk '{if ($0~/hsa/)print $0}' > miRNA.str
-        wget --random-wait --retry-connrefused -q -c -O mirbase.gff3 https://www.mirbase.org/ftp/21/genomes/hsa.gff3
+        wget --random-wait --retry-connrefused -q -c -O mirbase.gff3 https://mirbase.org/download/hsa.gff3
         #tdrmapper
         wget   --random-wait --retry-connrefused  --no-check-certificate -q -c -O trna_mature_pre.fa https://github.com/sararselitsky/tDRmapper/raw/master/hg19_mature_and_pre.fa
         # mintmap

ggd-recipes/mm10/mirbase.yaml

@@ -24,7 +24,7 @@ recipe:
         zcat mature.fa.gz |  awk '{if ($0~/>mmu/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g'  > mature.fa
         wget --random-wait --retry-connrefused  -q -c -O miRNA.str.gz https://www.mirbase.org/ftp/21/miRNA.str.gz
         zcat miRNA.str.gz | awk '{if ($0~/mmu/)print $0}' > miRNA.str
-        wget --random-wait --retry-connrefused -nv -c -O mirbase.gff3 https://www.mirbase.org/ftp/21/genomes/mmu.gff3
+        wget --random-wait --retry-connrefused -nv -c -O mirbase.gff3 https://mirbase.org/download/mmu.gff3
         wget --random-wait --retry-connrefused  --no-check-certificate -q -c -O Rfam_for_miRDeep.fa.gz https://github.com/lpantano/mirdeep2_core/raw/data/Rfam_for_miRDeep.fa.gz && gunzip Rfam_for_miRDeep.fa.gz
         # targetscan analysis
         # wget --no-check-certificate -q -c -O Summary_Counts.txt.zip http://www.targetscan.org/mmu_71/mmu_71_data_download/Summary_Counts.all_predictions.txt.zip && unzip Summary_Counts.txt.zip