Mercurial > repos > fubar > jbrowse2

view convertMAF.sh @ 22:2ddd41a0c2d5 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be4f98b07024b59ff5e1ae0d8b467eecb15c7521-dirty
author fubar
date Thu, 01 Feb 2024 01:58:58 +0000
parents d78175596286
children 94264fe60478
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#!/usr/bin/env bash
# https://github.com/cmdcolin/jbrowse-plugin-mafviewer/blob/master/bin/convert.sh
#  MAF file must contain the species name and chromosome name
#  e.g. hg38.chr1 in the sequence identifiers.
perl $3/maf2bed.pl $2 < $1 | sort -k1,1 -k2,2n > $4.sorted.bed
bgzip $4.sorted.bed
tabix -p bed $4.sorted.bed.gz