Mercurial > repos > fubar > jbrowse2

diff convertMAF.sh @ 0:d78175596286 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
author fubar
date Mon, 08 Jan 2024 09:20:33 +0000
parents
children 94264fe60478
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/convertMAF.sh	Mon Jan 08 09:20:33 2024 +0000
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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