Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 44:bea0916e1080 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 015c77d802595a85f78739ee2316b452c519c796-dirty
author fubar
date Fri, 01 Mar 2024 04:44:52 +0000
parents 3e7a4ed46551
children 4181e97c70a7
comparison
equal deleted inserted replaced
43:7e14b3f1f8e1 44:bea0916e1080
475 self.config_json["assemblies"] = assemblies 475 self.config_json["assemblies"] = assemblies
476 476
477 def make_assembly(self, fapath, gname): 477 def make_assembly(self, fapath, gname):
478 478
479 faname = gname + ".fa.gz" 479 faname = gname + ".fa.gz"
480 fadest = os.path.join(self.outdir, faname) 480 fadest = os.path.realpath(os.path.join(self.outdir, faname))
481 cmd = "bgzip -i -c %s -I %s.gzi > %s && samtools faidx %s" % ( 481 cmd = "bgzip -i -c %s -I %s.gzi > %s && samtools faidx %s" % (
482 fapath, 482 fapath,
483 fadest, 483 fadest,
484 fadest, 484 fadest,
485 fadest, 485 fadest,