+os.mkdir("/usr/local/share/bcbio-nextgen/galaxy/tool-data")
+
+with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/bowtie2_indices.loc", "w") as f:
+ f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(dir $(bowtie2_indices))\n"))
+
+with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/bwa_index.loc", "w") as f:
+ f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(bwa_index))\n"))
+
+with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/gatk_sorted_picard_index.loc", "w") as f:
+ f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(gatk_sorted_picard_index))\n"))
+
+with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/picard_index.loc", "w") as f:
+ f.write(subst.do_substitution(p, "GRCh37\tGRCh37\tHuman (GRCh37)\t$(file $(picard_index))\n"))
+
+with open("/usr/local/share/bcbio-nextgen/galaxy/tool-data/sam_fa_indices.loc", "w") as f:
+ f.write(subst.do_substitution(p, "index\tGRCh37\t$(file $(sam_fa_indices))\n"))
+
+with open("/tmp/crunch-job/freebayes-variant.yaml", "w") as f: