Commit faf33c6b authored by David Hoksza's avatar David Hoksza
Browse files

assemble treats csv

parent afa5acaf
......@@ -128,8 +128,8 @@ tr '\r' '\n' < ${ENRICHMENT_CONFIG} > ${ENRICHMENT_CONFIG_TMP}
#update paremters file
#the .bak is because MAC uses BSD version of sed which requires the backup for in-place replacements
sed -E -i.bak "s/(max_areas_per_map)(.*)/\1\t${ENRICH_MAX_AREAS_PER_MAP}/g" ${ENRICHMENT_CONFIG_TMP}
sed -E -i.bak "s/(max_areas_per_pathway_db)(.*)/\1\t${MAX_AREAS_PER_PATHWAY_DB}/g" ${ENRICHMENT_CONFIG_TMP}
sed -E -i.bak "s/(max_areas_per_map)(.*)/\1,${ENRICH_MAX_AREAS_PER_MAP}/g" ${ENRICHMENT_CONFIG_TMP}
sed -E -i.bak "s/(max_areas_per_pathway_db)(.*)/\1,${MAX_AREAS_PER_PATHWAY_DB}/g" ${ENRICHMENT_CONFIG_TMP}
rm ${ENRICHMENT_CONFIG_TMP}.bak
Rscript --vanilla ${ENRICHMENT_DIR}/enrich_maps.R ${genes_out_path} ${ENRICHMENT_CONFIG_TMP}
......
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