05561c4b23fbcf412ab896628db14146f9802143
max
  Tue Apr 4 06:00:14 2023 -0700
improving bigGuessDb a little before sending off to NCBI, refs #30316

diff --git src/utils/bigGuessDb/tests/makefile src/utils/bigGuessDb/tests/makefile
index 117b3b7..775206c 100644
--- src/utils/bigGuessDb/tests/makefile
+++ src/utils/bigGuessDb/tests/makefile
@@ -1,28 +1,30 @@
 kentSrc = ../../..
 include ../../../inc/common.mk
 
+INDEX=/cluster/home/max/public_html/bigGuessDb/bigGuessDb.txt.gz
+
 # test files were made with:
 #
 #bigWigToBedGraph /gbdb/mm10/encode3/atac/encode3RenAtacSignalStomachE16.bw stdout | randomLines stdin 20 stdout > mm10.bed
 #bedSort mm10.bed mm10.bed
 #bedGraphToBigWig mm10.bed /hive/data/genomes/mm10/chrom.sizes mm10.bw
 
 #bigBedToBed /gbdb/hg19/bbi/clinvar/clinvarCnv.bb stdout  | cut -f1-4 | randomLines stdin 20 stdout > hg19.bed
 #bedSort hg19.bed hg19.bed
 #bedToBigBed hg19.bed /hive/data/genomes/hg19/chrom.sizes hg19.bb
 
 all:
 	mkdir -p out
 	# alas, our automated tests cannot output anything to stderr, as otherwise emails will be sent
 	rm -f out/test.err
-	python2 ${DESTBINDIR}/bigGuessDb --indexFile ./guessAssembly.txt.gz in/hg19.bb > out/hg19.txt
-	python3 ${DESTBINDIR}/bigGuessDb --indexFile ./guessAssembly.txt.gz in/mm10.bw > out/mm10.txt
-	python3 ${DESTBINDIR}/bigGuessDb --indexFile ./guessAssembly.txt.gz in/mm10.bw --best > out/mm10.best.txt
+	python2 ${DESTBINDIR}/bigGuessDb --indexFile ${INDEX} in/hg19.bb > out/hg19.txt
+	python3 ${DESTBINDIR}/bigGuessDb --indexFile ${INDEX} in/mm10.bw > out/mm10.txt
+	python3 ${DESTBINDIR}/bigGuessDb --indexFile ${INDEX} in/mm10.bw --best > out/mm10.best.txt
 	diff out/hg19.txt expected/hg19.txt
 	diff out/mm10.txt expected/mm10.txt
 	diff out/mm10.best.txt expected/mm10.best.txt
 
 test: all
 
 clean:
 	rm -f out/*