afe1592acd7a4dd79f8ca81b390d10113cb6aadc
hiram
Tue Sep 20 09:40:42 2022 -0700
more complete accounting of all GenArk and UCSC assemblies to get them into the page refs #28930
diff --git src/hg/gar/garTable.sh src/hg/gar/garTable.sh
index 0e254df..b568d5d 100755
--- src/hg/gar/garTable.sh
+++ src/hg/gar/garTable.sh
@@ -71,36 +71,37 @@
interested in, you may request it using the "Can't find your assembly?"
button at the top of the page. Complete the request form (including the
NCBI GenBank or RefSeq assembly accession identifier). You will be notified
by email when your assembly is available for viewing in the UCSC Genome
Browser. This can take up to three weeks. The assembly browser will include
the following annotation tracks: Assembly mapping, Base position,
Gaps, GC Percent, Restriction Enzymes, Tandem Duplications,
CpG Islands, RefSeq mRNAs, Repeat Masking, and, if available:
NCBI RefSeq Genes and Ensembl Genes.
This page is optimized for use in Firefox and Safari.
For more details on using this page, please see this blog post.
\n"
-cut -d' ' -f3,5 \
+grep -v "^#" \
/cluster/home/hiram/kent/src/hg/makeDb/doc/asmHubs/master.run.list \
- | sort | awk '{printf "%s\t%s\n", $1, $2};' > asmId.sciName
+ | cut -d' ' -f3,5 | awk '{printf "%s\t%s\n", $1, $2};' | sort -k1,1 -u \
+ > asmId.sciName
-sort -k1,1 -u \
- /cluster/home/hiram/kent/src/hg/makeDb/doc/*AsmHub/*.orderList.tsv \
+ls /cluster/home/hiram/kent/src/hg/makeDb/doc/*AsmHub/*.orderList.tsv \
+ | grep -v others.orderList.tsv | xargs grep -h -v "^#" | sort -k1,1 -u \
> asmId.commonName;
sort -u /hive/data/outside/ncbi/genomes/reports/newAsm/*.suppressed.asmId.list \
> asmId.suppressed.list
join -t$'\t' asmId.sciName asmId.commonName > asmId.sciName.commonName
$srcDir/garTable.pl
# the column 1 tooltip display window, controlled in javaScript
printf "request
\n"
# add in the modal popUp request hidden window
printf "