6684918996cf61c1d1a7fb5ee3e6cb3a8a23f083 hiram Fri Feb 18 09:27:46 2022 -0800 version 0 before beginning modifications refs #28930 diff --git src/hg/gar/garTable.sh src/hg/gar/garTable.sh new file mode 100755 index 0000000..7bfeb76 --- /dev/null +++ src/hg/gar/garTable.sh @@ -0,0 +1,103 @@ +#!/bin/bash + +set -beEu -o pipefail + +export srcDir="$HOME/kent/src/hg/gar" + +rsync -aP hgdownload.soe.ucsc.edu::hubs/UCSC_GI.assemblyHubList.txt ./ \ + > /dev/null 2>&1 + +### starting html page output ############################################## +printf "<!DOCTYPE HTML 4.01 Transitional> +<!--#set var='TITLE' value='Genome assembly search and request' --> +<!--#set var='ROOT' value='.' --> + +<!--#include virtual='\$ROOT/inc/gbPageStartHardcoded.html' --> + +<link rel='stylesheet' type='text/css' href='<!--#echo var='ROOT' -->/style/gar.css'> + +" + +# coordinate these colors with the table.pl definitions +export criticalColor="#ff0000" +export endangeredColor="#dd6600" +export vulnerableColor="#663300" + +export leftHandPointer="☜" +export rightHandPointer="☞" + +# printf "<a id='pageTop'></a>\n" + +printf "<h2>Genome assembly search and request</h2>\n" + +printf "<div id='canNotFindDiv' class='pullDownMenu'>\n" +printf " <span id='canNotFindAnchor'>after searching page,<br>cannot find desired assembly here</span'>\n" +printf " <div class='pullDownMenuContent'>\n" +printf " <button id='specificRequest' type='button' onclick='gar.openModal(this)' name='specific'><label>%s request specific assembly not found here %s</label></button>\n", "${rightHandPointer}" "${leftHandPointer}" +printf " </div>\n" +printf "</div>\n" + +printf "<p>Please note discussion of <a href='http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#What' target=_blank>What does the Genome Browser do ?</a>\n" +printf "</p>\n" + +printf "<p>The information in this page allows navigation to +specific genome browsers when they are available. In the case where a +genome browser has not yet been constructed, the link for that species will +open a request form which will notify the U.C. Genome Browser staff as a request +to construct the genome browser for your species of interest. This is a new +and experimental service, we are interested to see if such requests are +many or few. Depending upon the level of activity, the expected processing +time for an assembly to appear in the genome browser should be on the order of +two weeks. +</p>\n" + +printf "<p>Please note, not all possible assemblies are shown here. There is +nothing here from the clade categories: <em>archaea, viruses, bacteria</em>. +This display attempts to show only whole genome assemblies. Some assemblies +have been eliminated when their total assembly size is much smaller than the +typical genome size for such species. For example, only the <em>exome</em> +of the organism has been sequenced. And in some cases there are too many +assemblies for the same species, for example there are over 1,000 assemblies for <em>Homo sapiens</em>. +</p>\n" + +printf "<p>This page works best in the <em>Firefox</em> and <em>Safari</em> +web browsers. The web browsers <em>Chrome</em> and <em>Edge</em> take +almost a minute to prepare the page for use. +</p>\n" + +printf "<p>Use your web browser <em>find in page</em> function to search +for names of interest on this page. Make the entire set visiible to allow +the search to find everything. Future enhancements to this page may include +a better search system. +</p>\n" + +# printf "<p>The numbers in parenthesis following the +# <em>Scientific name (1,234)</em> indicate the number of assemblies available +# for that species. +# </p>\n" + +# my @clades = qw( primates mammals birds fish vertebrate invertebrates plants fungi ); + +cut -d' ' -f3,5 \ + /cluster/home/hiram/kent/src/hg/makeDb/doc/asmHubs/master.run.list \ + | sort | awk '{printf "%s\t%s\n", $1, $2};' > asmId.sciName + +sort -k1,1 -u \ + /cluster/home/hiram/kent/src/hg/makeDb/doc/*AsmHub/*.orderList.tsv \ + > asmId.commonName; + +sort -u /hive/data/outside/ncbi/genomes/reports/newAsm/*.suppressed.asmId.list \ + > asmId.suppressed.list + +join -t$'\t' asmId.sciName asmId.commonName > asmId.sciName.commonName + +$srcDir/garTable.pl + +# add in the modal popUp request hidden window +printf "<!--#include virtual='\$ROOT/inc/garModal.html' --> +</div><!-- closing gbsPage from gbPageStartHardcoded.html --> +</div><!-- closing container-fluid from gbPageStartHardcoded.html --> +<!--#include virtual='\$ROOT/inc/gbFooterHardcoded.html' --> +<script src='<!--#echo var='ROOT' -->/js/sorttable.js'></script> +<script src='<!--#echo var='ROOT' -->/js/gar.js'></script> +</body></html>\n"