68e60a3ccfe0c3aaa48f2fa85f86ca700d681e81 hiram Tue Mar 31 12:08:22 2020 -0700 correct hub.txt not testHub.txt refs #23891 diff --git src/hg/makeDb/doc/asmHubs/mkHubIndex.pl src/hg/makeDb/doc/asmHubs/mkHubIndex.pl index d21d570..9402773 100755 --- src/hg/makeDb/doc/asmHubs/mkHubIndex.pl +++ src/hg/makeDb/doc/asmHubs/mkHubIndex.pl @@ -49,73 +49,79 @@ print <<"END"

$Name Genomes assembly hubs

Assemblies from NCBI/Genbank/Refseq sources, $subSetMessage.

How to view the hub

-You can load this hub from our -Public Hubs -page or by clicking these assembly links to any of our official websites: +Options: +

    +
  1. The links to the genome browser in the table below will attach that + one specific assembly to the genome browser. This is most likely what + you want.
    2. +
  2. Instead, you can attach the entire set of assemblies as one group to + the genome browser with the following links depending upon which of + our mirror site browsers you prefer to use: -

    - -

    -To manually attach all the assemblies in this hub to other genome browsers: +

    3. +
  3. To manually attach all the assemblies in this hub to genome browsers + that are not one of the three UCSC mirror sites:
      -
    1. - From the blue navigation bar, go to +
    2. From the blue navigation bar, go to My Data -> Track Hubs
      3. -
    3. - Then select the My Hubs tab and enter this URL into the textbox: +
    4. Then select the My Hubs tab and enter this URL into + the textbox:
      https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt
      5. -
    5. - Once you have added the URL to the entry form, press the Add Hub - button to add the hub.
      6. +
    6. Once you have added the URL to the entry form, + press the Add Hub button to add the hub.
      7. +
    +

After adding the hub, you will be redirected to the gateway page. The genome assemblies can be selected from the ${Name} Hub Assembly dropdown menu. Instead of adding all the assemblies in one collected group, use the individual link to genome browser in the table below.

-

See also: assembly statistics, track statistics


+

See also: assembly statistics, track statistics <== additional information for these assemblies.


Data resource links

+

NOTE: Click on the column headers to sort the table by that column
-The link to genome browser will attach only that single assembly to -the genome browser. +The common name/link to genome browser will attach only that single assembly to +the genome browser.
+The scientific name/and data download link provides access to the files for that one +assembly hub.
+The other links provide access to NCBI resources for these assemblies. +

END } # sub startHtml() ############################################################################## ### start the table output ############################################################################## sub startTable() { print <<"END" @@ -129,45 +135,46 @@ sub endTable() { print <<"END"
count common name
link to genome browser		 scientific name
and data download		 NCBI assembly bioSamplebioProject assembly date,
source link
END } # sub endTable() ############################################################################## ### end the HTML output ############################################################################## sub endHtml() { if ($asmHubName ne "viral") { - printf "

\n\n"; - printf "\n"; + printf "

\n

Assembly hubs index pages: 
\n"; + printf "\n"; + printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; - printf "\n"; - printf "\n"; - printf "\n"; - printf "\n"; - printf "\n"; + printf "\n"; + printf "\n"; + printf "\n"; + printf "\n"; + printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n"; printf "\n
Additional hubs with collections of assemblies
Assembly hubs index pages: PrimatesMammalsBirdsFishother vertebrates
Hubs assembly statistics: PrimatesMammalsBirdsFishother vertebratesPrimatesMammalsBirdsFishother vertebrates
Hubs track statistics: PrimatesMammalsBirdsFishother vertebrates
\n

\n"; } print <<"END"