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Forum How to update gatk tools doc to default to the latest version
cd ~/Workspace/gatk/
git pull
git checkout _versionnumber_
./gradlew gatkDoc
cd ~/Forum/
python3 cleanup_gatk_html.py -V 'The Gatk Version Number' -P ~/Workspace/gatk/build/docs/gatkdoc/
Login to gsaweb server. If you do not have access this server you can have BITS provide it to you.
ssh gsaweb
The various versions of GATK are in the folder "/local/htdocs/gatk/documentation/tooldocs/". In case you want to revert the tool docs to an earlier version, jump to the last step "Steps to run on gsaweb server" and create a soft link to that particular version.
cd /local/htdocs/gatk/documentation/tooldocs/
mkdir 4.0.12.0
In your local machine run the following steps. To be able to perform the following git commands, ensure that you have git initialized and clone the GATK repo in the CWD(current working directory).
git tag #gives you a list of all point releases, ensure they are all uptodate with the versions in tool docs
git pull #This pulls all the changes that have been pushed on that branch
git checkout 4.0.12.0
./gradlew -PphpDoc gatkDoc # this creates php docs of GTAK tools in the folder gatkdoc
cd build/docs/gatkdoc
sed -i -- 's/-SNAPSHOT//g' * #the gradle build command also creates a snapshot that needs to be removed
rm *--
rm *css
scp * bgandham@gsaweb:/local/htdocs/gatk/documentation/tooldocs/4.0.12.0/ #copy all the php files to gsaweb server
unlink current #this will unlink the last version the tool docs is tethered to
ln -s 4.0.12.0 current #this will link GATK tool docs to the specific version you want as the default.
Confirm the steps by going to this link: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/.
It should show the current GATK tools docs version.