oadinstitute.picard.2.18.10.source-code.release_picard.sh Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of picard Show documentation
Show all versions of picard Show documentation
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
#! /bin/bash
# The MIT License
#
# Copyright (c) $today.year The Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
echo "This release script has been DEPRECATED. Please use the gradle build file for releases."
#
# PROGNAME=`basename $0`
#
# function usage () {
# echo "USAGE: $PROGNAME " >&2
# echo "Tags Github Picard source, checks out and builds sources, uploads build results to Sourceforge.">&2
# echo "-t Build in . Default: $TMPDIR." >&2
# }
#
# function create_release () {
# local token="$1";
# local owner="$2";
# local repo="$3";
# local tag_name="$4";
# local target_commitish="$5";
# local name="$6";
# local body="$7";
# local draft="$8";
# local prerelease="$9";
#
# local payload="\"tag_name\":\"$tag_name\"";
# payload="$payload,\"target_commitish\":\"$target_commitish\"";
# payload="$payload,\"name\":\"$name\"";
# payload="$payload,\"body\":\"$body\"";
# payload="$payload,\"draft\":$draft";
# payload="$payload,\"prerelease\":$prerelease";
# payload="{$payload}";
#
# RELEASE_RESPONSE=$(curl --fail -s -S -X POST \
# https://api.github.com/repos/$owner/$repo/releases \
# -A "create-release" \
# -H "Accept: application/vnd.github.v3+json" \
# -H "Content-Type: application/json" \
# -H "Authorization: token $token" \
# -d "$payload");
#
# # NB: we must set the RELEASE_GITHUB_ID as the ID in the returned json response
# export RELEASE_GITHUB_ID=$(echo "$RELEASE_RESPONSE" | sed -e 's_",.*__g' -e 's_.*/__g')
# }
#
# function upload_asset () {
# local token="$1";
# local owner="$2";
# local repo="$3";
# local name="$4";
# local content_type="$5";
# local file="$6";
# local id="$7";
#
# curl --fail -s -S -X POST \
# https://uploads.github.com/repos/$owner/$repo/releases/$id/assets?name=$name \
# -A "upload-asset" \
# -H "Accept: application/vnd.github.v3+json" \
# -H "Content-Type: $content_type" \
# -H "Authorization: token $token" \
# --progress-bar \
# --data-binary @"$file";
# }
#
# function tag_exists() {
# git tag | grep -q "$1$"
# if test $? = 0
# then return 0
# else return 1
# fi
# }
#
# function remote_does_not_exist() {
# git ls-remote $1 2>/dev/null 1>/dev/null
# if test $? = 0
# then return 1
# else return 0
# fi
# }
#
# function remote_tag_does_not_exist() {
# git ls-remote --tags $2 | grep -q "$1$";
# if test $? = 0
# then return 0
# else return 1
# fi
# }
#
#
# # This method called once for picard and once for htsjdk
# function tag_it() {
#
# # tag must not exist
# if tag_exists $RELEASE_ID
# then echo "ERROR: Tag $RELEASE_ID locally already exists"
# return 1
# fi
#
# # remote must exist
# if remote_does_not_exist $REMOTE
# then echo "ERROR: Remote $REMOTE does not exist"
# return 1
# fi
#
# # tag at remote must not exist
# if remote_tag_does_not_exist $RELEASE_ID $REMOTE
# then echo "ERROR: Tag $RELEASE_ID at remote $REMOTE already exists"
# return 1
# fi
#
# # tag the branch locally then push to remote
# echo Tagging master as $RELEASE_ID and pushing the tag to $REMOTE
# # NB: we could use annotated tags in the future to store release notes, etc.
# git tag $RELEASE_ID
# git push $REMOTE $RELEASE_ID # TODO: should we check this return value in case someone made a tag since we last checked?
# }
#
# set -e
#
# while getopts "ht:" options; do
# case $options in
# t ) TMPDIR=$OPTARG;;
# h ) usage;;
# \? ) usage
# exit 1;;
# * ) usage
# exit 1;;
# esac
# done
# shift $(($OPTIND - 1))
#
# if [ -z $GITHUB_USER_TOKEN ]
# then echo "ERROR: environment variable GITHUB_USER_TOKEN must be set." >&2
# usage
# exit 1
# fi
#
# if (( $# != 1 ))
# then echo "ERROR: Incorrect number of arguments." >&2
# usage
# exit 1
# fi
#
# if [[ x"$EDITOR" == x ]]
# then echo "EDITOR environment variable must be set." >&2
# exit 1
# fi
#
# java_version=`java -version 2>&1 | fgrep -i version`
#
# [email protected]:broadinstitute/picard.git
# REMOTE=origin
# GHPAGES_BRANCH="gh-pages"
#
# RELEASE_ID=$1
#
# # Since releases are lexically sorted, need to filter in order to have 1.1xx be at the bottom.
# PICARD_PREV_RELEASE_ID=`git ls-remote --tags | grep -v "{}$" | awk '{print $2}' | sed -e "s_.*/__g" | egrep '[.]\d\d\d' | tail -1`
#
# if [[ -e $TMPDIR/picard ]]
# then echo "$TMPDIR/picard already exists. Please remove or specify a different TMPDIR." >&2
# exit 1
# fi
# echo "Using TMPDIR: $TMPDIR";
# cd $TMPDIR
#
# # clone
# git clone $PICARDGITROOT picard
# cd picard
# ant clone-htsjdk
# #by default clone will grab the latest release we need master
# cd htsjdk
# git checkout master
# cd ..
# ant clean # clean shouldn't be necessary, but no harm
#
# # Since releases are lexically sorted, need to filter in order to have 1.1xx be at the bottom.
# PICARD_PREV_RELEASE_ID=`git ls-remote --tags | grep -v "{}$" | awk '{print $2}' | sed -e "s_.*/__g" | egrep '[.]\d\d\d' | tail -1`
# HTSJDK_PREV_RELEASE_ID=$(cd htsjdk; git ls-remote --tags | grep -v "{}$" | awk '{print $2}' | sed -e "s_.*/__g" | egrep '[.]\d\d\d' | tail -1)
#
# # Tag in both repos
# for sandbox in . htsjdk
# do pushd $sandbox
# tag_it || exit 1
# popd
# done
#
# ant -lib lib/ant test-htsjdk test
#
# ant -lib lib/ant clean all javadoc
#
# mkdir -p deploy/picard-tools/$RELEASE_ID
#
# git log --name-status ${PICARD_PREV_RELEASE_ID}..${RELEASE_ID} > deploy/picard-tools/$RELEASE_ID/README.txt
#
# (cd htsjdk; git log --name-status ${HTSJDK_PREV_RELEASE_ID}..${RELEASE_ID}) >> deploy/picard-tools/$RELEASE_ID/README.txt
#
# echo 'Edit release notes and exit editor when finished.'
#
# $EDITOR deploy/picard-tools/$RELEASE_ID/README.txt
#
# cp dist/picard-tools-$RELEASE_ID.zip deploy/picard-tools/$RELEASE_ID/
#
# # Make all files to be pushed to Sourceforge writable by group so that another Picard admin can overwrite them.
#
# chmod -R gu+rw javadoc deploy dist
#
# find javadoc deploy dist -type d -exec chmod g+s '{}' ';'
#
# # Move the javadoc directory to a temporary location
# mv javadoc tmp_javadoc
#
# # Copy over javadoc for htsjdk since we are in the picard directory
# # NB: need to move javadoc to a tmp directory since the javadoc
# # directory in the gh-pages branch may already exist.
# cd htsjdk
# mkdir tmp_javadoc
# cp -r ../tmp_javadoc/htsjdk tmp_javadoc/.
# cd ../
#
# # Update the javadoc
# for sandbox in . htsjdk
# do pushd $sandbox
# if [ "." == $sandbox ]; then
# sandbox="picard";
# fi
# echo "Updating the javadoc for $sandbox"
# # Checkout the gh-pages branch
# git checkout -b $GHPAGES_BRANCH $REMOTE/$GHPAGES_BRANCH
# # Copy over from the tmp javadoc directory
# if [ ! -d javadoc ]; then
# mkdir javadoc;
# fi
# rsync -avP --delete-after tmp_javadoc/* javadoc/.
# # Remove the tmp directory as we no longer need it
# rm -r tmp_javadoc
# # Add the new javadoc files
# find javadoc/$sandbox | xargs git add
# # Commit!
# git commit -a --allow-empty -m "Updating javadoc for release: $RELEASE_ID"
# # NB: assumes the push will not fail
# git push $REMOTE $GHPAGES_BRANCH
# # Reset the repository to master
# git checkout master
# echo "Updated the javadoc for $sandbox"
# popd
# done
#
# # Publish a release and upload assets
# echo "Creating a release on github for htsjdk and picard"
# create_release $GITHUB_USER_TOKEN samtools htsjdk $RELEASE_ID "" $RELEASE_ID "Release $RELEASE_ID" "false" "false";
# create_release $GITHUB_USER_TOKEN broadinstitute picard $RELEASE_ID "" $RELEASE_ID "Release $RELEASE_ID" "false" "false";
# echo "Github release id: $RELEASE_GITHUB_ID"
# echo "Updating the release zip and README.txt to github"
# upload_asset $GITHUB_USER_TOKEN broadinstitute picard picard-tools-$RELEASE_ID.zip "application/zip" deploy/picard-tools/$RELEASE_ID/picard-tools-$RELEASE_ID.zip $RELEASE_GITHUB_ID;
# upload_asset $GITHUB_USER_TOKEN broadinstitute picard README.txt "application/zip" deploy/picard-tools/$RELEASE_ID/README.txt $RELEASE_GITHUB_ID;
#
# # Update the website
# echo "Updating the website"
# # Assumes the gh-pages branch is already locally created
# git checkout $GHPAGES_BRANCH;
# cd dist/html
# cp inc/*.html program_usage/*.html picard-metric-definitions.html ../../_includes/.
# cd ../../
# find _includes | xargs git add
# git commit -a --allow-empty -m "Adding website files for $RELEASE_ID"
# git push $REMOTE $GHPAGES_BRANCH
#
# # Move back to master just in case
# git checkout master
#
# echo "Release was successful!"