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[submodule "repseqio"] | ||
path = repseqio | ||
url = https://github.com/repseqio/repseqio.git |
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language: java | ||
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sudo: false | ||
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git: | ||
submodules: false | ||
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before_install: | ||
- sed -i 's/git@github.com:/https:\/\/github.com\//' .gitmodules | ||
- git submodule update --init --recursive | ||
- rm -rf ./repseqio/.cache | ||
- mv .cache ./repseqio/.cache | ||
- cd repseqio/milib && mvn clean install -DskipTests -B && cd .. | ||
- mvn clean install -DskipTests -B && cd .. | ||
- mv ./repseqio/.cache .cache | ||
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jdk: | ||
- openjdk7 | ||
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cache: | ||
directories: | ||
- $HOME/.m2 | ||
- .cache |
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#!/bin/bash | ||
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# Linux readlink -f alternative for Mac OS X | ||
function readlinkUniversal() { | ||
targetFile=$1 | ||
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cd `dirname $targetFile` | ||
targetFile=`basename $targetFile` | ||
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# iterate down a (possible) chain of symlinks | ||
while [ -L "$targetFile" ] | ||
do | ||
targetFile=`readlink $targetFile` | ||
cd `dirname $targetFile` | ||
targetFile=`basename $targetFile` | ||
done | ||
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# compute the canonicalized name by finding the physical path | ||
# for the directory we're in and appending the target file. | ||
phys_dir=`pwd -P` | ||
result=$phys_dir/$targetFile | ||
echo $result | ||
} | ||
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os=`uname` | ||
delta=100 | ||
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dir="" | ||
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case $os in | ||
Darwin) | ||
dir=$(dirname "$(readlinkUniversal "$0")") | ||
;; | ||
Linux) | ||
dir="$(dirname "$(readlink -f "$0")")" | ||
;; | ||
FreeBSD) | ||
dir=$(dirname "$(readlinkUniversal "$0")") | ||
;; | ||
*) | ||
echo "Unknown OS." | ||
exit 1 | ||
;; | ||
esac | ||
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if [[ ! -f ${dir}/repseqio/milib/pom.xml ]]; | ||
then | ||
echo "Please init git submodules. Try:" | ||
echo "git submodule update --init --recursive" | ||
exit 1 | ||
fi | ||
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function error_exit { | ||
echo -e "$1" | ||
exit "${2:-1}" | ||
} | ||
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GREEN='\033[0;32m' | ||
RED='\033[0;31m' | ||
NC='\033[0m' # No Color | ||
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echo "Building MiLib." | ||
cd ${dir}/repseqio/milib | ||
mvn clean install -DskipTests -B || error_exit "${RED}Problem building MiLib!${NC}" 1 | ||
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echo "Building RepSeq.IO util/lib" | ||
cd ${dir}/repseqio | ||
mvn clean install -DskipTests -B || error_exit "${RED}Problem building RepSeq.IO util!${NC}" 1 | ||
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echo "Building MiXCR." | ||
cd ${dir} | ||
mvn clean install -DskipTests -B || error_exit "${RED}Problem building MiXCR util!${NC}" 1 | ||
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echo -e "${GREEN}Build successfull!${NC}" | ||
echo "The following is the output of \"mixcr -v\" command:" | ||
${dir}/mixcr -v || error_exit "${RED}Something went wrong!${NC}" 1 | ||
echo -e "${GREEN}Everything seems OK!${NC}" | ||
echo "" | ||
echo "Add mixcr script from this folder to your PATH variable or add symlink to your bin folder." | ||
echo "" | ||
echo "MiXCR is free for Academic use. For commertial use please contact licensing@milaboratory.com ." | ||
echo "" | ||
echo "If you discover bugs or have any questions, contact us at https://github.com/milaboratory/mixcr/issues ." |
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