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#!/bin/bash
# ----------------------------------------------------------------------------
# SeqAn - The Library for Sequence Analysis
# ----------------------------------------------------------------------------
# Copyright (c) 2006-2016, Knut Reinert, FU Berlin
# All rights reserved.
#
# License: BSD 3-clause
# ----------------------------------------------------------------------------
# Author: Sabrina Krakau <sabrina.krakau@fu-berlin.de>
# Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
# ----------------------------------------------------------------------------
# Binary test helper script.
#
# This script downloads binary packages of SeqAn apps on remote Linux machines
# and calls the programs to test whether the applications can be executed at
# all and thus check whether the system's libraries are compatible.
#
# The following packages have to be installed in order to run on the operating
# systems:
#
# SUSE 64 Bit:
# zypper install libgomp1-32bit
#
# Fedora 64 Bit:
# yum install -y glibc.i686 libstdc++.i686 zlib.i686 libgomp.i686
# ----------------------------------------------------------------------------
# Global variables with user name and target host.
USER_NAME=$USER
SERVER_NAMES=
# Parse option values.
while getopts ":u:h:" opt
do
case $opt in
u)
USER_NAME=$OPTARG
;;
h)
SERVER_NAMES=$OPTARG
;;
\?)
echo "Invalid option: -$OPTARG" >&2
exit 1
;;
esac
done
# Check that ${USER_NAME} and ${SERVER_NAMES} are set.
if [[ "$USER_NAME" == "" || "$SERVER_NAMES" == "" ]]; then
echo "Missing option -h" >&2
exit 1
fi
# List of binary packages to tests.
BINARY_URLS=(
"http://packages.seqan.de/razers3/razers3-3.1.1-Linux-i686.tar.bz2"
"http://packages.seqan.de/razers3/razers3-3.1.1-Linux-x86_64.tar.bz2"
"http://packages.seqan.de/stellar/stellar-1.4.1-Linux-i686.tar.bz2"
"http://packages.seqan.de/stellar/stellar-1.4.1-Linux-x86_64.tar.bz2"
"http://packages.seqan.de/breakpoint_calculator/breakpoint_calculator-0.2.1-Linux-i686.tar.bz2"
"http://packages.seqan.de/breakpoint_calculator/breakpoint_calculator-0.2.1-Linux-x86_64.tar.bz2"
"http://packages.seqan.de/snp_store/snp_store-1.0.1-Linux-i686.tar.bz2"
"http://packages.seqan.de/snp_store/snp_store-1.0.1-Linux-x86_64.tar.bz2")
# Array with test calls for each package.
APP_CALLS=(
"./razers3 -o output.razers ../example/genome.fa ../example/reads.fa"
"./razers3 -o output.razers ../example/genome.fa ../example/reads.fa"
"./stellar -o ../example/mapped_reads.gff --minLength 30 ../example/NC_001477.fasta ../example/reads.fasta"
"./stellar -o ../example/mapped_reads.gff --minLength 30 ../example/NC_001477.fasta ../example/reads.fasta"
"./breakpoint_calculator -d2 ../example/alignment.maf"
"./breakpoint_calculator -d2 ../example/alignment.maf"
"./snp_store ../example/exampleGenome.fa ../example/exampleReads.gff -o output_snp.txt -id output_indel1.txt"
"./snp_store ../example/exampleGenome.fa ../example/exampleReads.gff -o output_snp.txt -id output_indel1.txt")
# Create tmp directory, download binaries, call program and return success/error message
#
# Arguments:
#
# $1 server to connect to
# $2 call to application
function test_app ()
{
USER_SERVER=$1
APP_CALL=$2
# Create temporary directory.
echo "testing ${F}" >&2
TMPDIR=$(ssh $USER_SERVER "mktemp -d")
# Download package.
echo -n " downloading ..." >&2
ssh $USER_SERVER "cd $TMPDIR && curl $F -o binaryName.tar.bz2 &>/dev/null"
if [[ "$?" = "0" ]]; then
echo " OK" >&2
else
echo " FAILED" >&2
echo "FAILED" # for caller
return
fi
# Extracting package.
echo -n " unpacking ..." >&2
ssh $USER_SERVER "cd $TMPDIR && tar -xjf binaryName.tar.bz2"
if [[ "$?" = "0" ]]; then
echo " OK" >&2
else
echo " FAILED" >&2
echo "FAILED" # for caller
return
fi
# Calling binary.
echo -n " calling test ..." >&2
FILE=$(mktemp)
MSG=`ssh $USER_SERVER "cd $TMPDIR && cd */bin && (${APP_CALL}) > file.stdout" &>${FILE}`
RET=$?
if [[ "${RET}" = "0" ]]; then
echo " OK" >&2
echo "OK" # for caller
return
else
echo " FAILED" >&2
echo " The program call returns: ${RET}." >&2
echo " Program output is >>>" >&2
cat ${FILE} >&2
rm -f ${FILE}
echo ${MSG}
echo "<<<" >&2
echo "FAILED" # for caller
return
fi
# Remove temporary directory.
ssh $USER_SERVER "rm -r $TMPDIR"
}
echo "Testing SeqAn Linux Binaries..." >&2
echo >&2
RESULTS=()
IFS=";";
# Execute tests for each server.
for SERVER_NAME in ${SERVER_NAMES[@]}; do
echo "testing on ${SERVER_NAME}"
USER_SERVER="$USER_NAME@$SERVER_NAME"
COUNTER=0
for F in ${BINARY_URLS[@]}; do
#echo "${APP_CALLS[$COUNTER]}" >&2
RET=`test_app $USER_SERVER "${APP_CALLS[$COUNTER]}"`
RESULTS+=("${RET}")
let COUNTER=COUNTER+1
done
done
# For each server and for each binary-url: Output test result
echo -e '\t'
for (( I = 0 ; I < ${#SERVER_NAMES[@]} ; I++ )) do
echo "Binary tests on ${SERVER_NAMES[$I]}:"
echo ""
for (( J = 0 ; J < ${#BINARY_URLS[@]} ; J++ )) do
K=$(($J+$I*${#BINARY_URLS[@]}))
echo -e "${BINARY_URLS[$J]}\t${RESULTS[$K]}"
done
done
|
