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#!/bin/bash
# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
echo $0 $*
#
# Download and test SRA Toolkit tarballs (see VDB-1345)
# Errors are reported to the specified email
#
# Parameters: $1 - working dir (will contain a copy of the latest md5sum.txt file)
# $2 - version of sra-toolkit, e.g. 2.10.7 ("current by default)
# $3 - version of ngs, e.g. 2.10.7 ("current by default)
# $4 - 'nojava' to skip anything that needs java
#
# return codes:
# 0 - tests passed
# 1 - wget sratoolkit failed
# 2 - gunzip sratoolkit failed
# 3 - tar sratoolkit failed
# 4 - wget GenomeAnalysisTK.jar failed
# 5 - wget ngs-sdk failed
# 6 - gunzip ngs-sdk failed
# 7 - tar ngs-sdk failed
# 8 - one of smoke tests failed
# 9 - example failed
DEF_WORKDIR="./temp"
WORKDIR="${1:-$DEF_WORKDIR}"
DEF_VERS="current"
VERS="${2:-$DEF_VERS}"
NGSVERS="${3:-$DEF_VERS}"
echo "Testing sra-tools tarballs, working directory = $WORKDIR"
case $(uname) in
Linux)
python3 -mplatform | grep -q Ubuntu && OS=ubuntu64 || OS=centos_linux64
TOOLS="${TOOLS} pacbio-load remote-fuser"
realpath() {
readlink -f $1
}
get() {
echo wget "$1"
wget -q --no-check-certificate "$1"
}
uname=linux
;;
Darwin)
OS=mac64
realpath() {
[[ $1 = /* ]] && echo "$1" || echo "$PWD/${1#./}"
}
get() {
echo curl "$1"
curl --fail --silent --insecure --remote-name "$1"
}
uname=mac
;;
esac
HOMEDIR=$(dirname $(realpath $0))
################################## sratoolkit ##################################
SDK_URL="https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${VERS}/"
TK_TARGET="sratoolkit.${VERS}-${OS}"
rm -rv ${WORKDIR}
mkdir -p ${WORKDIR}
OLDDIR=$(pwd)
cd ${WORKDIR}
df -h .
get "${SDK_URL}${TK_TARGET}.tar.gz" || exit 1
gunzip -f "${TK_TARGET}.tar.gz" || exit 2
TK_PACKAGE=$(tar tf "${TK_TARGET}.tar" | head -n 1)
rm -rf "${TK_PACKAGE}"
tar xf "${TK_TARGET}.tar" || exit 3
# extract version number from the package's name
[[ "${TK_PACKAGE}" =~ \.[0-9]+\.[0-9]+\.[0-9]+ ]] && VERSION="${BASH_REMATCH[0]:1}" # clip leading '.'
echo Current version: "${VERSION}"
################################## smoke-test ##################################
echo "/LIBS/GUID = \"8badf00d-1111-4444-8888-deaddeadbeef\"" >./${TK_PACKAGE}/bin/ncbi/local.kfg
VDB_CONFIG_FILE=`pwd`/${TK_PACKAGE}/bin/ncbi
echo VDB_CONFIG=${VDB_CONFIG_FILE} $HOMEDIR/smoke-test.sh ./${TK_PACKAGE} ${VERSION}
#ls `pwd`/${TK_PACKAGE}/bin/ncbi
VDB_CONFIG=${VDB_CONFIG_FILE} $HOMEDIR/smoke-test.sh ./${TK_PACKAGE} ${VERSION}
RC=$?
if [ "${RC}" != "0" ]
then
echo "Smoke test returned ${RC}"
exit 8
fi
# run an example
EXAMPLE="./${TK_PACKAGE}/bin/vdb-dump SRR000001 -R 1 "
VDB_CONFIG=${VDB_CONFIG_FILE} $EXAMPLE | grep -q EM7LVYS02FOYNU
if [ "$?" != "0" ]
then
echo "The example failed: $EXAMPLE"
exit 9
fi
# test a run with a vdbcache
EXAMPLE="./${TK_PACKAGE}/bin/vdb-dump --table_enum SRR390728 "
VDB_CONFIG=${VDB_CONFIG_FILE} $EXAMPLE | grep -q SEQUENCE
if [ "$?" != "0" ]
then
echo "The example failed: $EXAMPLE"
exit 9
fi
if [ "$4" != "nojava" ]
then
############################### GenomeAnalysisTK ###############################
GATK_TARGET=GenomeAnalysisTK.jar
get "${SDK_URL}${GATK_TARGET}" || exit 4
################################### ngs-sdk ####################################
NGS_URL="https://ftp-trace.ncbi.nlm.nih.gov/sra/ngs/${NGSVERS}/"
NGS_TARGET="ngs-sdk.${NGSVERS}-${uname}"
get "${NGS_URL}${NGS_TARGET}.tar.gz" || exit 5
gunzip -f "${NGS_TARGET}.tar.gz" || exit 6
NGS_PACKAGE=$(tar tf "${NGS_TARGET}.tar" | head -n 1)
rm -rf "${NGS_PACKAGE}"
tar xf "${NGS_TARGET}.tar" || exit 7
################################## smoke-test ##################################
echo "/LIBS/GUID = \"8badf00d-1111-4444-8888-deaddeadbeef\"" >./${TK_PACKAGE}/bin/ncbi/local.kfg
echo VDB_CONFIG=`pwd`/${TK_PACKAGE}/bin/ncbi $HOMEDIR/smoke-test-ngs.sh ./${TK_PACKAGE} ${VERSION}
#ls `pwd`/${TK_PACKAGE}/bin/ncbi
VDB_CONFIG=`pwd`/${TK_PACKAGE}/bin/ncbi $HOMEDIR/smoke-test-ngs.sh ./${TK_PACKAGE} ${VERSION}
RC=$?
if [ "${RC}" != "0" ]
then
echo "Smoke test returned ${RC}"
exit 8
fi
echo rm ${GATK_TARGET} ${NGS_PACKAGE} ${NGS_TARGET}.tar
rm -rf ${GATK_TARGET} ${NGS_PACKAGE} ${NGS_TARGET}.tar *vcf*
fi
echo rm ${TK_PACKAGE} ${TK_TARGET}.tar
rm -rf ${TK_PACKAGE} ${TK_TARGET}.tar
cd ${OLDDIR} && ( rm -rf ${WORKDIR} || ls ${WORKDIR} )
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