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1 #!/bin/sh
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2
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3 CMD=""
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4 PYTH_PATH="PYTHONPATH=/SHARE/USERFS/els7/users/galaxy/develop/usr-cluster/lib/p\
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5 ython2.7/site-packages/:/SHARE/USERFS/els7/users/biobank/lib/"
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6 runner="$(dirname ${BASH_SOURCE[0]})/"
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7 until [ -z $1 ]
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8 do
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9
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10 opt_host='--host='
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11 opt_user='--user='
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12 opt_passwd='--passwd='
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13 opt_interpreter='--interpreter='
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14 opt_runner='--runner='
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15 if [[ $1 == $opt_host* ]]; then
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16 host=`echo $1 | cut -d '=' -f2 | cut -d '.' -f1`
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17 if [ -z $host -o $host == 'None' ]; then
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18 echo 'ERROR. Missing omero host parameter. Please, set Omero Host in your user preferences' > /dev/null >&2
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19 exit -1
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20 fi
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21 PYTH_PATH+=$host
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22 HOST=`echo $1 | cut -d '=' -f2`
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23 CMD+=' '$1
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24 elif [[ $1 == $opt_user* ]]; then
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25 user=`echo $1 | cut -d '=' -f2`
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26 if [ -z $user -o $user == 'None' ]; then
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27 echo 'ERROR. Missing omero user parameter. Please, set Omero User in your user preferences' > /dev/null >&2
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28 exit -1
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29 fi
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30 CMD+=' '$1
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31 elif [[ $1 == $opt_passwd* ]]; then
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32 passwd=`echo $1 | cut -d '=' -f2`
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33 if [ -z $passwd -o $passwd == 'None' ]; then
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34 echo 'ERROR. Missing omero password parameter. Please, set Omero Password in your user preferences' > /dev/null >&2
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35 exit -1
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36 fi
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37 CMD+=' '$1
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38 elif [[ $1 == $opt_runner* ]]; then
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39 runner+=`echo $1 | cut -d '=' -f2`
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40 elif [[ $1 == $opt_interpreter* ]]; then
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41 interpreter=`echo $1 | cut -d '=' -f2`
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42 else
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43 CMD+=' '$1
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44 fi
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45 shift
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46 done
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47 export $PYTH_PATH/:$PYTHONPATH
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48 profile="/SHARE/USERFS/els7/users/biobank/lib/${HOST}.biobank.profile"
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49 if [ -f $profile ]; then
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50 source $profile
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51 CMD=$interpreter' '$runner$CMD
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52 $CMD
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53 else
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54 echo "ERROR. Biobank profile file doesn't exist. Please, check Omero Host in your user preferences" > /dev/null >&2
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55 exit -1
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56 fi
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