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annotate orthologs/ucsb_hamster/ucsb_hamster.sh @ 0:5b9a38ec4a39 draft default tip

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First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 #!/bin/sh
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2
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3 #############################################
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4 # UCSB HAMSTER #
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5 # #
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6 # Executes Hamster with given XML parameter #
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7 #############################################
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8
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 #the name of the script is here
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10 #script="/home/osiris/galaxy-dist/tools/osiris/orthologs/ucsb_hamster/hamstrsearch_local-hmmer3.pl"
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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11 script="hamstrsearch_local-hmmer3.pl"
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12
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13
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14
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15 #Variables input from xml
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16 # 1 - Sequence input file
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17 # 2 - Proteins Results Output file
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18 # 3 - cds Results Output file
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19 # 4 - Screen Log
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20 # 5 - Species Name
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21 # 6 - Whether to use -est flag (if D) or not (if P)
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22 # 7 - Core ortholog name
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23 # 8 - Base path for local core orthologs
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24 # 9 - Base path for local reference blast database
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25 #10 - Reference genome
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26
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27 input=$1
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28 proteins=$2
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29 cdsfile=$3
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30 screenlog=$4
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31 species=$5
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32 datatype=$6
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33 core=$7
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34 corepath=$8
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35 blastpath=$9
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36 genome=${10}
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37
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38 echo "ucsb_hamster.sh script parameters" >> $screenlog
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39 echo "Core ortholog name is $core " >> $screenlog
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40 echo "Reference genome name is $genome " >> $screenlog
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41 echo "Species name is $species " >> $screenlog
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42 echo "Datatype $datatype " >> $screenlog
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43
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44 #set flag based on input
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45 if [ $datatype = "P" ];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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46 then
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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47 estflag="-protein"
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48 else
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49 estflag="-est"
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50 fi
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51
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52 # First copy hmm's to working directory
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53 # Currently copies from Data directory
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54 mkdir $core
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55 mkdir $core/hmm_dir
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56 cp -r $corepath/* ./$core/
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57 echo "cp $corepath/hmm_dir/* ./$core/hmm_dir/" >> $screenlog
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58 cp -r $corepath/hmm_dir/* ./$core/hmm_dir/
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59
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60 # Currently copies from data directory
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61 mkdir $genome
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62 cp $blastpath/* ./$genome/
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63
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64 # Now call the actual Hamster Script
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65 #$script -sequence_file=$input $estflag -taxon=$species -hmmset=$core -refspec=$genome -galaxyout=$proteins -2galaxyout=$cdsfile >> $screenlog 2>log.txt
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66 $script -sequence_file=$input $estflag -taxon=$species -hmmset=$core -refspec=$genome -galaxyout=$proteins -2galaxyout=$cdsfile >> $screenlog
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