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comparison interproscan5/ips5.xml @ 2:d1d34608dba0 draft

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author mkh
date Fri, 29 Jan 2016 18:41:29 -0500
parents e2d4343d73ad
children 74cf3f49f10c
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1:e2d4343d73ad 2:d1d34608dba0
9 <requirement type="set_environment">INTERPROSCAN_SCRIPT_PATH</requirement> 9 <requirement type="set_environment">INTERPROSCAN_SCRIPT_PATH</requirement>
10 </requirements> 10 </requirements>
11 11
12 <command> 12 <command>
13 #import os 13 #import os
14 echo "Start timestamp: $(date)"; 14 echo "Start timestamp: \$(date)";
15 \$IPS_HOME/interproscan.sh 15 \$IPS_HOME/interproscan.sh
16 ## disables the precalculated lookup service, all calculation will be run locally 16 ## disables the precalculated lookup service, all calculation will be run locally
17 -dp 17 -dp
18 --input $infile 18 --input $infile
19 --seqtype $seqtype 19 --seqtype $seqtype
53 tar -C $svg_file.files_path -xvmzf $temp_archive_file; 53 tar -C $svg_file.files_path -xvmzf $temp_archive_file;
54 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_index.py $svg_file $svg_file.files_path; 54 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_index.py $svg_file $svg_file.files_path;
55 rm $temp_archive_file; 55 rm $temp_archive_file;
56 #end if 56 #end if
57 57
58 echo "End timestamp: $(date)" 58 echo "End timestamp: \$(date)"
59 </command> 59 </command>
60 60
61 <inputs> 61 <inputs>
62 <param name="infile" type="data" format="fasta" label="Sequence Fasta File"/> 62 <param name="infile" type="data" format="fasta" label="Sequence Fasta File"/>
63 63