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comparison data_manager/kraken_database_builder.xml @ 2:cdef63d8a141 draft

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Uploaded
author devteam
date Mon, 27 Apr 2015 16:13:06 -0400
parents 9e4d72083f9f
children 404ba485ec01
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1:9e4d72083f9f 2:cdef63d8a141
14 <![CDATA[ 14 <![CDATA[
15 #set $library_list = str($libraries).split(',') 15 #set $library_list = str($libraries).split(',')
16 mkdir kraken-database && cd kraken-database && 16 mkdir kraken-database && cd kraken-database &&
17 kraken-build --threads \${GALAXY_SLOTS:-1} --download-taxonomy --db "${database_name}" && 17 kraken-build --threads \${GALAXY_SLOTS:-1} --download-taxonomy --db "${database_name}" &&
18 #for $library in $library_list: 18 #for $library in $library_list:
19 kraken-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db "${database_name}" && 19 #if str($library) != 'None':
20 kraken-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db "${database_name}" &&
21 #end if
20 #end for 22 #end for
21 #for $fasta in $input_fasta: 23 #for $fasta in $input_fasta:
22 kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --add-to-library "$fasta" && 24 kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --add-to-library "$fasta" &&
23 #end for 25 #end for
24 kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} && 26 kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} &&