Mercurial > repos > devteam > data_manager_build_kraken_database

comparison data_manager/kraken_database_builder.xml @ 3:404ba485ec01 draft

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author devteam
date Thu, 30 Apr 2015 16:16:05 -0400
parents cdef63d8a141
children 1de1817a8a57
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2:cdef63d8a141 3:404ba485ec01
19 #if str($library) != 'None': 19 #if str($library) != 'None':
20 kraken-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db "${database_name}" && 20 kraken-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db "${database_name}" &&
21 #end if 21 #end if
22 #end for 22 #end for
23 #for $fasta in $input_fasta: 23 #for $fasta in $input_fasta:
24 kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --add-to-library "$fasta" && 24 #if str($fasta) != 'None':
25 kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --add-to-library "$fasta" &&
26 #end if
25 #end for 27 #end for
26 kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} && 28 kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} &&
27 cd .. && python \$KRAKEN_SCRIPT_PATH/data_manager/make_json.py --db "${database_name}" --out "${out_file}" 29 cd .. && python \$KRAKEN_SCRIPT_PATH/data_manager/make_json.py --db "${database_name}" --out "${out_file}"
28 ]]> 30 ]]>
29 </command> 31 </command>