Mercurial > repos > devteam > data_manager_build_kraken_database
comparison data_manager/kraken_database_builder.xml @ 3:404ba485ec01 draft
Uploaded
author | devteam |
---|---|
date | Thu, 30 Apr 2015 16:16:05 -0400 |
parents | cdef63d8a141 |
children | 1de1817a8a57 |
comparison
equal
deleted
inserted
replaced
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> |