Mercurial > repos > devteam > data_manager_build_kraken_database
comparison data_manager/kraken_database_builder.xml @ 2:cdef63d8a141 draft
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author | devteam |
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date | Mon, 27 Apr 2015 16:13:06 -0400 |
parents | 9e4d72083f9f |
children | 404ba485ec01 |
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1:9e4d72083f9f | 2:cdef63d8a141 |
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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} && |