Mercurial > repos > devteam > data_manager_build_kraken_database
changeset 3:404ba485ec01 draft
Uploaded
| author | devteam |
|---|---|
| date | Thu, 30 Apr 2015 16:16:05 -0400 |
| parents | cdef63d8a141 |
| children | 1de1817a8a57 |
| files | data_manager/kraken_database_builder.xml tool_dependencies.xml |
| diffstat | 2 files changed, 5 insertions(+), 3 deletions(-) [+] |
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--- a/data_manager/kraken_database_builder.xml Mon Apr 27 16:13:06 2015 -0400 +++ b/data_manager/kraken_database_builder.xml Thu Apr 30 16:16:05 2015 -0400 @@ -21,7 +21,9 @@ #end if #end for #for $fasta in $input_fasta: - kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --add-to-library "$fasta" && + #if str($fasta) != 'None': + kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --add-to-library "$fasta" && + #end if #end for kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} && cd .. && python \$KRAKEN_SCRIPT_PATH/data_manager/make_json.py --db "${database_name}" --out "${out_file}" @@ -45,4 +47,4 @@ <citations> <citation type="doi">10.1186/gb-2014-15-3-r46</citation> </citations> -</tool> \ No newline at end of file +</tool>
--- a/tool_dependencies.xml Mon Apr 27 16:13:06 2015 -0400 +++ b/tool_dependencies.xml Thu Apr 30 16:16:05 2015 -0400 @@ -4,7 +4,7 @@ <environment_variable action="set_to" name="KRAKEN_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> <package name="kraken" version="0.10.5"> - <repository changeset_revision="c949a8bd92ec" name="package_kraken_0_10_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="a3189c292911" name="package_kraken_0_10_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="jellyfish" version="1.1.11"> <repository changeset_revision="9529f5e46f4e" name="package_jellyfish_1_1_11" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />