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local-gluetools-config.xml
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local-gluetools-config.xml
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<gluetools>
<!-- GRANT ALL ON HCV_GLUE.* TO "hcvglue"@"localhost" identified by "hcvglue"; -->
<database>
<username>hcvglue</username>
<password>hcvglue</password>
<vendor>MySQL</vendor>
<jdbcUrl>jdbc:mysql://localhost:3306/HCV_GLUE?characterEncoding=UTF-8</jdbcUrl>
</database>
<properties>
<!-- BLAST related config -->
<property>
<name>gluetools.core.programs.blast.blastn.executable</name>
<value>/Users/joshsinger/blast/ncbi-blast-2.2.31+/bin/blastn</value>
</property>
<property>
<name>gluetools.core.programs.blast.tblastn.executable</name>
<value>/Users/joshsinger/blast/ncbi-blast-2.2.31+/bin/tblastn</value>
</property>
<property>
<name>gluetools.core.programs.blast.makeblastdb.executable</name>
<value>/Users/joshsinger/blast/ncbi-blast-2.2.31+/bin/makeblastdb</value>
</property>
<property>
<name>gluetools.core.programs.blast.search.threads</name>
<value>4</value>
</property>
<property>
<name>gluetools.core.programs.blast.db.dir</name>
<value>/Users/joshsinger/tmp/blastdbs</value>
</property>
<!-- RAxML-specific config -->
<property>
<name>gluetools.core.programs.raxml.raxmlhpc.executable</name>
<value>/Users/joshsinger/RAxML/bin/raxmlHPC-PTHREADS-AVX2</value>
</property>
<property>
<name>gluetools.core.programs.raxml.raxmlhpc.cpus</name>
<value>4</value>
</property>
<property>
<name>gluetools.core.programs.raxml.temp.dir</name>
<value>/Users/joshsinger/tmp/raxmlfiles</value>
</property>
<!-- MAFFT-specific config -->
<property>
<name>gluetools.core.programs.mafft.executable</name>
<value>/usr/local/bin/mafft</value>
</property>
<property>
<name>gluetools.core.programs.mafft.cpus</name>
<value>4</value>
</property>
<property>
<name>gluetools.core.programs.mafft.temp.dir</name>
<value>/Users/joshsinger/tmp/mafftfiles</value>
</property>
<!-- JModelTest -->
<property>
<name>gluetools.core.programs.jmodeltester.jar</name>
<value>/Users/joshsinger/jmodeltest/jmodeltest-2.1.10/jModelTest.jar</value>
</property>
<property>
<name>gluetools.core.programs.jmodeltester.temp.dir</name>
<value>/Users/joshsinger/jmodeltest/tmp</value>
</property>
<property>
<name>gluetools.core.programs.jmodeltester.cpus</name>
<value>4</value>
</property>
<!-- Cayenne -->
<property>
<name>cayenne.querycache.size</name>
<value>30000</value>
</property>
</properties>
</gluetools>