Mercurial > repos > peterjc > blast2go
changeset 19:7ed4187fc07c draft
Uploaded v0.0.8 preview 14, need June 2011 database for the test to pass.
| author | peterjc |
|---|---|
| date | Mon, 16 Sep 2013 06:54:39 -0400 |
| parents | cfef49c32fd0 |
| children | fe9dbe7817cc |
| files | blast2go/blast2go.xml blast2go/tool_dependencies.xml tool-data/blast2go.loc.sample |
| diffstat | 3 files changed, 10 insertions(+), 5 deletions(-) [+] |
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--- a/blast2go/blast2go.xml Sun Sep 15 15:30:53 2013 -0400 +++ b/blast2go/blast2go.xml Mon Sep 16 06:54:39 2013 -0400 @@ -27,7 +27,7 @@ <tests> <test> <param name="xml" value="blastp_sample.xml" ftype="blastxml"/> - <param name="prop" value="Spain_2012_August"/> + <param name="prop" value="Spain_2011_June"/> <output name="tab" file="blastp_sample.blast2go.tabular" ftype="tabular"/> </test> </tests>
--- a/blast2go/tool_dependencies.xml Sun Sep 15 15:30:53 2013 -0400 +++ b/blast2go/tool_dependencies.xml Mon Sep 16 06:54:39 2013 -0400 @@ -12,6 +12,11 @@ sed -i "s/Dbacces.dbname=b2g_apr12/Dbacces.dbname=b2g_aug12/g" Spain_2012_August.properties && sed -i "s/Dbacces.dbhost=10.10.100.203/Dbacces.dbhost=publicdb.blast2go.com/g" Spain_2012_August.properties </action> + <action type="shell_command"> +cp b2gPipe.properties Spain_2011_June.properties && +sed -i "s/Dbacces.dbname=b2g_apr12/Dbacces.dbname=b2g_jun11/g" Spain_2011_June.properties && +sed -i "s/Dbacces.dbhost=10.10.100.203/Dbacces.dbhost=publicdb.blast2go.com/g" Spain_2011_June.properties + </action> <action type="move_directory_files"><source_directory>.</source_directory><destination_directory>$INSTALL_DIR/</destination_directory></action> <!-- Set environment variable $B2G4PIPE so Python script knows where to look --> <action type="set_environment">
--- a/tool-data/blast2go.loc.sample Sun Sep 15 15:30:53 2013 -0400 +++ b/tool-data/blast2go.loc.sample Mon Sep 16 06:54:39 2013 -0400 @@ -13,7 +13,7 @@ # "General Settings", "DataAccess setting"). We also strongly recommend # configuring a local Blast2GO database. # -# The property filenames can be fullied qualified paths like +# The property filenames can be fully qualified paths like # /opt/b2g4pipe/Spain_2012_August.properties or provided they are # in the same folder as the Blast2GO JAR file, just the filename # like Spain_2012_August.properties instead. This is intended to @@ -22,6 +22,6 @@ # #Local_2011_May Local database (May 2011) Local_2011_May.properties #Spain_2010_May Database in Spain (May 2010) Spain_2010_May.properties -#Spain_2011_June Database in Spain (June 2011) Spain_2011_June.properties -#Spain_2012_August Database in Spain (August 2012) Spain_2012_August.properties -default Default settings b2gPipe.properties +Spain_2012_August Database in Spain (August 2012) Spain_2012_August.properties +Spain_2011_June Database in Spain (June 2011) Spain_2011_June.properties +#default Default settings b2gPipe.properties