details: http://www.bx.psu.edu/hg/galaxy/rev/5cc5e94345b8 changeset: 3566:5cc5e94345b8 user: fubar: ross Lazarus at gmail period com date: Fri Mar 26 12:02:22 2010 -0400 description: Add a tool_runner entry for hapmap - similar to the existing biomart one Updated WGA/SNP entries in tool_conf.xml.sample diffstat: .hgignore | 4 +++ lib/galaxy/web/controllers/tool_runner.py | 6 +++++ tool_conf.xml.sample | 35 +++++++++++++++++++----------- 3 files changed, 32 insertions(+), 13 deletions(-) diffs (93 lines): diff -r 5f927f52191c -r 5cc5e94345b8 .hgignore --- a/.hgignore Fri Mar 26 09:51:03 2010 -0400 +++ b/.hgignore Fri Mar 26 12:02:22 2010 -0400 @@ -1,5 +1,6 @@ syntax: glob +.hg* # Downloaded and locally built eggs eggs scripts/scramble/build @@ -10,6 +11,8 @@ database/beaker_sessions database/compiled_templates database/files +database/pbs +database/tmp database/*.sqlite # Python bytecode @@ -20,6 +23,7 @@ reports_wsgi.ini datatypes_conf.xml tool_conf.xml +static/welcome.html.* tool-data/*.loc # Test output diff -r 5f927f52191c -r 5cc5e94345b8 lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py Fri Mar 26 09:51:03 2010 -0400 +++ b/lib/galaxy/web/controllers/tool_runner.py Fri Mar 26 12:02:22 2010 -0400 @@ -25,6 +25,12 @@ """Catches the tool id and redirects as needed""" return self.index(trans, tool_id=tool_id, **kwd) + #test to get hapmap to work, ideally, we could pass tool_id to hapmap biomart and receive it back + @web.expose + def hapmapmart(self, trans, tool_id='hapmapmart', **kwd): + """Catches the tool id and redirects as needed""" + return self.index(trans, tool_id=tool_id, **kwd) + @web.expose def default(self, trans, tool_id=None, **kwd): """Catches the tool id and redirects as needed""" diff -r 5f927f52191c -r 5cc5e94345b8 tool_conf.xml.sample --- a/tool_conf.xml.sample Fri Mar 26 09:51:03 2010 -0400 +++ b/tool_conf.xml.sample Fri Mar 26 12:02:22 2010 -0400 @@ -235,24 +235,33 @@ <tool file="genetrack/genetrack_indexer.xml" /> <tool file="genetrack/genetrack_peak_prediction.xml" /> </section> - <section name="Rg Data" id="rgData1"> - <tool file="rgenetics/rgenetics_import.xml"/> - <tool file="rgenetics/rgLpedPbed.xml"/> + <section name="SNP/WGA: Data; Filters" id="rgdat"> + <label text="Data: Import and upload" id="rgimport" /> + <tool file="data_source/upload.xml"/> + <tool file="data_source/access_libraries.xml" /> + <tool file="data_source/hapmapmart.xml" /> + <label text="Data: Filter and Clean" id="rgfilter" /> <tool file="rgenetics/rgClean.xml"/> + <tool file="rgenetics/rgPedSub.xml"/> + <tool file="rgenetics/rgLDIndep.xml"/> + <label text="Simulate" id="rgsim" /> + <tool file="rgenetics/rgfakePhe.xml"/> + <tool file="rgenetics/rgfakePed.xml"/> + </section> + <section name="SNP/WGA: QC; LD; Plots" id="rgqcplot"> + <label text="QC; Eigenstrat" id="rgvisual" /> <tool file="rgenetics/rgQC.xml"/> + <tool file="rgenetics/rgEigPCA.xml"/> + <label text="LD; Manhattan/QQ; GRR" id="rgld" /> + <tool file="rgenetics/rgHaploView.xml"/> + <tool file="rgenetics/rgManQQ.xml"/> + <tool file="rgenetics/rgGRR.xml"/> </section> - <section name="Rg Simulate" id="rgSim1"> - <tool file="rgenetics/rgfakePhe.xml"/> - </section> - <section name="Rg Visualise" id="rgVis1"> - <tool file="rgenetics/rgQC.xml"/> - <tool file="rgenetics/rgEigPCA2.xml"/> - <tool file="rgenetics/rgQQ.xml"/> - </section> - <section name="Rg Model Data" id="rgModel1"> - <tool file="rgenetics/rgGLM.xml"/> + <section name="SNP/WGA: Statistical Models" id="rgmodel"> <tool file="rgenetics/rgCaCo.xml"/> <tool file="rgenetics/rgTDT.xml"/> + <tool file="rgenetics/rgGLM.xml"/> + <tool file="rgenetics/rgManQQ.xml"/> </section> <!-- TODO: uncomment the following EMBOSS section whenever