Mercurial > repos > peterjc > effectivet3
changeset 1:e607c342312f
Wrapper v0.0.8, includes effectiveT3.loc.sample file
| author | peterjc |
|---|---|
| date | Tue, 02 Aug 2011 07:06:13 -0400 |
| parents | 43436379876f |
| children | 5a8e09f115f8 |
| files | tool-data/effectiveT3.loc.sample tools/protein_analysis/effectiveT3.txt tools/protein_analysis/effectiveT3.xml |
| diffstat | 3 files changed, 39 insertions(+), 5 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/effectiveT3.loc.sample Tue Aug 02 07:06:13 2011 -0400 @@ -0,0 +1,26 @@ +# This is a three column tab separated file to define the modules (models) +# for the Effective T3 prediction tool. +# +# Column 1 - Module ID, string that Galaxy will save in its database +# Column 2 - Human readable name, Galaxy will show this in the UI +# Column 3 - Filename, Galaxy will use this when calling the tool +# +#NOTE: In EffectiveT3 v1.0.1, the modules are given as their filename +#(with the JAR extension) but without any path. They are expected to +#be located in a subdirectory called module under the working directory. +#For the galaxy wrapper, we assume this means under the folder where the +#main JAR file is, TTSS_GUI-1.0.1.jar +# +#e.g. +# +# /opt/EffectiveT3/TTSS_GUI-1.0.1.jar +# /opt/EffectiveT3/module/TTSS_STD-1.0.1.jar +# /opt/EffectiveT3/module/TTSS_ANIMAL-1.0.1.jar +# /opt/EffectiveT3/module/TTSS_PLANT-1.0.1.jar +# +#See files ../tools/protein_analysis/effectiveT3.* for more details, +#and http://effectors.org +# +standard Type III Effector prediction with standard set TTSS_STD-1.0.1.jar +animal Type III Effector prediction with animal set TTSS_ANIMAL-1.0.1.jar +plant Type III Effector prediction with plant set TTSS_PLANT-1.0.1.jar
--- a/tools/protein_analysis/effectiveT3.txt Tue Jun 07 17:21:30 2011 -0400 +++ b/tools/protein_analysis/effectiveT3.txt Tue Aug 02 07:06:13 2011 -0400 @@ -19,6 +19,10 @@ http://effectors.org/ + +Installation +=========== + You can change the path by editing the definition near the start of the Python script effectiveT3.py, but by default it expects the following files to be installed at these locations: @@ -35,6 +39,9 @@ * effectiveT3.py (the Python wrapper script) * effectiveT3.txt (this README file) +Also copy effectiveT3.loc.sample to effectiveT3.loc in the tool-data folder +(and edit if appropriate, e.g. to add or remove a model). + You will also need to modify the tools_conf.xml file to tell Galaxy to offer the tool. If you are using other protein analysis tools like TMHMM or SignalP, put it next to them. Just add the line: @@ -48,6 +55,7 @@ ======= v0.0.7 - Initial public release +v0.0.8 - Include effectiveT3.loc.sample in Tool Shed Developers @@ -59,7 +67,7 @@ For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder: -$ tar -czf effectiveT3.tar.gz tools/protein_analysis/effectiveT3.xml tools/protein_analysis/effectiveT3.py tools/protein_analysis/effectiveT3.txt +$ tar -czf effectiveT3.tar.gz tools/protein_analysis/effectiveT3.xml tools/protein_analysis/effectiveT3.py tools/protein_analysis/effectiveT3.txt tool-data/effectiveT3.loc.sample Check this worked: @@ -67,7 +75,7 @@ tools/protein_analysis/effectiveT3.xml tools/protein_analysis/effectiveT3.py tools/protein_analysis/effectiveT3.txt - +tool-data/effectiveT3.loc.sample Licence (MIT/BSD style) ======================= @@ -90,5 +98,5 @@ OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. -NOTE: This is the licence for the Galaxy Wrapper only. NLStradamus -is available and licenced separately. +NOTE: This is the licence for the Galaxy Wrapper only. +EffectiveT3 is available and licenced separately.
--- a/tools/protein_analysis/effectiveT3.xml Tue Jun 07 17:21:30 2011 -0400 +++ b/tools/protein_analysis/effectiveT3.xml Tue Aug 02 07:06:13 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="effectiveT3" name="Effective T3" version="0.0.7"> +<tool id="effectiveT3" name="Effective T3" version="0.0.8"> <description>Find bacterial effectors in protein sequences</description> <command interpreter="python"> effectiveT3.py $module.fields.path