| Previous changeset 3:6a9debe4b860 (2013-09-18) Next changeset 5:9485cdfca57e (2015-08-05) |
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Commit message:
Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML. |
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modified:
tools/clinod/README.rst tools/clinod/clinod.xml tools/clinod/tool_dependencies.xml |
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| diff -r 6a9debe4b860 -r 4d9a4a43861b tools/clinod/README.rst --- a/tools/clinod/README.rst Wed Sep 18 06:09:33 2013 -0400 +++ b/tools/clinod/README.rst Thu Nov 20 06:15:49 2014 -0500 |
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| @@ -18,35 +18,36 @@ This should be straightforward, Galaxy should automatically download and install the JAR file for clinod v1.3 and the batchman executable from the Stuttgart -Neural Network Simulator (SNNS), and set the $CLINOD to their folder. +Neural Network Simulator (SNNS), and set the ``$CLINOD`` to their folder. Manual Installation =================== This wrapper expects the java binary to be on the system PATH, and to be able -to access command line NoD as $CLINOD/clinod-1.3.jar which means if you used -/opt/clinod/clinod-1.3.jar set the environment variable $CLINOD to /opt/clinod +to access command line NoD as ``$CLINOD/clinod-1.3.jar`` which means if you +used ``/opt/clinod/clinod-1.3.jar`` set the environment variable ``$CLINOD`` +to ``/opt/clinod`` Internally NoD calls the binary batchman v1.0 from the Stuttgart Neural Network Simulator (SNNS) v4.2 or 4.3 software suite. This binary can either be on the -system path or located next to the JAR file, i.e. /opt/clinod/batchman +system path or located next to the JAR file, i.e. ``/opt/clinod/batchman`` To install the wrapper copy or move the following files under the Galaxy tools -folder, e.g. in a tools/clinod folder: +folder, e.g. in a ``tools/clinod`` folder: -* clinod.xml (the Galaxy tool definition) -* README.rst (this file) +* ``clinod.xml`` (the Galaxy tool definition) +* ``README.rst`` (this file) -You will also need to modify the tools_conf.xml file to tell Galaxy to offer the +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:: <tool file="clinod/clinod.xml" /> -If you wish to run the unit tests, also add this to tools_conf.xml.sample -and move/copy the test-data files under Galaxy's test-data folder. Then:: +If you wish to run the unit tests, also move/copy the ``test-data/`` files +under Galaxy's ``test-data/`` folder. Then:: - $ ./run_functional_tests.sh -id clinod + $ ./run_tests.sh -id clinod That's it. @@ -67,6 +68,8 @@ - Use reStructuredText for this README file. - Updated citation information (Cock et al. 2013). - Development moved to GitHub, https://github.com/peterjc/pico_galaxy +v0.0.7 - Use the new ``$GALAXY_SLOTS`` environment variable for thread count. + - Tool definition now embeds citation information. ======= ====================================================================== |
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| diff -r 6a9debe4b860 -r 4d9a4a43861b tools/clinod/clinod.xml --- a/tools/clinod/clinod.xml Wed Sep 18 06:09:33 2013 -0400 +++ b/tools/clinod/clinod.xml Thu Nov 20 06:15:49 2014 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.5"> +<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.7"> <description>Find nucleolar localization signals (NoLSs) in protein sequences</description> <requirements> <requirement type="binary">java</requirement> @@ -7,8 +7,7 @@ <command> ##The Galaxy Tool Shed installation should define $CLINOD to point at folder ##containing both clinod-1.3.jar and the batchman binary: -java -jar \$CLINOD/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t=2 -f=MEDIUM_TAB -nonols -clean_sequence -##I want the number of threads to be a Galaxy config option... +java -jar \$CLINOD/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t="\$GALAXY_SLOTS" -f=MEDIUM_TAB -nonols -clean_sequence ##TODO - Make the -clean_sequence argument a parameter? </command> <stdio> @@ -25,7 +24,7 @@ <tests> <test> <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" /> - <output name="tabular_file" file="four_human_proteins.clinod-1.3.tabular" ftype="tabular" /> + <output name="tabular_file" file="four_human_proteins.clinod-1.3.tabular" ftype="tabular" /> </test> </tests> <help> @@ -82,4 +81,9 @@ Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clinod </help> + <citations> + <citation type="doi">10.7717/peerj.167</citation> + <citation type="doi">10.1093/nar/gkq653</citation> + <citation type="doi">10.1186/1471-2105-12-317</citation> + </citations> </tool> |
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| diff -r 6a9debe4b860 -r 4d9a4a43861b tools/clinod/tool_dependencies.xml --- a/tools/clinod/tool_dependencies.xml Wed Sep 18 06:09:33 2013 -0400 +++ b/tools/clinod/tool_dependencies.xml Thu Nov 20 06:15:49 2014 -0500 |
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| @@ -9,7 +9,7 @@ </action> <!-- clinod requires the SNNS Batch Interpreter v1.0 executable --> <action type="shell_command">wget http://www.ra.cs.uni-tuebingen.de/downloads/SNNS/SNNSv4.3.tar.gz</action> - <action type="shell_command">tar -zxvf SNNSv4.3.tar.gz</action> + <action type="shell_command">tar -zxvf SNNSv4.3.tar.gz</action> <action type="move_file"><source>SNNSv4.3/tools/bin/x86_64-pc-unknown-linux-gnuoldld/batchman</source><destination>$INSTALL_DIR/</destination></action> <!-- clinod itself is just a JAR file --> <action type="shell_command">wget http://www.compbio.dundee.ac.uk/nod/downloads/clinod-1.3.jar</action> |