Mercurial > repos > peterjc > clinod
changeset 2:3213023deae1 draft
Uploaded v0.0.5 take 2, attempt auto-installation
| author | peterjc |
|---|---|
| date | Tue, 07 May 2013 10:29:57 -0400 |
| parents | a4881144d6f4 |
| children | a66a914c39b5 |
| files | tools/clinod/clinod.txt tools/clinod/clinod.xml |
| diffstat | 2 files changed, 25 insertions(+), 14 deletions(-) [+] |
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--- a/tools/clinod/clinod.txt Thu May 02 12:53:42 2013 -0400 +++ b/tools/clinod/clinod.txt Tue May 07 10:29:57 2013 -0400 @@ -13,15 +13,23 @@ http://toolshed.g2.bx.psu.edu/view/peterjc/clinod -Installation -============ +Automated Installation +====================== + +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. + + +Manual Installation +=================== This wrapper expects the java binary to be on the system PATH, and to be able -to access command line NoD as /opt/clinod/clinod-1.3.jar (edit clinod.xml if -you wish to use a different location). +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 $CLINOD to /opt/clinod -Internally NoD calls the binary batchman from the Stuttgart Neural Network -Simulator (SNNS) v 4.2 software suite. This binary can either be on the system -path or located next to the JAR file, i.e. /opt/clinod/batchman +Internally NoD calls the binary batchman v1.0 from the Stuttgart Neural Network +Simulator (SNNS) v4.2 or 4.3 software suite. This binary can either be on the +system path or located next to the JAR file, i.e. /opt/clinod/batchman To install the wrapper copy or move the following files under the Galaxy tools folder, e.g. in a tools/clinod folder: @@ -51,7 +59,7 @@ v0.0.3 - Describe output table in help v0.0.4 - Added unit test v0.0.5 - Link to Tool Shed added to help text and this documentation. - - Moved files pending automated tool installation. + - Automated tool installation. Developers
--- a/tools/clinod/clinod.xml Thu May 02 12:53:42 2013 -0400 +++ b/tools/clinod/clinod.xml Tue May 07 10:29:57 2013 -0400 @@ -1,9 +1,15 @@ <tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.5"> <description>Find nucleolar localization signals (NoLSs) in protein sequences</description> + <requirements> + <requirement type="binary">java</requirement> + <requirement type="package" version="1.3">clinod</requirement> + </requirements> <command> - java -jar /opt/clinod/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t=8 -f=MEDIUM_TAB -nonols -clean_sequence - ##I want the number of threads to be a Galaxy config option... - ##TODO - Make the -clean_sequence argument a parameter? +##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=8 -f=MEDIUM_TAB -nonols -clean_sequence +##I want the number of threads to be a Galaxy config option... +##TODO - Make the -clean_sequence argument a parameter? </command> <stdio> <!-- Assume anything other than zero is an error --> @@ -16,9 +22,6 @@ <outputs> <data name="tabular_file" format="tabular" label="NoD results" /> </outputs> - <requirements> - <requirement type="binary">java</requirement> - </requirements> <tests> <test> <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />