# HG changeset patch # User peterjc # Date 1367937123 14400 # Node ID a66a914c39b5bff03fa752b6d1c510d7b73a4226 # Parent 3213023deae162d079ad8660453c39bf7f9018b3 Uploaded v0.0.5 take 3, included the new tool_dependencies.xml file. diff -r 3213023deae1 -r a66a914c39b5 tools/clinod/clinod.txt --- a/tools/clinod/clinod.txt Tue May 07 10:29:57 2013 -0400 +++ b/tools/clinod/clinod.txt Tue May 07 10:32:03 2013 -0400 @@ -71,13 +71,14 @@ For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder: -$ tar -czf clinod.tar.gz tools/clinod/clinod.xml tools/clinod/clinod.txt test-data/four_human_proteins.fasta test-data/four_human_proteins.clinod-1.3.tabular +$ tar -czf clinod.tar.gz tools/clinod/clinod.xml tools/clinod/clinod.txt tools/clinod/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.clinod-1.3.tabular Check this worked: $ tar -tzf clinod.tar.gz tools/clinod/clinod.xml tools/clinod/clinod.txt +tools/clinod/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.clinod-1.3.tabular diff -r 3213023deae1 -r a66a914c39b5 tools/clinod/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/clinod/tool_dependencies.xml Tue May 07 10:32:03 2013 -0400 @@ -0,0 +1,30 @@ + + + + + + + http://www.ra.cs.uni-tuebingen.de/downloads/SNNS/SNNSv4.3.tar.gz + tools/bin/x86_64-pc-unknown-linux-gnuoldld/batchman$INSTALL_DIR/ + + http://www.compbio.dundee.ac.uk/nod/downloads/clinod-1.3.jar + clinod-1.3.jar$INSTALL_DIR + + $INSTALL_DIR + + + + +Downloads and installs the command line NoD (clinod) JAR file and the binary +dependency batchman, and sets $CLINOD to the folder used. + +We could download, compiles and install the SNNS Batch Interpreter v1.0 executable +(batchman) from Stuttgart Neural Network Simulator (SNNS) v4.2. However, we simplify +this by downloading SNNS v4.3 which includes the precompiled copy of batch man. + +For more details, see: +http://www.compbio.dundee.ac.uk/www-nod/downloads.jsp + + + +