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End to end test works. Add tests next
author ross lazarus ross.lazarus@gmail.com
date Sat, 02 Jun 2012 20:02:11 +1000
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1 = WARNING before you start = This tool should only ever be installed on a private Galaxy instance - NEVER use it on a public
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2 Galaxy because the risks are too awful to contemplate let alone manage. You have been warned.
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4 == Motivation == Simple transformation, filtering or reporting scripts get written, run and lost every day in most busy labs
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5 - even ours where Galaxy is in use. This 'dark script matter' is pervasive and generally not reproducible.
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7 == Benefits == For our group, this allows Galaxy to fill that important dark script gap - all those "small" bioinformatics
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8 tasks. Once a user has a working R (or python or perl) script that does something Galaxy cannot currently do (eg transpose a
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9 tabular file) and takes parameters the way Galaxy supplies them (see example below), they:
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11 1. Install the tool factory on a personal private instance
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13 2. Upload a small test data set
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15 3. Paste the script into the 'script' text box and iteratively run the insecure tool on test data until it works right -
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16 there is absolutely no reason to do this anywhere other than on a personal private instance.
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18 4. Once it works right, set the 'Generate toolshed gzip' option and run it again.
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20 5. A toolshed style gzip appears ready to upload and install like any other Toolshed entry.
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22 6. Upload the new tool to the toolshed
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24 7. Ask the local admin to check the new tool to confirm it's not evil and install it in the local production galaxy
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26 New mantra: Galaxy can efficiently soak up all your lab's dark script matter and make it reproducible and shareable.
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28 == Proof of concept ==
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30 === Obligatory screenshot ===
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31 [[http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png|proof of concept screengrab]]
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33 === Sample Rscript ===
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34 As a working example, this trivial Rscript transposes a tabular file:
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36 {{{
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37 ourargs = commandArgs(TRUE)
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38 inf = ourargs[1]
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39 outf = ourargs[2]
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40 inp = read.table(inf,head=F,row.names=NULL,sep='\t')
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41 outp = t(inp)
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42 write.table(outp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
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43 }}}
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45 == Licensing ==
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46 All project artefacts are copyright Ross Lazarus (ross period lazarus at gmail period com) 2012
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47 All rights reserved.
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48 You may accept a license from me under the LGPL if you want to use this code for any reason.
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49 Please see http://www.gnu.org/licenses/lgpl.html for details
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