fubar/brokenandnotdeletablebyowneroradmin: README.txt annotate

annotate README.txt @ 6:78044a3d4a21

Readme = wiki more or less now

author	Ross Lazarus <ross.lazarus@gmail.com>
date	Thu, 31 May 2012 10:49:22 +1000
parents	9c1a1e0e664a
children	7221619caefa

rev	line source
6 78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	1 = WARNING before you start =
78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	2 This tool should only ever be installed on a private instance - NEVER use it on a public Galaxy because the risks are too awful to contemplate let alone manage. You have been warned.
2 d95513e50c92 Add README.txt for bitbucket ross lazarus ross.lazarus@gmail.com parents: diff changeset	3
6 78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	4 == Motivation ==
78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	5 Simple transformation, filtering or reporting scripts get written, run and lost every day in most busy labs - even ours where Galaxy is in use. This 'dark script matter' is pervasive and generally not reproducible.
78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	6
78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	7 After considerable nagging, I wrote and installed a new tool locked down to allow only two other trusted bioinformatician users to paste and run (NO sandbox!) arbitrary scripts - see screenshot attached.
78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	8
78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	9 == Benefits ==
78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	10 For our group, this allows Galaxy to fill that important dark script gap - all those "small" bioinformatics tasks - because once a trusted user has a working R (or python or perl) script that takes parameters the way Galaxy supplies them (see example below), they:
2 d95513e50c92 Add README.txt for bitbucket ross lazarus ross.lazarus@gmail.com parents: diff changeset	11
d95513e50c92 Add README.txt for bitbucket ross lazarus ross.lazarus@gmail.com parents: diff changeset	12 1) run the new tool
d95513e50c92 Add README.txt for bitbucket ross lazarus ross.lazarus@gmail.com parents: diff changeset	13
d95513e50c92 Add README.txt for bitbucket ross lazarus ross.lazarus@gmail.com parents: diff changeset	14 2) paste their code into the tool 'script' text box
d95513e50c92 Add README.txt for bitbucket ross lazarus ross.lazarus@gmail.com parents: diff changeset	15
d95513e50c92 Add README.txt for bitbucket ross lazarus ross.lazarus@gmail.com parents: diff changeset	16 3) select the optional history input (and some other odds and ends - see screen shot) and
d95513e50c92 Add README.txt for bitbucket ross lazarus ross.lazarus@gmail.com parents: diff changeset	17
d95513e50c92 Add README.txt for bitbucket ross lazarus ross.lazarus@gmail.com parents: diff changeset	18 4) run the tool and thus the script.
d95513e50c92 Add README.txt for bitbucket ross lazarus ross.lazarus@gmail.com parents: diff changeset	19
6 78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	20 == Proposal - a Galaxy toolshed interface ==
78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	21 Rerunning the output of the existing script reruns the same script of course, so we're now better off than we were before. But what about adding some code to this script runner tool to generate a new Galaxy tool as a ready to install toolshed entry?
78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	22
78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	23 This (imho) will be a very low impedence way to generate new simple Galaxy tools - run them until they work then package them up and deploy/distribute for any user to use - no new security risks.
2 d95513e50c92 Add README.txt for bitbucket ross lazarus ross.lazarus@gmail.com parents: diff changeset	24
6 78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	25 Does this seem like a good idea to anyone else?
4 3755b2365fb0 More edits to readme ross lazarus ross.lazarus@gmail.com parents: 3 diff changeset	26
6 78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	27 == Proof of concept ==
2 d95513e50c92 Add README.txt for bitbucket ross lazarus ross.lazarus@gmail.com parents: diff changeset	28
6 78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	29 === Obligatory screenshot ===
78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	30 [[http://bitbucket.org/fubar/galaxytoolmaker/src/fda8032fe989/images/dynamicScriptTool.png\|proof of concept screengrab]]
4 3755b2365fb0 More edits to readme ross lazarus ross.lazarus@gmail.com parents: 3 diff changeset	31
6 78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	32 === Sample Rscript ===
78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	33 As a working example, this trivial Rscript replaces the score column in a bed file with a random number:
78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	34 {{{
4 3755b2365fb0 More edits to readme ross lazarus ross.lazarus@gmail.com parents: 3 diff changeset	35 ourargs = commandArgs(TRUE)
3755b2365fb0 More edits to readme ross lazarus ross.lazarus@gmail.com parents: 3 diff changeset	36 inf = ourargs[1]
3755b2365fb0 More edits to readme ross lazarus ross.lazarus@gmail.com parents: 3 diff changeset	37 outf = ourargs[2]
3755b2365fb0 More edits to readme ross lazarus ross.lazarus@gmail.com parents: 3 diff changeset	38 inp = read.table(inf,head=F,row.names=NULL,sep='\t')
3755b2365fb0 More edits to readme ross lazarus ross.lazarus@gmail.com parents: 3 diff changeset	39 inp[,5] = runif ( nrow(inp) )
6 78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	40 write.table(inp,outf, quote=FALSE, sep="\t",row.names=F,col.names=F)
78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	41 }}}
5 9c1a1e0e664a and again ross lazarus ross.lazarus@gmail.com parents: 4 diff changeset	42
6 78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	43 == Licensing ==
78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	44 All project artefacts are copyright Ross Lazarus (ross period lazarus at gmail period com) 2012
78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	45 All rights reserved.
78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	46 You may accept a license from me under the LGPL if you want to use this code for any reason.
78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	47 Please see http://www.gnu.org/licenses/lgpl.html for details
4 3755b2365fb0 More edits to readme ross lazarus ross.lazarus@gmail.com parents: 3 diff changeset	48
6 78044a3d4a21 Readme = wiki more or less now Ross Lazarus <ross.lazarus@gmail.com> parents: 5 diff changeset	49

Mercurial > repos > fubar > brokenandnotdeletablebyowneroradmin

annotate README.txt @ 6:78044a3d4a21