Hi all, I was recently introduced to the ProjectTemplate <http://projecttemplate.net/> package in R by a colleague which also creates a nice project directory structure (and automates some of the repetitive tedious parts like library loading and reading in data).
Regards, On 4 February 2015 at 09:19, Loyall, David <[email protected]> wrote: > Aron, > > > > If you have an existing github account, you can just click “edit” on his > script and it will automatically fork the repo, let you make changes, and > then present you with the option of sending them back to Dan in the form of > a Pull Request. > > > > This has already happened once! The script now will refuse to operate if > no argument was provided. :) > > > > Cheers, > > > > Dave Loyall > > State of Nebraska > > Office of the CIO > > Web Development Team > > [email protected] > > (402) 471-0677 > > > > *From:* Discuss [mailto:[email protected]] *On > Behalf Of *Aron Ahmadia > *Sent:* Tuesday, February 03, 2015 4:03 PM > *To:* Daniel Chen > *Cc:* [email protected] > *Subject:* Re: [Discuss] Script to organize computational biology projects > > > > Very cool Dan! My only suggestion would be to create a top-level README > file describing the directory structure (and possibly referring back to > your script's URL), or print that out to the screen for the user to create > their own file or append to their own. > > The shell experts will probably want to add a little error-handling. At > minimum, the script should probably turn clobbering off before writing to > files. > > > > On Tue, Feb 3, 2015 at 4:59 PM, Daniel Chen <[email protected]> wrote: > > Ever since Ivan showed Noble's PlosONE article [1] at the Harvard > workshop, I began to follow the template and teach it in workshops. > > > > I created a quick bash script [2] since I just started another project, > and thought it'd share with everyone. The code isn't pretty, but it does > the job. Improvements welcome! > > > > And hopefully it'll be a less barrier to entry for people to setup project > folders after they attend a workshop. > > > > > > [1] > http://journals.plos.org/ploscollections/article?id=10.1371/journal.pcbi.1000424 > > [2] https://github.com/chendaniely/computational-project-cookie-cutter > > > > > > - Dan > > > _______________________________________________ > Discuss mailing list > [email protected] > > http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org > > > > _______________________________________________ > Discuss mailing list > [email protected] > > http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org > -- ---- Scott Ritchie, BCompSci, MSc, Ph.D. Student, Medical Systems Biology Group, Department of Pathology, Faculty of Medicine, Dentistry, and Health Sciences, The University of Melbourne Parkville, Victoria, Australia W: http://www.inouyelab.org P: +61 3 9035 8916 E: [email protected] Research Community Co-ordinator for the Life Sciences & Software Carpentry Instructor for R and Data Science. Department of Research Platforms, The University of Melbourne. W: http://resbaz.tumblr.com/ W: http://software-carpentry.org/ President, Bioinformatics Graduate Student Association (BGSA), The University of Melbourne. W: http://bioinformatics.asn.au/bgsa/ F: https://www.facebook.com/groups/BGSA.melbourne/ E: [email protected] General Committee, COMBINE: The Regional Student Group (RSG) Australia; for the International Society for Computational Biology (ISCB) W: http://combine.org.au/ http://www.iscb.org/ ----
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