Hi Ilenia, I am sorry for the delay in my reply. I have been very busy lately and haven't had the time to complete all documentation etc.
The source code may be downloaded from http://madr.lcb.uu.se/browser/plugins/se/lu/thep/affymetrix/branches/APT . I have not yet decided if this should be a separate package or an extension to the affymetrix package (I posted a question regarding this some time ago on the mailing list but have not received any response yet). It is currently a separate package called se.uu.lcb.APT that includes AbstractExternalBinaryPlugin.java from the se.lu.thep.affymetrix package. Some additional documentation is needed and I will add this as soon as possible. The README file has not yet been completed and the INSTALL file is a modification of the one from the affymetrix package. I have also modified the Makefile from the affymetrix package. Some tweaks/ changes could be made here. A simple make works though. Cheers, Robin On Jan 15, 2008, at 10:04 AM, Ilenia Zara wrote: >> >> Jim, >> >> I have been working a while building plugins for the apt-probeset- >> summarize and apt-probeset-genotype command line tools. These two >> plugins implement the AbstractExternalBinaryPlugin in affymetrix.jar. >> >> Some additional testing is needed before I release the package for >> the BASE community. I haven't tried the apt-cel-extract tool yet but >> understand the usefulness of such a plugin if raw data need to be >> deposited in the database prior to further analyses. >> >> In contrast to the Plier plugin that just do the plier-mm analysis >> (using apt-probeset-summarize), I have made all possible analysis >> parameters to these tools available in the plugins. >> >> Perhaps you can reuse some of the code in these plugins. I will let >> you know when the code is ready for release. >> >> /Robin >> >> >> > > [...] > > Hi Robin, hi All, > > we are very interested in the BASE plugin for the apt-probeset- > genotype > command line tools for SNPs. > We would like to use it as soon as possible. > When will the compiled and source code versions be available? > Let me know if we can help by running some tests ... hope this is > helpful! > Thank you! > > Ilenia > > > -- > Ilenia Zara > CRS4 - Bioinformatics > Phone +39 070 9250 437 > Loc. Pixina Manna Edificio 1 Pula 09010 (CA), Italy > http://www.bioinformatica.crs4.org > > > ------------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > _______________________________________________ > basedb-devel mailing list > basedb-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/basedb-devel --- Robin Andersson, PhD student Linnaeus Centre for Bioinformatics Uppsala University BMC, Box 598, SE-751 24 Uppsala, Sweden phone: +46 18 471 66 86 (admin: 66 90) fax: +46 18 471 66 98 office: BMC, C6:315a email: [EMAIL PROTECTED] http://www.lcb.uu.se/~robina/ ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
