I have built a 64-bit version for AMD's 64-bit and Intel's Core 2 machines. It's available here: http://gel.ahabs.wisc.edu/mauve/downloads/mauve_linux_x64_2.0.0.tar.gz
I am working on 64-bit Mac builds, but there are some issues with apple's compiler that need to be sorted out. It worries me when my code crashes the compiler. For those who have other types of 64-bit computers, there are build instructions here: http://asap.ahabs.wisc.edu/mauve-aligner/mauve-developer-guide/compiling-mauvealigner-from-source.html When aligning large plant and animal genomes, one of the undocumented features of the command-line mauveAligner may come in handy. mauveAligner can use two hard drives to do creation of the .sml files "outside-of-core-memory", which basically amounts to an out-of-core sort. We used that feature to generate the synteny maps for mammalian genomes published in the 2004 Genome Research paper, and later for a full alignment of the mammalian genomes. To trigger the feature, simply add the command-line parameters: --scratch-path=/path/to/disk1 --scratch-path=/path/to/disk2 More than two scratch disks can be used, just add another --scratch-path= to the command-line. The important thing is that each path should really be on a separate hard drive, otherwise lots and lots of drive head seeking will result and the SML construction will probably take days instead of an hour or two. It should be possible to use network drives or file servers, but that may be slow as well. Beware that there's a bug which causes mauveAligner to crash immediately after finishing the SML construction, at least on linux. The SML still gets created and executing the exact same mauveAligner command a second time will read the SML that the previous run had created. So it's necessary to run mauveAligner once per SML and once to actually perform the alignment. -Aaron Stephan Ossowski wrote: > Hi, > We would also be interested in a 64 bit version of Mauve 2 > for Linux OS. All our servers use AMD Opterons (64 bit). > > Currently we try to run whole genome alignments for plant > genomes. This takes too much memory for our Intel desktop > computers to run properly. > > Thanks for your help. > Stephan Ossowski > > On Tue, 30 Jan 2007 20:45:18 -0500 > "David J. Schneider" <[EMAIL PROTECTED]> wrote: > >> Aaron, >> >> I am interested in being able to perform a simultaneous >> alignment of all of >> the fully sequenced Pseudomonas spp. Attempts with >> previous versions of >> Mauve have been unsuccessful, apparently due to the 32 >> bit addressing limit. >> However, I have access to a Mac G5-based cluster with 8 >> Gbytes/node. How >> difficult would it be to produce a 64 bit version of >> Mauve for the G5? >> >> By the way, the recently released progressive version >> works great and >> appears to be significantly faster when aligning the >> three fully sequenced >> pathovars of P. syringae. The new search features are >> extremely helpful. >> >> Dave Schneider >> >> Computational biologist >> Pseudomonas syringae systems biology group >> USDA Agricultural Research Service >> >> >> >> >> > ------------------------------------------------------------------------- > >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the >> chance to share your >> opinions on IT & business topics through brief surveys - >> and earn cash >> >> > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > >> _______________________________________________ >> Mauve-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/mauve-users >> >> >> > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier. > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Mauve-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/mauve-users > ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier. Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
