Good Afternoon Greg: I'll check this in my CygWin environment later today to see what the error is. A simple cast of some type should eliminate this particular error. It has been some time since I've tried the compile under CygWin, I don't know if there may be other errors lurking. They should be manageable.
--Hiram Gregory Dougherty wrote: > I love when my situation changes on the fly. > > I'm now getting a dedicated (virtual) server. Were hoping to run isPcr or > gfPcr AND Tomcat (serving up a Google Web Toolkit application) on a 2 CPU, 4 > GB RAM server. xxPcr will only be serving up the human genome. This is > expected to work, yes? > > I'm trying to build the isPcr source tree using Cygwin. aliType.c builds > correctly, but apacheLog.c fails. cc1 informs me that it is treating > warnings as errors, and that at lines 92 and 119 , in function > apacheAccessLogParse "error: array subscript as type 'char'". > > I have gcc 4.3.4. > > Should I be able to build this under Cygwin? Am I doing something stupid? I > believe I completely followed the instruction in the isPcrSrc README. > > TIA, > > Greg > > ----- Original Message ----- > From: "Jim Kent" <[email protected]> > To: "Gregory Dougherty" <[email protected]> > Cc: [email protected] > Sent: Thursday, July 22, 2010 8:25:11 AM GMT -06:00 US/Canada Central > Subject: Re: [Genome] Finding where Primers hit > > It sounds like in your usage case you'll want to go with gfPcr. > > On Jul 21, 2010, at 5:39 PM, Gregory Dougherty wrote: > >> Hi Jim, >> >> Unfortunately, the nodes in the cluster I'll probably be using only have 2GB >> per CPU, so I'll be better off if I can partition the task into two 2GB >> chunks. >> >> So, the situation is that I don't have a dedicated server. I have users who >> might have (at most) 20 pairs of primers that they will want to validate at >> once (i.e. "do these primers target my gene / region of interest?" "What's >> the size of the product they'll produce?" "Is there anything else they >> target?"). It's for a research lab at Mayo Clinic, and it MIGHT get used, >> at most, a couple of times a day. >> >> My reading is that while we could send our users to the UCSC In-Silico PCR >> Web page, we can NOT access it from our own program. Correct? >> >> Am I going to be spending minutes launching isPcr, and then seconds actually >> getting results? Is it possible to pre-compute the indexes, and then just >> load them in as necessary? >> >> Thank you, >> >> Greg >> >> ----- Original Message ----- >> From: "Jim Kent" <[email protected]> >> To: "Gregory Dougherty" <[email protected]> >> Cc: [email protected] >> Sent: Tuesday, July 20, 2010 7:45:52 PM GMT -06:00 US/Canada Central >> Subject: Re: [Genome] Finding where Primers hit >> >> Hi - if you are doing a lot of primers at once usually you want to use >> isPcr. If you want to have a server set up that will quickly align a few >> primers at a time use gfPcr. The memory these days is generally not a >> problem. I think 4 gig is enough for the whole genome for isPcr. >> >> >> On Jul 20, 2010, at 11:56 PM, Gregory Dougherty wrote: >> >>> Thank you Hiram and Jim for pointing me in the right direction. >>> >>> Looking at the code, for my situation I have two workable choices: gfPcr or >>> isPcr. >>> >>> Questions: >>> 1: Is gfPcr actually a workable choice? I.E. will it let me search for >>> hits from 18 base primers, and will it be as successful as isPcr at finding >>> hits? >>> >>> 2: The ReadMe says that isPcr "builds its own index". Is it creating it's >>> own index, or loaded an already calculated one from files? >>> >>> 3; For isPcr, roughly how much is "a lot of memory"? In particular, >>> roughly how much space does it take from Chr1, and roughly how much does it >>> take for the whole human genome? >>> >>> Thanks again, >>> >>> Greg >>> >>> ----- Original Message ----- >>> From: "Jim Kent" <[email protected]> >>> To: "Gregory Dougherty" <[email protected]> >>> Cc: [email protected] >>> Sent: Tuesday, July 20, 2010 1:52:22 PM GMT -06:00 US/Canada Central >>> Subject: Re: [Genome] Finding where Primers hit >>> >>> Please use In Silico PCR, which was designed just for this purpose. >>> >>> On Jul 20, 2010, at 4:51 PM, Gregory Dougherty wrote: >>> >>>> Hi all, >>>> >>>> I hope this isn't a FAQ, I couldn't find any way to search the archives. >>>> >>>> I am writing a program that takes pairs of PCR Primer sequences, and >>>> returns the products they will produce when used w/ human DNA. My first >>>> thought was to use BLAT to figure out where the primers match the genome. >>>> While this has worked well with test primers that are 20+ bases long, BLAT >>>> won't run on smaller Primers, and my users have Primers as small as 18 >>>> bases. >>>> >>>> Is BLAT a reasonable tool to use for solving this problem? If we download >>>> the source, change the 20 base limit to 18, and then run that BLAT, will >>>> that work? Work only if the sequence is a perfect match? Fail miserably? >>>> >>>> May be OT: Can I get Blast to tell me WHERE the primer hit in the item it >>>> hit in? "Homo sapiens chromosome 17 genomic contig, GRCh37 reference >>>> primary assembly, Length=21169982" really isn't a very useful hit report. >>>> >>>> Thanks in advance, >>>> >>>> Greg _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
