From tolu at soccer-unltd.com Sun Mar 9 18:22:58 2008 From: tolu at soccer-unltd.com (=?windows-1251?B?0eXw4+XpIMji4O3u4uj3?=) Date: Sun, 09 Mar 2008 14:22:58 -0800 Subject: ***SPAM*** Акционеру - Оптимизация налогов Message-ID: <6299891302.20080309142258@soccer-unltd.com> ??? ??? ?????????? ????? ?? ??????????? ???????! ???? ???????? ??????? ?????????????? ??????!!! ?????????? ?????????????-????????????? ???????? ?? 480 ?????????. (????? + ?D) ???????????? ?????????? ???????? 40 ???? + 60 ???? = 100 % ?????????? ????????? ???????????? 40 ???? ??????????? ??????? ? ???????? ? ????????? ?????????? (?? CD ?????), ?????????????? ?????????? ????????? ????. ????? ? ?????????, ???????????? ????????? ??????? ?????????????? ?????????? ? ????? ?? ????? http://www.1069.su/ ??????? ?? ???????? /495/ 585-10-68 From paolo_siniselli at yahoo.it Tue Mar 25 21:49:12 2008 From: paolo_siniselli at yahoo.it (paolo siniselli) Date: Wed, 26 Mar 2008 01:49:12 +0000 (GMT) Subject: [Biococoa-dev] BioCocoa linux install Message-ID: <829663.37998.qm@web26713.mail.ukl.yahoo.com> Hi, I don't have a Mac. So I installed GNUstep (all the packages I needed) on my Linux distribution (Debian Etch). I also installed BioCocoa.app 1.6 using apt (it's the new one in debian stable rep.) The fact is that I tried to run "make" using GNUmake file of the Ultraconserved project downloaded from BioCocoa repos. The first message error says: BioCocoa/BCFoundation.h not found How is it possible, I installed BioCocoa.app and it works... Could you help me? Thanks Inviato da Yahoo! Mail. Tanti modi per restare in contatto con chi vuoi. http://it.docs.yahoo.com/mail/overview/index.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From schristley at mac.com Wed Mar 26 00:26:53 2008 From: schristley at mac.com (Scott Christley) Date: Wed, 26 Mar 2008 00:26:53 -0400 Subject: [Biococoa-dev] BioCocoa linux install In-Reply-To: <829663.37998.qm@web26713.mail.ukl.yahoo.com> References: <829663.37998.qm@web26713.mail.ukl.yahoo.com> Message-ID: <20E83570-38B3-4A5A-8E7C-54EA8CC5FB19@mac.com> Hello Paolo, I'm not sure what BioCocoa.app 1.6 is, I think that may be an old version of something. BioCocoa is a library, not an application. If you have the sources from the BioCocoa repository, go into the trunk/GNUstep directory and type "make install", that will compile and install the BioCocoa library. Then you should be able to "make" the Ultraconserved project. cheers Scott On Mar 25, 2008, at 9:49 PM, paolo siniselli wrote: > Hi, > I don't have a Mac. > So I installed GNUstep (all the packages I needed) on my Linux > distribution (Debian Etch). > I also installed BioCocoa.app 1.6 using apt (it's the new one in > debian stable rep.) > The fact is that I tried to run "make" using GNUmake file of the > Ultraconserved project downloaded from BioCocoa repos. > The first message error says: > BioCocoa/BCFoundation.h not found > > How is it possible, I installed BioCocoa.app and it works... > Could you help me? > Thanks > > > > Inviato da Yahoo! Mail. > Tanti modi per restare in contatto con chi vuoi. > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/biococoa-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From sweetcocoa at mac.com Wed Mar 26 04:44:12 2008 From: sweetcocoa at mac.com (Peter Schols) Date: Wed, 26 Mar 2008 09:44:12 +0100 Subject: [Biococoa-dev] BioCocoa linux install In-Reply-To: <20E83570-38B3-4A5A-8E7C-54EA8CC5FB19@mac.com> References: <829663.37998.qm@web26713.mail.ukl.yahoo.com> <20E83570-38B3-4A5A-8E7C-54EA8CC5FB19@mac.com> Message-ID: <9BC1F1FC-1436-42C6-A1CB-BE6E29AD790C@mac.com> Hi Paolo, BioCocoa 1.6 was an experiment to compile BioCocoa on GNUStep. It uses the BioCocoa 1.0 framework, while we are currently at version 2. Scott's advice should get you started with the latest version. best wishes, Peter On 26 Mar 2008, at 05:26, Scott Christley wrote: > Hello Paolo, > > I'm not sure what BioCocoa.app 1.6 is, I think that may be an old > version of something. BioCocoa is a library, not an application. > > If you have the sources from the BioCocoa repository, go into the > trunk/GNUstep directory and type "make install", that will compile > and install the BioCocoa library. Then you should be able to "make" > the Ultraconserved project. > > cheers > Scott > > On Mar 25, 2008, at 9:49 PM, paolo siniselli wrote: >> Hi, >> I don't have a Mac. >> So I installed GNUstep (all the packages I needed) on my Linux >> distribution (Debian Etch). >> I also installed BioCocoa.app 1.6 using apt (it's the new one in >> debian stable rep.) >> The fact is that I tried to run "make" using GNUmake file of the >> Ultraconserved project downloaded from BioCocoa repos. >> The first message error says: >> BioCocoa/BCFoundation.h not found >> >> How is it possible, I installed BioCocoa.app and it works... >> Could you help me? >> Thanks >> >> >> >> Inviato da Yahoo! Mail. >> Tanti modi per restare in contatto con chi vuoi. >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/biococoa-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From paolo_siniselli at yahoo.it Wed Mar 26 13:24:21 2008 From: paolo_siniselli at yahoo.it (paolo siniselli) Date: Wed, 26 Mar 2008 18:24:21 +0100 (CET) Subject: [Biococoa-dev] BioCocoa linux install Message-ID: <250162.37149.qm@web26709.mail.ukl.yahoo.com> Ok, I installed BioCocoa 2 and ultraconserved tools witho no errors But now, when I try to use construct_sarray I get this error: debian:/home/paolo/biococoa_ultraconserved/Ultraconserved.r132/trunk/shared_obj# ls construct_sarray intersect_mcp.d mcp_sarray.o print_sarray trim_mcp.d union_mcp.o construct_sarray.d intersect_mcp.o print_mcp print_sarray.d trim_mcp.o construct_sarray.o mcp_sarray print_mcp.d print_sarray.o union_mcp intersect_mcp mcp_sarray.d print_mcp.o trim_mcp union_mcp.d debian:/home/paolo/biococoa_ultraconserved/Ultraconserved.r132/trunk/shared_obj# ./construct_sarray /home/paolo/S_Cerevisae\ Genome/chr1.fa ./construct_sarray: error while loading shared libraries: libBioCocoa.so.0: cannot open shared object file: No such file or directory debian:/home/paolo/biococoa_ultraconserved/Ultraconserved.r132/trunk/shared_obj# locate libBioCocoa.so.0 /home/paolo/Biococoa2/GNUstep/BioCocoa.framework/Versions/A/libBioCocoa.so.0 /home/paolo/Biococoa2/GNUstep/BioCocoa.framework/Versions/A/libBioCocoa.so.0.0.1 /usr/local/lib/GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/A/libBioCocoa.so.0 /usr/local/lib/GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/A/libBioCocoa.so.0.0.1 /usr/local/lib/GNUstep/Local/Library/Libraries/libBioCocoa.so.0 /usr/local/lib/GNUstep/Local/Library/Libraries/libBioCocoa.so.0.0.1 Any suggestions? Thank for your help Paolo --- Scott Christley wrote: > ... "make install", > that will compile > and install the BioCocoa library. Then you should > be able to "make" > the Ultraconserved project. > > cheers > Scott R ___________________________________ Scopri il Blog di Yahoo! Mail: trucchi, novit?, consigli... e la tua opinione! http://www.ymailblogit.com/blog/ From schristley at mac.com Wed Mar 26 14:40:07 2008 From: schristley at mac.com (Scott Christley) Date: Wed, 26 Mar 2008 14:40:07 -0400 Subject: [Biococoa-dev] BioCocoa linux install In-Reply-To: <250162.37149.qm@web26709.mail.ukl.yahoo.com> References: <250162.37149.qm@web26709.mail.ukl.yahoo.com> Message-ID: <1124985A-4652-4C8E-BA9E-8860F81552C9@mac.com> Your GNUstep environment is likely not setup properly in that terminal window. It should have added the appropriate paths to the LD_LIBRARY_PATH environment variable so that it finds the shared libraries. Alternatively you can manually add /usr/local/GNUstep/ Local/Library/Libraries to your LD_LIBRARY_PATH environment variable, but I don't recommend do it manually because there are other settings required which may cause things to fail unexpectedly. cheers Scott On Mar 26, 2008, at 1:24 PM, paolo siniselli wrote: > Ok, I installed BioCocoa 2 and ultraconserved tools > witho no errors > But now, when I try to use construct_sarray I get this > error: > > debian:/home/paolo/biococoa_ultraconserved/Ultraconserved.r132/ > trunk/shared_obj# > ls > construct_sarray intersect_mcp.d mcp_sarray.o > print_sarray trim_mcp.d union_mcp.o > construct_sarray.d intersect_mcp.o print_mcp > print_sarray.d trim_mcp.o > construct_sarray.o mcp_sarray print_mcp.d > print_sarray.o union_mcp > intersect_mcp mcp_sarray.d print_mcp.o > trim_mcp union_mcp.d > > debian:/home/paolo/biococoa_ultraconserved/Ultraconserved.r132/ > trunk/shared_obj# > ./construct_sarray /home/paolo/S_Cerevisae\ > Genome/chr1.fa > ./construct_sarray: error while loading shared > libraries: libBioCocoa.so.0: cannot open shared object > file: No such file or directory > > debian:/home/paolo/biococoa_ultraconserved/Ultraconserved.r132/ > trunk/shared_obj# > locate libBioCocoa.so.0 > /home/paolo/Biococoa2/GNUstep/BioCocoa.framework/Versions/A/ > libBioCocoa.so.0 > /home/paolo/Biococoa2/GNUstep/BioCocoa.framework/Versions/A/ > libBioCocoa.so.0.0.1 > /usr/local/lib/GNUstep/Local/Library/Frameworks/BioCocoa.framework/ > Versions/A/libBioCocoa.so.0 > /usr/local/lib/GNUstep/Local/Library/Frameworks/BioCocoa.framework/ > Versions/A/libBioCocoa.so.0.0.1 > /usr/local/lib/GNUstep/Local/Library/Libraries/libBioCocoa.so.0 > /usr/local/lib/GNUstep/Local/Library/Libraries/libBioCocoa.so.0.0.1 > > Any suggestions? > Thank for your help > Paolo > > > > --- Scott Christley wrote: > > >> ... "make install", >> that will compile >> and install the BioCocoa library. Then you should >> be able to "make" >> the Ultraconserved project. >> >> cheers >> Scott > R > > > ___________________________________ > Scopri il Blog di Yahoo! Mail: trucchi, novit?, consigli... e la > tua opinione! > http://www.ymailblogit.com/blog/ > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/biococoa-dev From paolo_siniselli at yahoo.it Thu Mar 27 13:08:02 2008 From: paolo_siniselli at yahoo.it (paolo siniselli) Date: Thu, 27 Mar 2008 18:08:02 +0100 (CET) Subject: [Biococoa-dev] BioCocoa linux install Message-ID: <140121.35391.qm@web26709.mail.ukl.yahoo.com> Ok, I did this, to solve it: debian:/home/kei/biococoa_ultraconserved/Ultraconserved.r132/trunk/obj# . /usr/share/GNUstep/Makefiles/GNUstep.sh debian:/home/kei/biococoa_ultraconserved/Ultraconserved.r132/trunk/obj# ./construct_sarray /home/kei/S_Cerevisae\ Genome/chr1.fa outputchr1 f Constructing suffix array. .:3: validity error : Validation failed: no DTD found ! ^ .:3: validity error : Validation failed: no DTD found ! ^ .:3: validity error : Validation failed: no DTD found ! ^ totSize: 1841672 maxMem: 1327878144 Sufficient memory for all sequences. 230209 bytes Allocating 230211 bytes. total size 230209 (bp) Saving suffix array. I don't know what those errors mean, and I don't know know about the parameter f and r which ared used in construct_sarray. Anyway, is the output file correct? Thanks Paolo --- Scott Christley wrote: > Your GNUstep environment is likely not setup > properly in that > terminal window. It should have added the > appropriate paths to the > LD_LIBRARY_PATH environment variable so that it > finds the shared > libraries ___________________________________ Scopri il Blog di Yahoo! Mail: trucchi, novit?, consigli... e la tua opinione! http://www.ymailblogit.com/blog/ From schristley at mac.com Thu Mar 27 15:29:40 2008 From: schristley at mac.com (Scott Christley) Date: Thu, 27 Mar 2008 15:29:40 -0400 Subject: [Biococoa-dev] BioCocoa linux install In-Reply-To: <140121.35391.qm@web26709.mail.ukl.yahoo.com> References: <140121.35391.qm@web26709.mail.ukl.yahoo.com> Message-ID: <20419F84-7F53-4CEA-A2D0-D8AC44D1A029@mac.com> Hello Paolo, On Mar 27, 2008, at 1:08 PM, paolo siniselli wrote: > debian:/home/kei/biococoa_ultraconserved/Ultraconserved.r132/trunk/ > obj# > . /usr/share/GNUstep/Makefiles/GNUstep.sh Correct, sourcing that script sets up the GNUstep environment. If you do not want to type it each time you open a terminal window, you can add it to your .bashrc or .bash_profile script in your home directory. > > .:3: validity error : Validation failed: no DTD found > ! > > ^ > .:3: validity error : Validation failed: no DTD found > ! > > ^ > .:3: validity error : Validation failed: no DTD found > ! > > ^ These messages do not look good. Seems to indicate that something is wrong with the XML parsing in GNUstep. It is necessary for the XML parsing to be enabled and functional with GNUstep in order for BioCocoa to work. > > I don't know what those errors mean, and I don't know > know about the parameter f and r which ared used in > construct_sarray. The f/r parameter is to specify just the forward or reverse strand to be used. It is an optional parameter and normally do not specify so that both strands are used. cheers Scott From paolo_siniselli at yahoo.it Thu Mar 27 17:08:03 2008 From: paolo_siniselli at yahoo.it (paolo siniselli) Date: Thu, 27 Mar 2008 22:08:03 +0100 (CET) Subject: [Biococoa-dev] BioCocoa linux install In-Reply-To: <20419F84-7F53-4CEA-A2D0-D8AC44D1A029@mac.com> Message-ID: <766970.74592.qm@web26701.mail.ukl.yahoo.com> I installed all the XMl library I could but I've got the same errors. I found this googling around: NB. MacOS-X generates illegal XML for some strings - those which contain characters not legal in XML. GNUstep always generates legal XML, at the cost of a certain degree of compatibility. GNUstep XML property lists use a backslash to escape illegal chatracters, and consequently any string containing either a backslash or an illegal character will be written differently to the same string on MacOS-X. http://www.gnustep.org/resources/documentation/Developer/Base/ProgrammingManual/manual_13.html Do you think this is the problem? Thank you very much Paolo --- Scott Christley wrote: > These messages do not look good. Seems to indicate > that something is > wrong with the XML parsing in GNUstep. It is > necessary for the XML > parsing to be enabled and functional with GNUstep in > order for > BioCocoa to work. > ___________________________________ Scopri il Blog di Yahoo! Mail: trucchi, novit?, consigli... e la tua opinione! http://www.ymailblogit.com/blog/ From schristley at mac.com Fri Mar 28 10:45:12 2008 From: schristley at mac.com (Scott Christley) Date: Fri, 28 Mar 2008 10:45:12 -0400 Subject: [Biococoa-dev] BioCocoa linux install In-Reply-To: <766970.74592.qm@web26701.mail.ukl.yahoo.com> References: <766970.74592.qm@web26701.mail.ukl.yahoo.com> Message-ID: <9FCB62DB-78E5-4E35-BA89-554BAA11823D@mac.com> Hello Paolo, Yeah there are issues with Apple XML being read by GNUstep, so I created GNUstep compatible XML in BioCocoa. Anyways, you created a suffix array file with your chromosome, try using the "print_sarray" command to output the contents of that suffix array. That command needs to read an XML file (hold the suffix array meta data), so if it displays the suffix array data correctly then it should have read the XML fine. cheers Scott On Mar 27, 2008, at 5:08 PM, paolo siniselli wrote: > I installed all the XMl library I could but I've got > the same errors. I found this googling around: > > NB. MacOS-X generates illegal XML for some strings - > those which contain characters not legal in XML. > GNUstep always generates legal XML, at the cost of a > certain degree of compatibility. GNUstep XML property > lists use a backslash to escape illegal chatracters, > and consequently any string containing either a > backslash or an illegal character will be written > differently to the same string on MacOS-X. > http://www.gnustep.org/resources/documentation/Developer/Base/ > ProgrammingManual/manual_13.html > > Do you think this is the problem? > Thank you very much > Paolo > > --- Scott Christley wrote: > > >> These messages do not look good. Seems to indicate >> that something is >> wrong with the XML parsing in GNUstep. It is >> necessary for the XML >> parsing to be enabled and functional with GNUstep in >> order for >> BioCocoa to work. >> > > > ___________________________________ > Scopri il Blog di Yahoo! Mail: trucchi, novit?, consigli... e la > tua opinione! > http://www.ymailblogit.com/blog/ From paolo_siniselli at yahoo.it Fri Mar 28 11:23:10 2008 From: paolo_siniselli at yahoo.it (paolo siniselli) Date: Fri, 28 Mar 2008 16:23:10 +0100 (CET) Subject: [Biococoa-dev] BioCocoa linux install In-Reply-To: <9FCB62DB-78E5-4E35-BA89-554BAA11823D@mac.com> Message-ID: <295624.68251.qm@web26713.mail.ukl.yahoo.com> Hi Scott, I gave the command below. I don't if it is look good or not. Should I change something or just keep going? Anyway I appreciated your time. Thanks Paolo debian:/home/kei/biococoa_ultraconserved/Ultraconserved.r132/trunk/obj# ./print_sarray outputchr1 | more .:3: validity error : Validation failed: no DTD found ! ^ .:3: validity error : Validation failed: no DTD found ! ^ .:3: validity error : Validation failed: no DTD found ! ^ offset: 237262 strand: R id: chr1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAATGTGTCTAT ... offset: 237263 strand: R id: chr1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAATGTGTCTATC ... offset: 237264 strand: R id: chr1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAATGTGTCTATCT ... offset: 237265 strand: R id: chr1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAATGTGTCTATCTT ... offset: 237266 strand: R id: chr1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAATGTGTCTATCTTC ... offset: 237267 strand: R id: chr1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAATGTGTCTATCTTCA ... offset: 237268 strand: R id: chr1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAATGTGTCTATCTTCAT ... offset: 237269 strand: R id: chr1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAATGTGTCTATCTTCATA ... offset: 237270 strand: R id: chr1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAATGTGTCTATCTTCATAA ... offset: 237271 strand: R id: chr1 --- Scott Christley wrote: > Anyways, you created a suffix array file with your > chromosome, try > using the "print_sarray" command to output the > contents of that > suffix array. ___________________________________ Scopri il Blog di Yahoo! Mail: trucchi, novit?, consigli... e la tua opinione! http://www.ymailblogit.com/blog/