Dear biojava-l-request: Hi, Mark, We are the center of bioinformatics of Peking University (Beijing,P.R. China) which is national node of EMBnet. I would like to do the chinese version of biojava in Anger if you agree .
======= 2003-08-11 您在来信中写道：======= >Send Biojava-l mailing list submissions to > [EMAIL PROTECTED] > >To subscribe or unsubscribe via the World Wide Web, visit > http://biojava.org/mailman/listinfo/biojava-l >or, via email, send a message with subject or body 'help' to > [EMAIL PROTECTED] > >You can reach the person managing the list at > [EMAIL PROTECTED] > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Biojava-l digest..." > > >Today's Topics: > > 1. RE: problems installing biojava on Windows 2000 (Matthew Pocock) > 2. biojava-acedb (Suman Kanuganti) > 3. Re: biojava-acedb (Suman Kanuganti) > 4. Announcing: BJIA in Japanese (Schreiber, Mark) > 5. RE: Re: biojava-acedb (Francois Pepin) > 6. Running apps with Java (Schreiber, Mark) > 7. Re: Running apps with Java (Thomas Down) > 8. Re: Running apps with Java (Francois Pepin) > 9. Re: Running apps with Java (Patrick McConnell) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Sun, 10 Aug 2003 18:43:48 +0100 (BST) >From: Matthew Pocock <[EMAIL PROTECTED]> >Subject: RE: [Biojava-l] problems installing biojava on Windows 2000 >To: David Millis <[EMAIL PROTECTED]>, "'Schreiber, Mark'" > <[EMAIL PROTECTED]> >Cc: [EMAIL PROTECTED] >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset=iso-8859-1 > >Since 1.4 seems to come bundled with net-beans now, >should we update the docs to say how to get biojava >working in netbeans? Love it or hate it, everyone is >going to have it. > >Matthew > > --- David Millis <[EMAIL PROTECTED]> wrote: > >Mark - >> >> Thanks for your response to my message. >> >> I am using the netBeans 3.5 IDE for editing and >> compiling Java files. I >> have found that if I mount the >> biojava-1.30-jdk14.jar archive inside the >> IDE, the Java compiler is able to find all the files >> it needs, even if I >> don't edit the Windows PATH variable. I have finally >> been able to get >> one of the example from "BioJava In Anger" to >> compile without any >> errors. This is so much easier than trying to get >> the PATH variable set >> exactly right in Windows that I will just use this >> strategy. >> >> David Millis. >> >> -----Original Message----- >> From: Schreiber, Mark >> [mailto:[EMAIL PROTECTED] >> Sent: Thursday, August 07, 2003 5:44 PM >> To: David Millis; [EMAIL PROTECTED] >> Subject: RE: [Biojava-l] problems installing biojava >> on Windows 2000 >> >> Hi - >> >> Your class path looks OK but you can check that it >> has actually been set >> by running set command with no arguments from the >> command prompt. If the >> CLASSPATH variable is not displaying properly there >> then it is not >> properly set (possibly incorrect syntax). >> >> If you are running BioJava 1.3 or less you will also >> need the >> Jakarta-Regexp jar on your path. >> >> - Mark >> >> >> -----Original Message----- >> From: David Millis [mailto:[EMAIL PROTECTED] >> Sent: Friday, 8 August 2003 6:04 a.m. >> To: [EMAIL PROTECTED] >> Subject: [Biojava-l] problems installing biojava on >> Windows 2000 >> >> >> >> Hello, >> >> I am new to using biojava. I am trying to install >> biojava on a PC >> running Windows 2000 Professional. I am using Java 2 >> SDK version 1.4.2. >> I have downloaded the files in the "binaries" >> directory in the download >> area of the biojava server to the directory >> "C:\biojava" on my computer. >> I have added the >> string >> >> >> >"C:\biojava;C:\biojava\biojava.jar;C:\biojava\xerces.jar;C:\biojava\byte >> code.jar;" >> >> to my PATH variable. When I try to compile one of >> the simple demo files, >> like AlphabetExample.java, I get error messages >> saying that the packages >> "org.biojava.bio.symbol.*" and >> "org.biojava.bio.seq.*" can't be found. >> Is there something else I have to do to get the >> biojava files installed >> correctly? >> >> Thanks - >> David Millis. >> >> _______________________________________________ >> Biojava-l mailing list - [EMAIL PROTECTED] >> http://biojava.org/mailman/listinfo/biojava-l > >________________________________________________________________________ >Want to chat instantly with your online friends? Get the FREE Yahoo! >Messenger http://uk.messenger.yahoo.com/ > >------------------------------ > >Message: 2 >Date: Sun, 10 Aug 2003 15:13:19 -0700 (PDT) >From: Suman Kanuganti <[EMAIL PROTECTED]> >Subject: [Biojava-l] biojava-acedb >To: [EMAIL PROTECTED] >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset=us-ascii > >Is there any jar for acedb-biojava for running its >programs. I downloaded biojava-acedb.tar but couldnt >figure how to build corresponding .jar to add it in my >path. > >Could any one tell me about this? > >Suman K > >__________________________________ >Do you Yahoo!? >Yahoo! SiteBuilder - Free, easy-to-use web site design software >http://sitebuilder.yahoo.com > >------------------------------ > >Message: 3 >Date: Sun, 10 Aug 2003 15:40:06 -0700 (PDT) >From: Suman Kanuganti <[EMAIL PROTECTED]> >Subject: [Biojava-l] Re: biojava-acedb >To: [EMAIL PROTECTED] >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset=us-ascii > >I figured out something that I need to use ant to >build the acedb-biojava, with the build.xml provided >by the package. Now the problem: > >[EMAIL PROTECTED] bin]$ ant -buildfile >~/biojava-acedb/build.xml >Buildfile: /home/newton/biojava-acedb/build.xml > >init: > >prepare: > >BUILD FAILED >file:/home/newton/biojava-acedb/build.xml:61: >Directory /home/newton/biojava-acedb/ant-build >creation was not successful for an unknown reason > >Total time: 1 second > >Any suggestions, >Suman K > > >--- Suman Kanuganti <[EMAIL PROTECTED]> >wrote: >> Is there any jar for acedb-biojava for running its >> programs. I downloaded biojava-acedb.tar but couldnt >> figure how to build corresponding .jar to add it in >> my >> path. >> >> Could any one tell me about this? >> >> Suman K >> >> __________________________________ >> Do you Yahoo!? >> Yahoo! SiteBuilder - Free, easy-to-use web site >> design software >> http://sitebuilder.yahoo.com >> > > >===== >Suman K >BioInformatics Associate, >Genomics Research, >University of Missouri - Columbia. > >__________________________________ >Do you Yahoo!? >Yahoo! SiteBuilder - Free, easy-to-use web site design software >http://sitebuilder.yahoo.com > >------------------------------ > >Message: 4 >Date: Mon, 11 Aug 2003 11:30:34 +1200 >From: "Schreiber, Mark" <[EMAIL PROTECTED]> >Subject: [Biojava-l] Announcing: BJIA in Japanese >To: <[EMAIL PROTECTED]>, <[EMAIL PROTECTED]> >Message-ID: > <[EMAIL PROTECTED]> >Content-Type: text/plain; charset="us-ascii" > >Hello all, > >The unexpectidly popular biojava in anger site has now been translated >into Japanese. A big thanks to the Translators Takeshi Sasayama and >Kentaro Sugino and possibly others, let me know if I haven't credited >every one. > >Just follow the link off the main page: >http://www.biojava.org/docs/bj_in_anger/index.htm. This site requires >you to have the font MS Michu to display Kanji but you can easily get it >off the web. There is also a link to a French version (by Sylvain >Foisey) on the main page. Anyone want to do a Chinese or Spanish >version so we can cover 90 of the world? > >I have also recently added a tutorial on the use of Edit objects in the >Basic Sequence Manipulaton section >(http://www.biojava.org/docs/bj_in_anger/edit.htm) > >I'm always open to suggestions for or donations of new tutorials, >comments and bugfixes. > >Enjoy > >- Mark > >Mark Schreiber PhD >AgResearch Joint Bioinformatics Institute >School of Biological Sciences >Universtity of Auckland >3a Symonds St >Private Bag 92-019 Auckland New Zealand > >PH: +64 9 3737599 ext 84290 >FAX: +64 9 3737414 > > >======================================================================= >Attention: The information contained in this message and/or attachments >from AgResearch Limited is intended only for the persons or entities >to which it is addressed and may contain confidential and/or privileged >material. Any review, retransmission, dissemination or other use of, or >taking of any action in reliance upon, this information by persons or >entities other than the intended recipients is prohibited by AgResearch >Limited. If you have received this message in error, please notify the >sender immediately. >======================================================================= > > >------------------------------ > >Message: 5 >Date: Sun, 10 Aug 2003 19:53:43 -0400 >From: "Francois Pepin" <[EMAIL PROTECTED]> >Subject: RE: [Biojava-l] Re: biojava-acedb >To: "'Suman Kanuganti'" <[EMAIL PROTECTED]>, > <[EMAIL PROTECTED]> >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset="us-ascii" > >Hi Suman, > >My guess is that you have a permission problem somewhere, or that your >disk is full or something similar. > >Try to see if you can create that directory by yourself. > >The error seems to be about being able to create the directory itself. >It happened before any of the code was touched for compilation, so the >problem would not be with the code, but with the machine that you're >building on. > >Francois > >-----Original Message----- >From: [EMAIL PROTECTED] >[mailto:[EMAIL PROTECTED] On Behalf Of Suman Kanuganti >Sent: 10 aout, 2003 18:40 >To: [EMAIL PROTECTED] >Subject: [Biojava-l] Re: biojava-acedb > > >I figured out something that I need to use ant to >build the acedb-biojava, with the build.xml provided >by the package. Now the problem: > >[EMAIL PROTECTED] bin]$ ant -buildfile ~/biojava-acedb/build.xml >Buildfile: /home/newton/biojava-acedb/build.xml > >init: > >prepare: > >BUILD FAILED >file:/home/newton/biojava-acedb/build.xml:61: >Directory /home/newton/biojava-acedb/ant-build >creation was not successful for an unknown reason > >Total time: 1 second > >Any suggestions, >Suman K > > >--- Suman Kanuganti <[EMAIL PROTECTED]> >wrote: >> Is there any jar for acedb-biojava for running its >> programs. I downloaded biojava-acedb.tar but couldnt >> figure how to build corresponding .jar to add it in >> my >> path. >> >> Could any one tell me about this? >> >> Suman K >> >> __________________________________ >> Do you Yahoo!? >> Yahoo! SiteBuilder - Free, easy-to-use web site >> design software >> http://sitebuilder.yahoo.com >> > > >===== >Suman K >BioInformatics Associate, >Genomics Research, >University of Missouri - Columbia. > >__________________________________ >Do you Yahoo!? >Yahoo! SiteBuilder - Free, easy-to-use web site design software >http://sitebuilder.yahoo.com >_______________________________________________ >Biojava-l mailing list - [EMAIL PROTECTED] >http://biojava.org/mailman/listinfo/biojava-l > > >------------------------------ > >Message: 6 >Date: Mon, 11 Aug 2003 11:59:46 +1200 >From: "Schreiber, Mark" <[EMAIL PROTECTED]> >Subject: [Biojava-l] Running apps with Java >To: <[EMAIL PROTECTED]> >Message-ID: > <[EMAIL PROTECTED]> >Content-Type: text/plain; charset="us-ascii" > >Hi - > >I know this has come up a few times on the list but I'm not sure we have >ever come to any agreement on it so I'm going to raise it again as I >think it is important. > >What is the best way to invoke a native bioinformatics program in Java. >People have reported that controlling processes directly has been patchy >in Java, is this still the case or have JVMs evolved? If not then what >is the alternative? Wrapping the program in a perl or python webservice? >If this was the prefered method then we could borrow quite a bit from >the Bio::Pipeline::Runnable package. > >Ultimately the reason for asking is that J2EE (particularly the message >driven beans) would make for a pretty good pipelining system (drawing on >all its inherent transaction control, roll back etc). My expectation >would be that biojava could exist server side to provide parsing support >and possibly connection to BioSQL although J2EE could also do that >without biojava. It would also be useful in local EJBs (no serialization >slowdown) to do some manipulation of sequence data. The only missing >component is some kind of BioRunnable that could reliably kick off the >jobs and capture the output for parsing with the biojava parsers. > >Any thoughts? > >- Mark > > >Mark Schreiber PhD >AgResearch Joint Bioinformatics Institute >School of Biological Sciences >Universtity of Auckland >3a Symonds St >Private Bag 92-019 Auckland New Zealand > >PH: +64 9 3737599 ext 84290 >FAX: +64 9 3737414 > > >======================================================================= >Attention: The information contained in this message and/or attachments >from AgResearch Limited is intended only for the persons or entities >to which it is addressed and may contain confidential and/or privileged >material. Any review, retransmission, dissemination or other use of, or >taking of any action in reliance upon, this information by persons or >entities other than the intended recipients is prohibited by AgResearch >Limited. If you have received this message in error, please notify the >sender immediately. >======================================================================= > > >------------------------------ > >Message: 7 >Date: Mon, 11 Aug 2003 09:11:08 +0100 >From: Thomas Down <[EMAIL PROTECTED]> >Subject: Re: [Biojava-l] Running apps with Java >To: "Schreiber, Mark" <[EMAIL PROTECTED]> >Cc: [EMAIL PROTECTED] >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset=us-ascii > >On Mon, Aug 11, 2003 at 11:59:46AM +1200, Schreiber, Mark wrote: >> >> What is the best way to invoke a native bioinformatics program in Java. >> People have reported that controlling processes directly has been patchy >> in Java, is this still the case or have JVMs evolved? If not then what >> is the alternative? Wrapping the program in a perl or python webservice? >> If this was the prefered method then we could borrow quite a bit from >> the Bio::Pipeline::Runnable package. > >I think it *is* possible to write good-quality wrappers to >external tools in Java: it's just that the Runtime.exec >APIs are substantially more complicated than the equivalents >in $PREFERRED_SCRIPTING_LANGUAGE. If you're using stdin/stdout/stderr >on the external program, you need to make heavy use of Threads >in Java. I think that's the main barrier to entry. > >A lot of these issues could probably be addressed by something >like: > >public class ExecTools { > /** > * Execute an external program and wait for it to complete. > * > * @param args the command line to run. > * @param input some data to feed to the program's standard input, > * or null if no data. > * @param stdout a StringBuffer to receive the program's output, > * or null to ignore them. > * @param stderr a StringBuffer to receive the program's error > * stream, or null to ignore this. > * @returns the program's return code. > */ > > public static int exec( > String[] args, > String input, > StringBuffer stdout, > StringBuffer stderr > ); >} > >All the necessary thread code for most practical uses of exec could >be hidden in there. I might code this up this afternoon if nobody >objects -- it's code I write reasonably regularly, and the API above >would certainly save me time. Anyone else? > > >As for the web service approach, AppLap might be relevant: > > http://industry.ebi.ac.uk/applab/ > >Thomas. > >------------------------------ > >Message: 8 >Date: Mon, 11 Aug 2003 10:03:55 -0400 (EDT) >From: Francois Pepin <[EMAIL PROTECTED]> >Subject: Re: [Biojava-l] Running apps with Java >To: [EMAIL PROTECTED] >Message-ID: <[EMAIL PROTECTED]> >Content-Type: TEXT/PLAIN; charset=US-ASCII > >I have code that did that, but it wasn't reliable enough to use like >that. For unknown reasons, there are programs that I couldn't call at >all. > >The only reliable method that I found was to write a one-liner shell >script to be executed by sh, but this is an ugly, ugly hack. > >The grabbing of stdin and stdout wasn't working as advertised either. > >This is with Linux. I don't know about Windows, but I'm sure I'm not the >only one who needs to call Linux apps. > >Maybe like Mark said it got more reliable with 1.4. > >Personally I'd much rather use a system like that than to have to depend >on Perl or Python to do it. > >Francois > >On Mon, 2003-08-11 at 04:11, Thomas Down wrote: >> On Mon, Aug 11, 2003 at 11:59:46AM +1200, Schreiber, Mark wrote: >> > >> > What is the best way to invoke a native bioinformatics program in >Java. >> > People have reported that controlling processes directly has been >patchy >> > in Java, is this still the case or have JVMs evolved? If not then what >> > is the alternative? Wrapping the program in a perl or python >webservice? >> > If this was the prefered method then we could borrow quite a bit from >> > the Bio::Pipeline::Runnable package. >> >> I think it *is* possible to write good-quality wrappers to >> external tools in Java: it's just that the Runtime.exec >> APIs are substantially more complicated than the equivalents >> in $PREFERRED_SCRIPTING_LANGUAGE. If you're using stdin/stdout/stderr >> on the external program, you need to make heavy use of Threads >> in Java. I think that's the main barrier to entry. >> >> A lot of these issues could probably be addressed by something >> like: >> >> public class ExecTools { >> /** >> * Execute an external program and wait for it to complete. >> * >> * @param args the command line to run. >> * @param input some data to feed to the program's standard input, >> * or null if no data. >> * @param stdout a StringBuffer to receive the program's output, >> * or null to ignore them. >> * @param stderr a StringBuffer to receive the program's error >> * stream, or null to ignore this. >> * @returns the program's return code. >> */ >> >> public static int exec( >> String[] args, >> String input, >> StringBuffer stdout, >> StringBuffer stderr >> ); >> } >> >> All the necessary thread code for most practical uses of exec could >> be hidden in there. I might code this up this afternoon if nobody >> objects -- it's code I write reasonably regularly, and the API above >> would certainly save me time. Anyone else? >> >> >> As for the web service approach, AppLap might be relevant: >> >> http://industry.ebi.ac.uk/applab/ >> >> Thomas. >> _______________________________________________ >> Biojava-l mailing list - [EMAIL PROTECTED] >> http://biojava.org/mailman/listinfo/biojava-l > > >------------------------------ > >Message: 9 >Date: Mon, 11 Aug 2003 10:28:14 -0400 >From: "Patrick McConnell" <[EMAIL PROTECTED]> >Subject: Re: [Biojava-l] Running apps with Java >To: [EMAIL PROTECTED] >Message-ID: > <[EMAIL PROTECTED]> > >Content-Type: text/plain; charset=us-ascii > > > > > > >We do something similar, and I have not ran into any problems. The biggest >problem is when stdout and stderr are not handled in separate threads. > >Personally, I would like to see API's developed for specific applications. >Something ilke: > > public static int execNCBIBlast( > String executable, > String inputFile, > String outputFile > String program, > String database, > String input, > StringBuffer stdout, > StringBuffer stderr > ); > >Or, even better would be some sort of Parameters class to encapsulate all >those parameters, providing optional parameters. Then, you could do >something like this: > > NCBIBlastParameters params = new NCBIBlastParameters(); > params.addParameter("p", "blastn"); > params.addParameter("d", "nt"); > params.addParameter("m", "7"); > StringBuffer outputXML = new StringBuffer(); > int success = NCBIBlast.exec( > "c:\\blast\\blastall", > params, > inputFasta, > outputXML, > null > ); > System.out.println(outputXML); > >I think this would be more convenient to people for developing >applications. If you wanted to get fancy, you could have the exec method >throw an exception for missing or invalid parameters. Perhaps a method to >turn off this parameter checking would also be necessary. > >-Patrick > > > > > >Thomas Down <[EMAIL PROTECTED]>@biojava.org on 08/11/2003 04:11:08 AM > >Sent by: [EMAIL PROTECTED] > > >To: "Schreiber, Mark" <[EMAIL PROTECTED]> >cc: [EMAIL PROTECTED] > >Subject: Re: [Biojava-l] Running apps with Java > >On Mon, Aug 11, 2003 at 11:59:46AM +1200, Schreiber, Mark wrote: >> >> What is the best way to invoke a native bioinformatics program in Java. >> People have reported that controlling processes directly has been patchy >> in Java, is this still the case or have JVMs evolved? If not then what >> is the alternative? Wrapping the program in a perl or python webservice? >> If this was the prefered method then we could borrow quite a bit from >> the Bio::Pipeline::Runnable package. > >I think it *is* possible to write good-quality wrappers to >external tools in Java: it's just that the Runtime.exec >APIs are substantially more complicated than the equivalents >in $PREFERRED_SCRIPTING_LANGUAGE. If you're using stdin/stdout/stderr >on the external program, you need to make heavy use of Threads >in Java. I think that's the main barrier to entry. > >A lot of these issues could probably be addressed by something >like: > >public class ExecTools { > /** > * Execute an external program and wait for it to complete. > * > * @param args the command line to run. > * @param input some data to feed to the program's standard input, > * or null if no data. > * @param stdout a StringBuffer to receive the program's output, > * or null to ignore them. > * @param stderr a StringBuffer to receive the program's error > * stream, or null to ignore this. > * @returns the program's return code. > */ > > public static int exec( > String[] args, > String input, > StringBuffer stdout, > StringBuffer stderr > ); >} > >All the necessary thread code for most practical uses of exec could >be hidden in there. I might code this up this afternoon if nobody >objects -- it's code I write reasonably regularly, and the API above >would certainly save me time. Anyone else? > > >As for the web service approach, AppLap might be relevant: > > http://industry.ebi.ac.uk/applab/ > >Thomas. >_______________________________________________ >Biojava-l mailing list - [EMAIL PROTECTED] >http://biojava.org/mailman/listinfo/biojava-l > > > > > >------------------------------ > >_______________________________________________ >Biojava-l mailing list - [EMAIL PROTECTED] >http://biojava.org/mailman/listinfo/biojava-l > > >End of Biojava-l Digest, Vol 8, Issue 6 >*************************************** >. = = = = = = = = = = = = = = = = = = = = Best wishes for you! Yours faithfully, wux [EMAIL PROTECTED] 2003-08-12 ***************************************************** WuXin Ph.D student of CBI (Center of Bioinformatics) Peking University 100871 P.R.China Email: [EMAIL PROTECTED] Tel: 010-62762409 (dorm) 010-62755206 (office) Address: Building 47#2026 Peking University ***************************************************** _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
