What GNU/Linux distribution are you using ? On 02/12/2013 11:21 AM, frederic texier wrote: > Hi, > > I don't unerstand because I have zlib and I have always the samer errors. > > mpicxx -lz -lbz2 code/TheRayGenomeAssembler.a RayPlatform/libRayPlatform.a > -o Ray > code/TheRayGenomeAssembler.a(FastqGzLoader.o): In function > `FastqGzLoader::open(std::basic_string<char, std::char_traits<char>, > std::allocator<char> >, int)': > FastqGzLoader.cpp:(.text+0x39): undefined reference to `gzopen' > FastqGzLoader.cpp:(.text+0x6f): undefined reference to `gzgets' > FastqGzLoader.cpp:(.text+0x8d): undefined reference to `gzclose' > FastqGzLoader.cpp:(.text+0x9a): undefined reference to `gzopen' > code/TheRayGenomeAssembler.a(FastqGzLoader.o): In function > `FastqGzLoader::load(int, ArrayOfReads*, MyAllocator*, int)': > FastqGzLoader.cpp:(.text+0x15e): undefined reference to `gzgets' > FastqGzLoader.cpp:(.text+0x1b4): undefined reference to `gzclose' > code/TheRayGenomeAssembler.a(BzReader.o): In function > `BzReader::readLine(char*, int)': > BzReader.cpp:(.text+0x82a): undefined reference to `BZ2_bzRead' > BzReader.cpp:(.text+0x8f5): undefined reference to `BZ2_bzReadOpen' > BzReader.cpp:(.text+0x9fa): undefined reference to `BZ2_bzReadGetUnused' > BzReader.cpp:(.text+0xa27): undefined reference to `BZ2_bzReadClose' > collect2: ld a retourné 1 code d'état d'exécution > make: *** [Ray] Erreur 1 > > Could you help me please? > Thank you. > > Best regards > Frederic Texier. > > -----Message d'origine----- > De : Sébastien Boisvert [mailto:[email protected]] > Envoyé : mardi 12 février 2013 14:55 > À : frederic texier > Cc : [email protected] > Objet : Re: Ray output > > > > On 02/12/2013 05:15 AM, frederic texier wrote: >> Bonjour de nouveau, >> >> J'ai un problème quand je veux installer avec l'otpion HAVE_LIBZ=y. >> Faut-il un module supplémentaire à installer avant? >> > > Yes, you need zlib headers. > > On Debian or Ubuntu or other Debian-derived distributions: > > sudo apt-get install -y zlib1g-dev > > > On Fedora or CentOS or other similar distribution: > > sudo yum install -y zlib-devel > > > There is also the option HAVE_LIBBZ2=y that provides native support for > fastq.bz2 files. > >> Je vous remercie. >> Cordialement >> Frédéric Texier. >> >> -----Message d'origine----- >> De : Sébastien Boisvert [mailto:[email protected]] >> Envoyé : vendredi 8 février 2013 18:05 À : frederic texier Cc : >> [email protected] >> Objet : Re: Ray output >> >> Bonjour Frédéric, >> >> There is a work-in-progress to add this feature [1], although it's not >> in the current backlog [2]. >> >> Current available courses of action are: >> >> 1. use -amos option to generate a AMOS file with Ray and then parse >> this to obtain the information you want (used reads, and so on). >> >> 2. Map your reads on contigs (or on scaffolds) with a aligner and then >> pipe this in a existing tool (I am sure there exists tools for that >> that take a SAM file as input). >> >> >> Also, if you want to visualize your assemblies to do some quality >> controls (usually production departments like to do quality controls), >> you can use Ray Cloud Browser. >> >> >> Demo: http://genome.ulaval.ca/corbeillab/Ray-Cloud-Browser/ >> Source code: https://github.com/sebhtml/Ray-Cloud-Browser >> Deployment instructions: >> https://raw.github.com/sebhtml/Ray-Cloud-Browser/master/Documentation/ >> Deploy >> ment.txt >> >> >> --- >> [1] https://github.com/sebhtml/ray/issues/65 >> [2] https://github.com/sebhtml/ray/issues?milestone=5&state=open >> >> >> >> >> Sébastien Boisvert >> Community Manager, Ray Genomics Software Suite PhD student, Université >> Laval >> >> On 02/08/2013 09:05 AM, frederic texier wrote: >>> Hello, >>> >>> I have used Ray to assemble bacterial genome but I don't know where >>> find >> the number of reads really used and the numer of reads not used in the >> output. >>> >>> could you help me to find this, please? >>> >>> Thank you. >>> -- >>> >>> Frédéric Texier >>> >>> Téléphone: +33(0)359317403 >>> E-mail: [email protected] >>> >>> Genoscreen >>> Campus Pasteur - 1 rue du Pr Calmette >>> 59000 Lille >>> Téléphone: +33(0)320877153 >>> >>> ********************************************************************* >>> * >>> ****** Ce message et toutes les pièces jointes sont confidentiels et >>> établis à l'intention exclusive de son ou ses destinataires. Si vous >>> avez reçu ce message par erreur, merci d'en avertir immédiatement >>> l'émetteur et de détruire le message ainsi que les pièces jointes. >>> Toute modification, édition, utilisation ou diffusion non autorisée >>> est interdite. L'émetteur décline toute responsabilité au titre de ce >>> message s'il a été modifié, déformé, falsifié, infecté par un virus >>> ou encore édité ou diffusé sans autorisation. >>> >>> This message and any attachments are confidential and intended for >>> the named >>> addressee(s) only. >>> If you have received this message in error, please notify immediately >>> the sender, then delete the message and the attachments. Any >>> unauthorized modification, edition, use or dissemination is >>> prohibited. The sender does not be liable for this message if it has >>> been modified, altered, falsified, infected by a virus or even edited >>> or >> disseminated without authorization. >>> ********************************************************************* >>> * >>> ****** >> >
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