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. >> ********************************************************************* >> * >> ****** > ------------------------------------------------------------------------------ Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
