I had the same problem with ubuntu 12.04 and 12.10 and the stable Ray release. I was able to successfully compile the program and be able to use .gz files after following the instructions in this mailing list entry
http://lists.debian.org/debian-med/2012/11/msg00015.html But this version works - ie. simply putting the $LD_FLAGS after the input files on line 189 of the Makefile: tbooth@balisaur[ray_2.1.0]mpicxx -Wl,-Bsymbolic-functions -Wl,-z,relro code/TheRayGenomeAssembler.a RayPlatform/libRayPlatform.a -lz -lbz2 -o Ray Anthony On 13/02/2013, at 5:14 AM, Sébastien Boisvert wrote: 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. [cid:[email protected]] Anthony Borneman Principal Research Scientist - Molecular Biology | The Australian Wine Research Institute Waite Precinct, Hartley Grove cnr Paratoo Road, Urrbrae (Adelaide) SA 5064 | <http://www.awri.com.au/contact/map.asp> Map<http://www.awri.com.au/contact/maps-to-the-awri/> PO Box 197, Glen Osmond SA 5064, Australia •+61 8 83136613 (direct) |Ê+61 8 83136601 | | [cid:[email protected]] @The_AWRI<https://twitter.com/#!/The_AWRI> | The.AWRI<http://www.facebook.com/#!/The.AWRI> • www.awri.com.au<http://www.awri.com.au/> | AWRI Events<http://www.awri.com.au/industry_support/courses-seminars-workshops/events/> This communication, including attachments, is intended only for the addressee(s) and contains information which might be confidential and/or the copyright of The Australian Wine Research Institute (AWRI) or a third party. If you are not the intended recipient of this communication please immediately delete and destroy all copies and contact the sender. If you are the intended recipient of this communication you should not copy, disclose or distribute any of the information contained herein without the consent of the AWRI and the sender. Any views expressed in this communication are those of the individual sender except where the sender specifically states them to be the views of the AWRI. No representation is made that this communication, including attachments, is free of viruses. Virus scanning is recommended and is the responsibility of the recipient. -----Message d'origine----- De : Sébastien Boisvert [mailto:[email protected]] Envoyé : mardi 12 février 2013 14:55 À : frederic texier Cc : [email protected]<mailto:[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]<mailto:[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]<mailto:[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
<<inline: imagef9eb54.JPG>>
<<inline: imageb6264e.JPG>>
<<inline: image09b72d.JPG>>
------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb
_______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
