Hi, Indeed, this is a bug in v2.1.0. This issue was fixed by this commit:
https://github.com/sebhtml/ray/commit/450f1074ad492a89bcac32a6ec5ceea45597e60a and will be included in v2.2.0. I compiled Ray (from git) on Ubuntu 12.10 on Amazon EC2 (t1.micro spot instance) and it compiles without this error. Thanks ! -Séb --- $ ssh -i GoldThor.pem [email protected] ubuntu@ip-10-127-111-120:~/ray$ sudo apt-get install -y git make g++ pentium-builder openmpi-bin openmpi-dev libbz2-dev libz-dev ubuntu@ip-10-127-111-120:~/ray$ git clone git://github.com/sebhtml/RayPlatform.git ubuntu@ip-10-127-111-120:~/ray$ git clone git://github.com/sebhtml/ray.git ubuntu@ip-10-127-111-120:~/ray$ cd ray ubuntu@ip-10-127-111-120:~/ray$ make HAVE_LIBZ=y HAVE_LIBBZ2=y ubuntu@ip-10-127-111-120:~/ray$ ldd Ray On 02/12/2013 10:19 PM, Anthony Borneman wrote: > 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. >>> > > > *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 | | @The_AWRI > <https://twitter.com/#!/The_AWRI> | The.AWRI > <http://www.facebook.com/#!/The.AWRI> > 8 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. 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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 > ------------------------------------------------------------------------------ Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! 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