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  • compiling SRA Toolkit on a 64bit Ubunti machine

    Hi there, my first post here ... hope to have reached the right section of the forum.

    I wanted to install the latest SRA Toolkit on my 64bit Ubuntu server.

    While for the 2.1.8 release seems there are no apparent problems compiling it from souces (link) I do have them for the 2.1.10 (the latest as I am writing)...

    Code:
    $ uname -a
    
    Linux popeye 2.6.32-35-server #78-Ubuntu SMP Tue Oct 11 16:26:12 UTC 2011 x86_64 GNU/Linux
    and

    Code:
    $ cat /etc/lsb-release 
    
    DISTRIB_ID=Ubuntu
    DISTRIB_RELEASE=10.04
    DISTRIB_CODENAME=lucid
    DISTRIB_DESCRIPTION="Ubuntu 10.04.4 LTS"
    after giving the make command the systems run then ends with these errors:

    Code:
    gcc -c  -D_DEBUGGING -g -m64  -std=c99 -ansi -pedantic -D_STATIC -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -D_ARCH_BITS=64 -DLIBPREFIX=lib -DSHLIBEXT=so -I/home/nicola/Downloads/sra_sdk-2.1.10/tools/sra-load/linux -I/home/nicola/Downloads/sra_sdk-2.1.10/tools/sra-load/unix -I/home/nicola/Downloads/sra_sdk-2.1.10/tools/sra-load -I/home/nicola/Downloads/sra_sdk-2.1.10/interfaces -I/home/nicola/Downloads/sra_sdk-2.1.10/interfaces/cc/gcc/x86_64 -I/home/nicola/Downloads/sra_sdk-2.1.10/interfaces/cc/gcc -I/home/nicola/Downloads/sra_sdk-2.1.10/interfaces/os/linux -I/home/nicola/Downloads/sra_sdk-2.1.10/interfaces/os/unix -I/home/nicola/Downloads/sra_sdk-2.1.10/interfaces/ext -MD -o writer-ion-torrent.o -Wall -Wno-variadic-macros /home/nicola/Downloads/sra_sdk-2.1.10/tools/sra-load/writer-ion-torrent.c
    gcc -c  -D_DEBUGGING -g -m64  -std=c99 -ansi -pedantic -D_STATIC -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -D_ARCH_BITS=64 -DLIBPREFIX=lib -DSHLIBEXT=so -I/home/nicola/Downloads/sra_sdk-2.1.10/tools/sra-load/linux -I/home/nicola/Downloads/sra_sdk-2.1.10/tools/sra-load/unix -I/home/nicola/Downloads/sra_sdk-2.1.10/tools/sra-load -I/home/nicola/Downloads/sra_sdk-2.1.10/interfaces -I/home/nicola/Downloads/sra_sdk-2.1.10/interfaces/cc/gcc/x86_64 -I/home/nicola/Downloads/sra_sdk-2.1.10/interfaces/cc/gcc -I/home/nicola/Downloads/sra_sdk-2.1.10/interfaces/os/linux -I/home/nicola/Downloads/sra_sdk-2.1.10/interfaces/os/unix -I/home/nicola/Downloads/sra_sdk-2.1.10/interfaces/ext -MD -o fastq-fmt.o -Wall -Wno-variadic-macros /home/nicola/Downloads/sra_sdk-2.1.10/tools/sra-load/fastq-fmt.c
    gcc -o /home/nicola/sra/linux/dbg/gcc/x86_64/bin/fastq-load.2.1.13 -g -Wl,--export-dynamic pstring.o common-xml.o experiment-xml.o run-xml.o loader-file.o loader-fmt.o sra-writer.o loader.o writer-illumina.o writer-454.o writer-ion-torrent.o fastq-fmt.o -L/home/nicola/sra/linux/dbg/gcc/x86_64/lib -L/home/nicola/sra/linux/dbg/gcc/x86_64/ilib -Wl,-Bstatic -Wl,-whole-archive -lwsradb -lwsraxf -lkapp -lwvxf -lwvdb -lwkdb -lvfs -lkrypto -lkfg -lload -lkfs -lksrch -lkxml -lkxfs -lklib -lkproc -Wl,-no-whole-archive -Wl,-Bdynamic -lm -Wl,-Bstatic -Wl,-whole-archive -lkq -Wl,-no-whole-archive -Wl,-Bdynamic -lxml2 -lz -lbz2 -ldl -lpthread
    /usr/bin/ld: cannot find -lxml2
    collect2: ld returned 1 exit status
    make[3]: *** [/home/nicola/sra/linux/dbg/gcc/x86_64/bin/fastq-load] Error 1
    make[3]: Leaving directory `/home/nicola/sra/linux/dbg/gcc/x86_64/obj/tools/sra-load'
    make[2]: *** [std] Error 2
    make[2]: Leaving directory `/home/nicola/Downloads/sra_sdk-2.1.10/tools/sra-load'
    make[1]: *** [sra-load] Error 2
    make[1]: Leaving directory `/home/nicola/Downloads/sra_sdk-2.1.10/tools'
    make: *** [tools] Error 2
    Libxml2 is correctly installed on my machine as
    Code:
    dpkg -l libxml2
    Desired=Unknown/Install/Remove/Purge/Hold
    | Status=Not/Inst/Cfg-files/Unpacked/Failed-cfg/Half-inst/trig-aWait/Trig-pend
    |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
    ||/ Name                                 Version                              Description
    +++-====================================-====================================-========================================================================================
    ii  libxml2                              2.7.6.dfsg-1ubuntu1.4                GNOME XML library
    Anyone has an idea on how to solve this ?
    SysAdmin & ICT consultant
    http://about.me/nicola.losito

  • #2
    You probably need the libxml2-dev package as well, to get the include files for linking.

    Comment


    • #3
      Seems that I've solved this alone.

      I tested the xml2 installation with:
      Code:
      xml2-config --prefix
      which gave me
      Code:
      The program 'xml2-config' is currently not installed.  You can install it by typing:
      sudo apt-get install libxml2-dev
      so I did and after having installed it the toolkit installed without any further issue!

      Thanks anyway!
      SysAdmin & ICT consultant
      http://about.me/nicola.losito

      Comment


      • #4
        Originally posted by arvid View Post
        You probably need the libxml2-dev package as well, to get the include files for linking.
        Yes! you suggested me the right solution while I was writing down my previous post. Thanks !!!
        SysAdmin & ICT consultant
        http://about.me/nicola.losito

        Comment

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