Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • BWA and Samtools installation failing

    Hi.

    First post, so please be gentle

    First, I would like to say that I am not very familiar with Linux/Unix so I need advice to be addressed in a manner so that I can understand. I hope this is not stopping you from giving me some advice.

    System, Ubuntu 12.04 LTS 64-bit, Intel core i7-2640M CPU, 8 GB memory.

    I would like to set up a few tools in order to perform ananlysis of my RNA-sequencing (Illumina HiSeq). So far I have figured out that I would like to try the combination of the following software:

    - BWA
    - Cufflinks
    - Samtools
    - Bowtie
    - TopHat

    Cufflinks and tophat is working (at least if I type cufflinks --help or tophat --help).

    Now, I am having trouble with Samtools and BWA, and it appears that I am not able to install them (by using the make command).

    I am getting the following error:

    JamesT-XPS-L412Z:~/Samtools/samtools-0.1.18$ make
    make[1]: Entering directory `/home/jim/Samtools/samtools-0.1.18'
    make[2]: Entering directory `/home/jim/Samtools/samtools-0.1.18'
    gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
    In file included from bgzf.c:36:0:
    bgzf.h:29:18: fatal error: zlib.h: No such file or directory
    compilation terminated.
    make[2]: *** [bgzf.o] Error 1
    make[2]: Leaving directory `/home/jim/Samtools/samtools-0.1.18'
    make[1]: *** [lib-recur] Error 1
    make[1]: Leaving directory `/home/jim/Samtools/samtools-0.1.18'
    make: *** [all-recur] Error 1

    JamesT-XPS-L412Z:~/bwa/bwa-0.6.2$ make
    gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwa.c -o bwa.o
    In file included from bwa.c:8:0:
    bntseq.h:32:18: fatal error: zlib.h: No such file or directory
    compilation terminated.
    make: *** [bwa.o] Error 1

    From searching the web for a few days I think the problem is with the library, however, my Ubuntu tells me that the zlib1g-dev is installed. Is there any other library I need? Do I need to make changes to the make file? Or is the problem elsewhere.

    -James
    Last edited by JamesT; 06-28-2012, 03:18 AM. Reason: problem solved

  • #2
    I did the following:

    JamesT-XPS-L412Z:~$sudo apt-get update
    JamesT-XPS-L412Z:~$sudo apt-get install zlib1g-dev libncurses5-dev
    JamesT-XPS-L412Z:~/Samtools/samtools-0.1.18$ make
    JamesT-XPS-L412Z:~/bwa/bwa-0.6.2$ make

    Both commands finished without errors, so I assume things are ok.

    Comment


    • #3
      Originally posted by JamesT View Post
      Hi.

      First, I would like to say that I am not very familiar with Linux/Unix so I need advice to be addressed in a manner so that I can understand. I hope this is not stopping you from giving me some advice.
      Don't worry... I'm sure most of us without a backgroud in linux have been stumped by the zlib/ncurses thing at some point or the other

      Comment


      • #4
        Well, at least I managed to make it work Thanks for the positive remark, it is helpful when you are entering a new field (NGS and Linux).

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Strategies for Sequencing Challenging Samples
          by seqadmin


          Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
          03-22-2024, 06:39 AM
        • seqadmin
          Techniques and Challenges in Conservation Genomics
          by seqadmin



          The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

          Avian Conservation
          Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
          03-08-2024, 10:41 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 03-27-2024, 06:37 PM
        0 responses
        12 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-27-2024, 06:07 PM
        0 responses
        11 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        53 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        69 views
        0 likes
        Last Post seqadmin  
        Working...
        X