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  • pepsimax
    Junior Member
    • May 2012
    • 9

    #1

    Installing SplitRead

    Hi,

    I'm fairly new to this sort of work, and I've been having trouble installing SplitRead (http://splitread.sourceforge.net/manual.html). It requires MrsFast and Samtools, both of which I've installed and got working properly. I'm running Fedora 16, I downloaded the tar.gz, decompressed it and got Code-Release. That contains
    breakReads.c Make.sh split_match_sam.c
    fastqdeloea.c Paired-end_match_sam.c SplitOEA_match.c
    Finalevents_v5.c pair_match_v5.c SplitReadAll_lite.c
    getFinalevents.sh pairToSC.sh

    I tried
    Code:
    Bash Make.sh
    and
    Code:
    sh Make.sh
    after making it executable with
    Code:
    chmod -x
    . All I get in return is a string of errors.

    Code:
    bash-4.2$ bash Make.sh
    mkdir: cannot create directory `/___': File exists
    /usr/bin/ld: cannot find -lm
    /usr/bin/ld: cannot find -lc
    collect2: ld returned 1 exit status
    /usr/bin/ld: cannot find -lm
    /usr/bin/ld: cannot find -lc
    collect2: ld returned 1 exit status
    /usr/bin/ld: cannot find -lm
    /usr/bin/ld: cannot find -lc
    collect2: ld returned 1 exit status
    Paired-end_match_sam.c: In function ‘myfopen’:
    Paired-end_match_sam.c:242:9: warning: assignment from incompatible pointer type [enabled by default]
    /usr/bin/ld: cannot find -lm
    /usr/bin/ld: cannot find -lc
    collect2: ld returned 1 exit status
    pair_match_v5.c: In function ‘myfopen’:
    pair_match_v5.c:516:9: warning: assignment from incompatible pointer type [enabled by default]
    /usr/bin/ld: cannot find -lm
    /usr/bin/ld: cannot find -lc
    collect2: ld returned 1 exit status
    split_match_sam.c: In function ‘myfopen’:
    split_match_sam.c:227:9: warning: assignment from incompatible pointer type [enabled by default]
    /usr/bin/ld: cannot find -lm
    /usr/bin/ld: cannot find -lc
    collect2: ld returned 1 exit status
    SplitOEA_match.c: In function ‘myfopen’:
    SplitOEA_match.c:245:9: warning: assignment from incompatible pointer type [enabled by default]
    /usr/bin/ld: cannot find -lm
    /usr/bin/ld: cannot find -lc
    collect2: ld returned 1 exit status
    /usr/bin/ld: cannot find -lm
    /usr/bin/ld: cannot find -lc
    collect2: ld returned 1 exit status
    cp: cannot stat `breakReads': No such file or directory
    cp: cannot stat `fastqdeloea': No such file or directory
    cp: cannot stat `events5': No such file or directory
    cp: cannot stat `Paired-end_match_sam': No such file or directory
    cp: cannot stat `pair_match_v5': No such file or directory
    cp: cannot stat `split_match_sam': No such file or directory
    cp: cannot stat `SplitOEA_match': No such file or directory
    cp: cannot stat `SplitReadAll_lite': No such file or directory
    I guess I'm missing something simple... please help!

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