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  • FLASH : command not found

    Hi there,
    I'm a newbie in bioinformatics and I encounter a simple problem with FLASH (Fast Length Adjustment for SHort reads).
    I'm working on Mac OS X and followed the instructions to download, untar the tarball and compile using $make:
    $ make
    cc -O2 -Wall -std=c99 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -pthread -c -o flash.o flash.c
    cc -O2 -Wall -std=c99 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -pthread -c -o combine_reads.o combine_reads.c
    cc -O2 -Wall -std=c99 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -pthread -c -o fastq.o fastq.c
    cc -O2 -Wall -std=c99 -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -pthread -c -o util.o util.c
    cc -pthread flash.o combine_reads.o fastq.o util.o -lz -o flash
    clang: warning: argument unused during compilation: '-pthread'

    But when I ran the command I got an error message:
    $ flash -o flashout_trimmed --interleaved-output trimmedR1.fastq trimmedR2.fastq
    -bash: flash: command not found

    Can anyone help with that?
    Thank you very much in advance!

  • #2
    you just need to add the directory flash was installed in to your .bash_profile.

    Alternatively you could copy it to something like /usr/local/bin/ or /usr/bin/

    What I do on my machine is to create local "bin" directory at just /home/username/bin which is added to my path in .bash_profile. I then make a symlink to the executable file, or just copy the executable over.

    Comment


    • #3
      Thank you!

      That worked, thank you very much!

      Comment

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