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Old 04-17-2013, 10:09 PM   #1
opencell
Junior Member
 
Location: Singapore

Join Date: Apr 2013
Posts: 2
Default 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!
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Old 04-17-2013, 11:03 PM   #2
Wallysb01
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Location: San Francisco, CA

Join Date: Feb 2011
Posts: 286
Default

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.
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Old 04-17-2013, 11:07 PM   #3
opencell
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Location: Singapore

Join Date: Apr 2013
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Default Thank you!

That worked, thank you very much!
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