Hi Admin,
I followed the INSTALL.txt guideline as attached to install Ray but i have
no clue to go further.
Could you please guide me how to enable .gz support?
Thanks
Jason
On Tue, Nov 15, 2016 at 9:12 PM, Sébastien Boisvert <s...@boisvert.info>
wrote:
> Hi Jason,
>
>
> Please post your questions to the mailing list (in CC).
>
> Did you enable .gz support when you built the software Ray from source ?
>
> ------------------------------
> *From:* Jason Tan <jasonta...@gmail.com>
> *Sent:* November 15, 2016 3:47 AM
> *To:* s...@boisvert.info
> *Subject:* Request for guidance
>
> Dear Admin,
>
> Thank you for contributing this useful piece of software.
>
> I am using Ubuntu as my working platform but i received an error "Rank 0 :
> no input files, aborting" when i executed Ray program of Ray-2.3.1.tar.bz2
> which is downloaded from this website
>
> https://sourceforge.net/projects/denovoassembler/files/
> Ray, a de novo assembler using MPI 2.2 - Browse Files at ...
> <https://sourceforge.net/projects/denovoassembler/files/>
> sourceforge.net
> Ray -- Parallel genome assemblies for parallel DNA sequencing
>
> The command that i entered was
>
> mpiexec -n 2 ray-build/Ray -detect-sequence-files SRR1633365 -show
> memory-usage
>
> and the file SRR1633365.fastq.gz is in the folder SRR1633365
>
> However, when i installed the Ray by using this command, it can be
> executed successfully.
>
> sudo apt-get install Ray
> mpiexec -n 2 Ray -detect-sequence-files SRR1633365 -show memory-usage
>
>
> Could you please guide me the solution to this problem?
>
> Thanks
> Jason
>
You need:
- A C++ compiler (C++ 1998 or later)
- An MPI implementation
- make
== Quickstart on GNU/Linux ==
On GNU/Linux, you can use GNU C++ (g++) and Open-MPI.
Then, type
make PREFIX=ray-build
make install
ls ray-build
mpiexec -n 1 ray-build/Ray -o test -p test_1.fastq test_2.fastq -k 31
== Options ==
You can provide compilation options to the Makefile.
MPICXX The path to the C++ compiler wrapper (usually called
mpicxx)
PREFIX Where to install stuff
MAXKMERLENGTH maximum k-mer length, default is MAXKMERLENGTH=32
FORCE_PACKING save memory by not aligning addresses, default is
FORCE_PACKING=n
ASSERT run assertions too, default is ASSERT=n
For other options, read the Makefile header.
== Working compilers ==
Anything that supports C++ 1998.
see Documentation/COMPILERS.txt
------------------------------------------------------------------------------
_______________________________________________
Denovoassembler-users mailing list
Denovoassembler-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
