[Bug 872783] Review Request: Ray - Parallel genome assemblies for parallel DNA sequencing

[bugzilla at redhat.com]

https://bugzilla.redhat.com/show_bug.cgi?id=872783

--- Comment #11 from Sébastien Boisvert <seb at boisvert.info> ---
Spec URL:
https://raw.github.com/sebhtml/ray-packaging-for-Fedora/for-review/ray-2.1.0-2/2.1.0/ray.spec
SRPM URL:
https://raw.github.com/sebhtml/ray-packaging-for-Fedora/for-review/ray-2.1.0-2/2.1.0/ray-2.1.0-2.fc17.src.rpm
Description: Parallel genome assemblies for parallel DNA sequencing
Fedora Account System Username: sebhtml

The package now builds in mock:

$ mock -r fedora-17-x86_64 rebuild ray-2.1.0-2.fc17.src.rpm &>
ray-2.1.0-2.fc17.src.rpm.mock
$ tail -n1 ray-2.1.0-2.fc17.src.rpm.mock
Finish: run

* Fri Nov 4 2012 Sébastien Boisvert <sebastien.boisvert.3 at ulaval.ca> - 2.1.0-2
- Added build dependency help2man 
- Added OMPI_MCA_orte_rsh_agent to pass mock builds

> The package does not build in mock. You're missing BuildRequires: help2man.

Fixed.

> And even after that I get
>
> + help2man --no-info -n 'assemble genomes in parallel using the message-passing interface' /builddir/build/BUILD/Ray-v2.1.0/Ray
> help2man: can't get `--help' info from /builddir/build/BUILD/Ray-v2.1.0/Ray
> Try `--no-discard-stderr' if option outputs to stderr

Fixed by adding 

    export OMPI_MCA_orte_rsh_agent=/bin/false

before calling help2man

I started reviewing submissions:

  https://fedoraproject.org/wiki/User:Sebhtml#Finding_a_sponsor

For this "SHOULD: The reviewer should test that the package functions as
described.",
here are two system tests if you want to try Ray.

# Test 1

module load openmpi-x86_64
mpiexec -n 32 Ray$MPI_SUFFIX -o test \
-test-network-only
module unload openmpi-x86_64

# Test 2

wget
ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA001/SRA001125/SRX000429/SRR001665_1.fastq.bz2
wget
ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA001/SRA001125/SRX000429/SRR001665_2.fastq.bz2
wget
ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA001/SRA001125/SRX000430/SRR001666_1.fastq.bz2
wget
ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA001/SRA001125/SRX000430/SRR001666_2.fastq.bz2

module load openmpi-x86_64
mpiexec -n 32 Ray$MPI_SUFFIX -k 23 -o Ecoli \
-p SRR001665_1.fastq.bz2 SRR001665_2.fastq.bz2 \
-p SRR001666_1.fastq.bz2 SRR001666_1.fastq.bz2 
module unload openmpi-x86_64

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