On 05/23/2013 02:39 PM, Jens Timmerman wrote:
Hi,

why are all these package to-do list?
Manly because I am really crappy at putting lists together.

BWA -- we need 0.7.4 (there is already a PR for the config and an updated block)

BEAGLE -- should definitely not have been in the list.

Some of the others we had a problem building the first time around so they did not go "green" in my spreadsheet. I will check once again and report...

Thanks!

George

They are already included
see https://github.com/hpcugent/easybuild/wiki/List-of-supported-software-packages

abyss https://github.com/hpcugent/easybuild-easyconfigs/tree/develop/easybuild/easyconfigs/a/ABySS bioperl: https://github.com/hpcugent/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/p/Perl/Perl-5.16.3-goolf-1.4.10.eb and https://github.com/hpcugent/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-goolf-1.4.10-Perl-5.16.3.eb bowtie https://github.com/hpcugent/easybuild-easyconfigs/tree/master/easybuild/easyconfigs/b/Bowtie bwa https://github.com/hpcugent/easybuild-easyconfigs/tree/develop/easybuild/easyconfigs/b/BWA mrbayes https://github.com/hpcugent/easybuild-easyconfigs/tree/develop/easybuild/easyconfigs/m/MrBayes beagle https://github.com/hpcugent/easybuild-easyconfigs/tree/develop/easybuild/easyconfigs/b/BEAGLE

regards
Jens Timmerman


On 23 May 2013 12:46, George Tsouloupas <g.tsoulou...@cyi.ac.cy <mailto:g.tsoulou...@cyi.ac.cy>> wrote:

    Dear EasyFriends,

    While duplication of work is a really good way to catch errors, we
    could reduce it a bit;
    Here are the packages we are working on these days at The Cyprus
    Institute with respect to Bioinformatics:


    "Packages" with a pull request already submitted or to be
    submitted within a few days (I'm not sure if we'll make the freeze):
    PLINK
    AllPathslg
    bam2fastq
    bwa
    EMBOSS
    paml
    GATK

    "Packages" with configs/blocks in easybuild.experimental
    MUSCLE
    CD-HIT
    RaxML
    RepeatMasker
    GPU-BLAST
    CUDA-BLASTP

    "Packages" on our immediate to-do list:
    BioPython
    Bioconductor
    Bioperl
    Oases
    bamtools
    blat
    bowtie
    fasta
    fastqc
    freebayes
    mrbayes
    beagle lib
    Picard-tools
    glimmer

    "Packages" on no-so-immediate to-do list:
    Phrap
    Phred
    Consed
    Abyss
    lastz


    All feedback is welcome!

    Thanks!

    George Tsouloupas,
    HPC Operations
    CaSToRC, the Cyprus Institute.





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