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.