On 23 May 2013, at 12:46, George Tsouloupas 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):
To make the freeze, PRs should be open before tomorrow 9am (CET), see https://github.com/hpcugent/easybuild/wiki/Release-schedule. We'll be fairly strict about this, otherwise it's impossible to make the planned release date. Do open the PRs though, then they'll be included quickly and be shipped in v1.6 (currently roughly planned for end of June). > PLINK > AllPathslg > bam2fastq > bwa > EMBOSS There are two PRs open for EMBOSS, see https://github.com/hpcugent/easybuild-easyconfigs/pull/265 and https://github.com/hpcugent/easybuild-easyconfigs/pull/269 . I'll make sure they get merged properly. In particular, your version (#269) does something extra, so that's likely to be the one that will be included. > paml > GATK > > "Packages" with configs/blocks in easybuild.experimental > MUSCLE > CD-HIT We have installed CD-HIT before with EB, but the support is not ported yet. Who is working on this? I can send them our (old/outdated) stuff, it could give some inspiration. See https://github.com/hpcugent/easybuild/wiki/List-of-supported-software-packages/ede46976d7367a86fe76ae79adba7b8e9fd9f118 for a list of legacy supported packages. If you find anything there that might be interesting for you, let us know, and we can share old stuff that needs to be ported (which is usually not too hard). > RaxML I opened a PR for this yesterday, see https://github.com/hpcugent/easybuild-easyconfigs/pull/277 . > RepeatMasker > GPU-BLAST > CUDA-BLASTP > > "Packages" on our immediate to-do list: > BioPython We have legacy support for BioPython. > Bioconductor Several Bioconductor R packages are installed as a part of the R easyconfig. It should be fairly easy to compose stand-alone easyconfigs for Bioconductor R libs. > Bioperl > Oases > bamtools > blat > bowtie > fasta > fastqc > freebayes > mrbayes > beagle lib > Picard-tools > glimmer We already have several of these, see Jens' mail and https://github.com/hpcugent/easybuild/wiki/List-of-supported-software-packages. > > "Packages" on no-so-immediate to-do list: > Phrap > Phred > Consed > Abyss We already have ABySS. > lastz > > > All feedback is welcome! > > Thanks! > > George Tsouloupas, > HPC Operations > CaSToRC, the Cyprus Institute. > > >
