On 23 May 2013, at 14:02, George Tsouloupas wrote: > 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)
I'll jump on that ASAP, should go in for v1.5. > > 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... If you have problems with building individual packages that are already support in EB v1.4 (or earlier), please open issues for those with the error messages popping up. Depending on the problem, either open the issue in the easyblocks repository (e.g. when the Python code crashes), or in easyconfigs (missing dependencies, doesn't work for a newer version, etc.). Then these can be followed up piece by piece efficiently. regards, Kenneth > > 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 <[email protected]> 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. >> >> >> >> >
