Hi Adam, much of the needed “machinery” is provided via HPCBIOS_Bioinfo easyconfig (essentially, most of deps). Hint: trim down to the essential; it’s a complicated one and it’s common to spit out errors.
Watch out with samtools/htslib though, because AFAIK recent versions are not truly backwards compatible, so you will need to handle that in some way. F. On Sep 14, 2015, at 11:51 AM, Adam Huffman <[email protected]> wrote: > Hello > > I’ve started an easyconfig for alleleCount > (http://cancerit.github.io/alleleCount/), which is a combination of Perl and > C code. > There’s a shell script provided that downloads and builds samtools and > htslib, then the remaining Perl dependencies, then installs the > binaries/scripts. > > Is there an easyconfig that replicates a similar approach, which I can use > for inspiration? > > The bare outline I have so far is at: > > https://github.com/verdurin/easybuild-easyconfigs-devel/blob/master/alleleCount-2.1.1.eb > > Cheers, > Adam > > — > > Adam Huffman > Senior HPC and Virtualization Systems Engineer > The Francis Crick Institute > Gibbs Building > 215 Euston Road > London NW1 2BE > > T: 020 7611 2244 > E: [email protected] > W: www.crick.ac.uk > > > > > The Francis Crick Institute Limited is a registered charity in England and > Wales no. 1140062 and a company registered in England and Wales no. 06885462, > with its registered office at 215 Euston Road, London NW1 2BE. cheers, Fotis -- echo "sysadmin know better bash than english" | sed s/min/mins/ \ | sed 's/better bash/bash better/' # signal detected in a CERN forum
