UPDATE (161216): My IT support determined that the current version of SHAPEIT is incompatible with our current system software (but doesn't know why), but was able to get the previous version of SHAPEIT to function. However, with a similar installation of the Linux module of extractPIRs, he/we cannot get past a "cannot execute binary file" error.
I REALLY need the extractPIRs for my project. I haven't been able to locate any other programs doing the same thing, so suggestions of workarounds/fixes or other applications would be greatly appreciated!
Thx, Bobbi
*Qualification: Novice at NGS analyses. (Old school Sanger sequencing, microsatellites, population/phylogenetics experience...)
I need to install extractPIRs and ShapeIt to phase haplotypes for a resequencing analysis of unrelated individuals (2 species/7 subspecies geese).
I cannot locate detailed system requirements/compatibilities or installation instructions for the software and have been unable to post at the OXSTATGEN mailing list for clarification. (I HAVE e-mailed the list owners.) (https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#download)
When attempting to run either extractPIRs or ShapeIt with the example files provided, I keep getting "Command Not Found."
I've located one thread that indicates the ShapeIt File needs to be copied into the usr\bin, but am awaiting our IT folks, since "permission denied" to copy it there.
In searching for others having installation/execution errors, I've also read about people using "Homebrew" to install "Boost" before using ShapeIt and extractPIRs. I was under the assumption that, if there's a Max OS version for download, it should run if installed correctly. Are there additional system requirements?
A co-worker indicated the Linux versions should work from the Mac terminal without recompiling in any way. Is this correct information?
Many thanks in advance for any guidance!
Bobbi
Install attempt on: Mac Pro running OS 10.11.6 El Capitan
Update 2 and additional Q's:
Still no suggestions from OXSTATGEN or from here...
Additional question: the extractPIRs website (https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#readaware) indicates "We developed a small tool, extractPIRs, to extract the PIRs from BAM files that relies on the samtools API for efficiency."
Does this mean that extractPIRs is somehow added within Samtools or simply uses portions of its code to execute? What does this mean for installation and running of extractPIRs?
Please, any help? I realize this may be too elementary for many of you, but I need to know if these should run on a Mac Pro running OS 10.11.6 at its terminal without Ubuntu or other Linux platform????
Thanks, Bobbi