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rsc 03-03-2014 10:34 AM

Sambamba, ldmd2, BioD - on RHEL 6

I'm trying to install Sambamba ( ) which is written in "D" and requires the LDMD2 compiler and includes undocumented references to "rdmd" and "BioD".

Worse, I'm trying to do it on RedHat Enterprise Linux 6 (which means the pre-built binaries don't work and which means re-building a heck of a lot of the tool chains.)

I'm an experienced system administrator - but not a Bioinformatics person, and not familiar with the "D" language or it's 3 compilers (MDC, GDC, or LDC.)

When I try to follow the Sambama instructions, I get:

[rsc@buffer3 sambama-20140227]$ make sambamba-ldmd2-64
mkdir -p build/
rdmd --build-only --force --compiler=ldmd2 -O2 -m64 -noboundscheck -release -inline -IBioD/ -ofbuild/sambamba main.d
sambamba/view.d(25): Error: module region is in file 'bio/bam/region.d' which cannot be read
import path[0] = BioD/
import path[1] = .
import path[2] = /usr/local/include/d/ldc
import path[3] = /usr/local/include/d
Failed: ["ldmd2", "-O2", "-m64", "-noboundscheck", "-release", "-inline", "-IBioD/", "-v", "-o-", "main.d", "-I."]
make: *** [sambamba-ldmd2-64] Error 1
[rsc@buffer3 sambama-20140227]$

I've tried installing "BioD" in the Sambamba distribution directory, and in the "ldc" import directory ("/usr/local/include/d" on my system.)

Does anyone have any suggestions?

Thank you in advance.

--- Richard

rsc 03-04-2014 08:55 AM

I grabbed BioD from the wrong place. With the right BioD in place, everything's fine.

--- Richard

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