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# guix-bioinformatics
Bioinformatics packages for GNU Guix that are used in
http://genenetwork.org/. See
[Guix Notes](https://github.com/pjotrp/guix-notes/blob/master/HACKING.org)
for installing and hacking GNU Guix.
Simply set the GUIX_PACKAGE_PATH to point to the root of this directory
before running Guix. E.g.
git clone https://github.com/genenetwork/guix-bioinformatics.git
export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/
guix package -A cwl
or using a checked out Guix repo with
env GUIX_PACKAGE_PATH=$genenetwork/guix-bioinformatics/ ./pre-inst-env guix package -A cwl
Some (or most) of these package definitions should make it upstream
into the GNU Guix repository when tested and stable.
## LLVM D compiler
Install with
git clone https://github.com/genenetwork/guix-bioinformatics.git
export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/
guix package -i ldc
ldc2 --version
LDC - the LLVM D compiler (0.16.0):
based on DMD v2.067.1 and LLVM 3.6.2
Default target: x86_64-unknown-linux-gnu
Host CPU: corei7-avx
http://dlang.org - http://wiki.dlang.org/LDC
Registered Targets:
aarch64 - AArch64 (little endian)
aarch64_be - AArch64 (big endian)
amdgcn - AMD GCN GPUs
arm - ARM
arm64 - ARM64 (little endian)
armeb - ARM (big endian)
cpp - C++ backend
hexagon - Hexagon
mips - Mips
mips64 - Mips64 [experimental]
mips64el - Mips64el [experimental]
mipsel - Mipsel
msp430 - MSP430 [experimental]
nvptx - NVIDIA PTX 32-bit
nvptx64 - NVIDIA PTX 64-bit
ppc32 - PowerPC 32
ppc64 - PowerPC 64
ppc64le - PowerPC 64 LE
r600 - AMD GPUs HD2XXX-HD6XXX
sparc - Sparc
sparcv9 - Sparc V9
systemz - SystemZ
thumb - Thumb
thumbeb - Thumb (big endian)
x86 - 32-bit X86: Pentium-Pro and above
x86-64 - 64-bit X86: EM64T and AMD64
xcore - XCore
## Common Workflow Language (CWL)
Install the common workflow language tool cwltool with
git clone https://github.com/genenetwork/guix-bioinformatics.git
export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/
guix package -i python2-cwltool
cwtool --version
1.0.20150916041152
## R/qtl
R-qtl is now part of main stream GNU Guix:
guix package -i r-qtl r
# Development tips
## Override individual packages
The cheerful way of overriding a version of a package:
(use-modules (guix) (gnu packages emacs))
(package
(inherit emacs)
(name "emacs-snapshot")
(source "/path/to/some-file-or-directory.tar.gz"))
and then run:
guix package --install-from-file=that-file.scm
## LICENSE
These package descriptions (so-called Guix expressions) are
distributed by the same license as GNU Guix, i.e. GPL3+
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