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Diffstat (limited to 'README.md')
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1 files changed, 54 insertions, 9 deletions
@@ -5,37 +5,82 @@ http://genenetwork.org/. See [Guix Notes](https://github.com/pjotrp/guix-notes/blob/master/HACKING.org) for installing and hacking GNU Guix. -Set the GUIX_PACKAGE_PATH to point to the root of this directory +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=$PWD/guix-bioinformatics/ guix package -A cwl -or using a checked out Guix repo +or using a checked out Guix repo with env GUIX_PACKAGE_PATH=$genenetwork/guix-bioinformatics/ ./pre-inst-env guix package -A cwl -Some of these package definitions should make it upstream into the GNU -Guix repository when tested and stable. +Some (or most) of these package definitions should make it upstream +into the GNU Guix repository when tested and stable. -## Install Common Workflow Language (CWL) +## 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 -## Install R/qtl +## R/qtl -R-qtl is part of main stream GNU Guix: +R-qtl is now part of main stream GNU Guix: guix package -i r-qtl r - R - library(qtl) # Development tips |