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-rw-r--r--README.md63
1 files changed, 54 insertions, 9 deletions
diff --git a/README.md b/README.md
index 5cb1dd7..c5c690d 100644
--- a/README.md
+++ b/README.md
@@ -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