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authorMuriithi Frederick Muriuki2021-08-30 12:01:54 +0300
committerMuriithi Frederick Muriuki2021-08-30 12:01:54 +0300
commitb8777bcfee70325263d5389367e3a93ec2842f69 (patch)
treeb851dd3a31b059be92c4364c6b84fe1ec8e9bd97
parent58f59b8f7df82969b58a604070aec095d17e0501 (diff)
downloadgenenetwork3-b8777bcfee70325263d5389367e3a93ec2842f69.tar.gz
Update documentation on genotype files
* Provide documentation on downloading and using the genotype files.
-rw-r--r--README.md17
1 files changed, 15 insertions, 2 deletions
diff --git a/README.md b/README.md
index b54015f..61ca539 100644
--- a/README.md
+++ b/README.md
@@ -14,7 +14,7 @@ guix environment --load=guix.scm
Also, make sure you have the [guix-bioinformatics](https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics) channel set up.
```bash
-env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment --load=guix.scm
+env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment --expose=$HOME/genotype_files/ --load=guix.scm
python3
import redis
```
@@ -22,7 +22,7 @@ python3
Better run a proper container
```
-env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C --network --load=guix.scm
+env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C --network --expose=$HOME/genotype_files/ --load=guix.scm
```
If you get a Guix error, such as `ice-9/boot-9.scm:1669:16: In procedure raise-exception:
@@ -121,6 +121,19 @@ pip freeze --path venv/lib/python3.8/site-packages > requirements.txt
```
+## Genotype Files
+
+You can get the genotype files from http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL and save them on your host machine at, say `$HOME/genotype_files` with something like:
+
+```bash
+$ mkdir -p $HOME/genotype_files
+$ cd $HOME/genotype_files
+$ yes | 7z x genotype_files.tar.7z
+$ tar xf genotype_files.tar
+```
+
+The `genotype_files.tar.7z` file seems to only contain the **BXD.geno** genotype file.
+
## QTLReaper (rust-qtlreaper) and Trait Files
To run QTL computations, this system makes use of the [rust-qtlreaper](https://github.com/chfi/rust-qtlreaper.git) utility.