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Minor updates for installing xtail 1.2.0 into R on macOS without Docker #26

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Minor updates for installing xtail 1.2.0 into R on macOS without Docker #26

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1 change: 1 addition & 0 deletions DESCRIPTION
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Expand Up @@ -9,6 +9,7 @@ Authors@R:
person("Yu", "Liu", role = "aut"),
person("Xuerui", "Yang", role = "aut"),
person("Rongyao", "Huang", email = "THUhry12[at]163.com", role = "ctb"))
Maintainer: Zhengtao Xiao <xzt13@tsinghua.org.cn>; Rongyao Huang <THUhry12@163.com>
Description:
The xtail package is designed to identify genes exhibiting differential
translation between two experimental conditions by simultaneously analyzing
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33 changes: 32 additions & 1 deletion INSTALL
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Expand Up @@ -32,4 +32,35 @@ Download the binary package from "releases", e.g. xtail_1.1.5.zip;
For Windows and Mac OS X, users can install Xtail using R's package installer;
For linux, type the following in an R command window: install.packages("xtail_1.1.5.tar.gz")
Please make sure that the working directory is the same as the downloading directory , or use the full path, for example,
install.packages("/Users/username/xtail_1.1.5-source.tar.gz")
install.packages("/Users/username/xtail_1.1.5-source.tar.gz")

# xtail 1.2.0 INSTALL INSTRUCTIONS FOR R INSTALL on MacOS (not using Docker)
1. Install R as above

2. Install DESeq2 as above

3. Install gfortran
# I used conda
conda install -c conda-forge gfortran

3. Clone xtail git repo from Github
git clone https://github.com/xryanglab/xtail.git

4. Create a Makevars file for .R to find the gfortran install
# if /Users/[USER]/.R does not exist
mkdir /Users/[USER]/.R

nano /Users/[USER]/.R/Makevars

# Paste the following lines into the Makevars
# Path should point to your gfortran install (should have a similar directory structure regardless of method)
FC = /opt/miniconda3/bin/gfortran
F77 = /opt/miniconda3/bin/gfortran
FLIBS = -L/opt/miniconda3/lib/gcc

5. In R, install xtail from local git repo using devtools
library(devtools)
devtools::install(/ABSOLUTE/PATH/TO/XTAIL/REPO/DIR)

6. You can delete the /Users/[USER]/.R/Makevars file once the xtail package is installed on R.
rm /Users/[USER]/.R/Makevars