Just a heads up, we don't have a huge amount of space on this machine, ~750 GB for the git repos. We can include some data in the projects, but really big datasets will need to remain elsewhere. For anyone new to Git, this is a fairly good place to start: http://gitref.org/index.html Documentation for Gitlab is available here: http://doc.gitlab.com/

Commit ffb4e668 authored by Khalid Kunji's avatar Khalid Kunji

Update README.md

parent 8b1c0e8d
......@@ -8,15 +8,20 @@ Somewhat modern version of g++ if you need to recompile the binaries, we haven't
#### Getting GIGI-Quick
##### With Git
git clone https://cse-git.qcri.org/Imputation/GIGI-Quick.git
Run the following command to clone the repository with git (git is a version management program started by Linus Torvalds https://git-scm.com/downloads)
```git clone https://cse-git.qcri.org/Imputation/GIGI-Quick.git```
##### With a browser
Go to this url: https://cse-git.qcri.org/Imputation/GIGI-Quick/tree/master
Click on the icon with the download arrow above the column "Last Update" on the right hand side.
There are several download options with different compressions, if you get run_GIGI this way, then you will need to decompress it before proceeding
There are several download options with different compressions. If you get run_GIGI this way, then you will need to decompress it before proceeding.
#### Installation
Once you have the files, there are executables compiled on Red Hat, 64 bit Linux, if this is not your system, then you may need to recompile them:
Starting from the folder where you downloaded run_GIGI
Once you have the files, there are executables compiled on Red Hat, 64 bit Linux, if this is not your system, then you may need to recompile them,
but this is usually not necessary unless your system has a different architecture (e.g., 32 bit x86, PowerPC, ARM):
To recompile, starting from the folder where you downloaded run_GIG:
```cd GIGI-Quick/SPLIT/```
......@@ -26,8 +31,12 @@ Starting from the folder where you downloaded run_GIGI
```g++ -O2 GIGIMerge.cpp -o gigimerge```
That's it, GIGI-Quick is installed, they main file/command to run it is run_GIGI
If you like you can now add GIGI-Quick to your path, the examples assume that you have, you can do this by adding the folling to your .bashrc (located in your home folder)
```cd ../GIGI/src/GIGI_v1.06.1```
```g++ -O2 GIGI.cpp -o ../../GIGI```
That's it, GIGI-Quick is installed, the main file/command to run it is run_GIGI
If you like you can now add GIGI-Quick to your path, the examples assume that you have, you can do this by adding the following to your .bashrc (located in your home folder)
```export PATH=${PATH}:/path/to/folder/where/you/put/run_GIGI```
......@@ -35,6 +44,11 @@ Then source your .bashrc to apply the changes right away
```source ~/.bashrc```
The folder structure of GIGI-Quick should not be separated, GIGI-Quick depends on relative paths to locate the scripts and executables included other than run_GIGI.
To add run_GIGI to the path system-wide for all users you can create a symlink in /usr/bin pointing to the run_GIGI script:
```ln -s /path/to/run_GIGI/script /usr/bin/run_GIGI```
#### Usage
Note: The parameter file is the same as you would use for GIGI normally, but if you are using the long format, then pass the "-l" option
......@@ -73,6 +87,16 @@ If there is a problem that makes GIGI stop before completion, then the output fi
If you are unsure where the failure occurred, then the safest approach will be to remove the output files before rerunning (e.g. rm -R [OUTPUT FOLDER]/[RUN NAME]), always use rm with caution as always
e.g. if the 2nd example failed, I would "rm -R ./OUTPUTS/test_run" before rerunning.
The -n option is largely redundant, as it is equivalent to using the -o option with a longer path giving the subfolder, e.g.
```./run_GIGI ./INPUTS/Sample_Input/param-v1_06.txt -o ./OUTPUTS -n test_run```
is equivalent to:
```./run_GIGI ./INPUTS/Sample_Input/param-v1_06.txt -o ./OUTPUTS/test_run```
The inclusion of -n is mostly a semantic convenience.
##### Logs
With the addition of -v and cleanup of output, you may notice that even with -v you don't see the output of split, gigi, and merge any longer. These are now written to their own individual log files in the output directory/run subdirectory.
......
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