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 7e297e0a authored by Khalid Kunji's avatar Khalid Kunji

Updated help text and fixed typo

parent 017e7aeb
......@@ -203,11 +203,16 @@ then
echo "-n [RUN NAME] : This is a path relative to the [OUTPUT FOLDER] to use to keep the outputs from more than one run of run_GIGI separated."
echo "-t [THREADS] : The number of threads to use for run_GIGI, and also the number of chunks to split the input into."
echo "-m [MEMORY IN MB] : The amount of RAM that run_GIGI will restrict its use to, please set up the cgroup first"
echo "-q [QUEUE LENGTH] : How many copies of GIGI to run concurrently, always use -m when using -q"
echo "-l : Specifies that the input is in the long format."
echo "-v : Display the version of GIGI-Quick"
echo "-V : Verbose mode, output from run_GIGI is much quiter now, you can see much more of what it is doing and what variables are set to at various stages with -v. "
echo "-v : Display the version of GIGI-Quick and exit."
echo "-V : Verbose mode, output from run_GIGI is much quieter now, you can see much more of what it is doing and what variables are set to at various stages with -v. "
echo "-h : Display this help text"
echo "-r [START] [END] : Run on only a selected region, starting at start and ending at end, this region will be selected before any further splitting."
echo "-q [THREADS] : Run in queued mode, this mode will run up to THREADS instances of GIGI at a time and will attempt to keep the total amount of memory being used less than "
echo " [MEMORY IN MB] using an estimate of the amount of memory GIGI may need. If -m [MEMORY IN MB] wasn't given, then it will use the amount of memory available "
echo " as shown by 'free.' For older kernels this isn't shown and we use an estimate that is no longer accurate for modern systems (amount free + amount of buff/cache). "
echo " https://git.kernel.org/pub/scm/linux/kernel/git/torvalds/linux.git/commit/?id=34e431b0ae398fc54ea69ff85ec700722c9da773 Also, -t is ignored when -q is given."
echo "-e [MEMORY IN MB] : Not yet implemented, manual estimate of how much memory GIGI will need for queued mode in case the calculated estimate is too inaccurate"
echo "For further information please see the included readme file and or the same text online on the project page: https://cse-git.qcri.org/Imputation/Impute_Beaming"
exit 0
;;
......
......@@ -39,7 +39,7 @@ run_GIGI parameter_file -o [OUTPUT FOLDER] -n [RUN NAME] -t [THREADS] -m [MEMORY
-t [THREADS] : The number of threads to use for run_GIGI, and also the number of chunks to split the input into.
-m [MEMORY IN MB] : The amount of RAM that run_GIGI will restrict its use to, not yet implemented
-l : Specifies that the input is in the long format.
-V : Verbose mode, output from run_GIGI is much quiter now, you can see much more of what it is doing and what variables are set to at various stages with -v.
-V : Verbose mode, output from run_GIGI is much quieter now, you can see much more of what it is doing and what variables are set to at various stages with -v.
-v : Display the version of GIGI-Quick and exit.
-h : Display this help text.
-r [START] [END] : Run on only a selected region, starting at start and ending at end, this region will be selected before any further splitting.
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment