From d69856ae92eda02b6974df4c32c842f5afd06c14 Mon Sep 17 00:00:00 2001 From: martinghunt Date: Fri, 27 May 2016 13:34:46 +0000 Subject: [PATCH] Add tmp dir description --- README.md | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/README.md b/README.md index 5160de06..6432ebe5 100644 --- a/README.md +++ b/README.md @@ -68,6 +68,46 @@ that you compiled and downloaded in your home directory (assuming BASH): export ARIBA_SAMTOOLS=$HOME/samtools-1.2/samtools +### Temporary files + +ARIBA can temporarily make a large number of files whilst running, which +are put in a temporary directory made by ARIBA. The total size of these +files is small, but there can be a many of them. This can be a +problem when running large numbers (100s or 1000s) of jobs simultaneously +on the same file system. +By default, ARIBA creates a temporary directory for these files +inside the output directory of each run. + +Each temporary directory +is unique to one run of ARIBA, and is automatically deleted at the end +of the run (even if ARIBA was killed by the user or crashed). +The parent directory of the temporary +directory can be changed using the environment variable +`$ARIBA_TMPDIR`. The temporary directory for each run will be made +inside `$ARIBA_TMPDIR`. For example, + + export $ARIBA_TMPDIR=/tmp + +will result in the creation of a new directory inside `/tmp`, which +will have a name of the form + + /tmp/ariba.tmp.abcdef + +where the suffix `abcdef` is a random string of characters, chosen +such that `/tmp/ariba.tmp.abcdef` does not already exist. + +The temporary directory can also be changed using the option +`--tmp_dir` when running `ariba run`. Using this option takes precedence +over the environment variable `$ARIBA_TMPDIR`. If neither are +set, then ARIBA creates the temporary directory inside +the output directory given to `ariba run`. + +The exception to the above is if the option `--noclean` is used. +This forces the temporary directory to be placed in the output +directory, and temporary files are kept. It is intended for +debugging. + + Usage -----