From bd9480e305b0f943bdd748f2f16d95f970bfd944 Mon Sep 17 00:00:00 2001 From: Chloe Pacyna Date: Sun, 16 Oct 2022 15:36:28 +0100 Subject: [PATCH] fix -J order text --- 05-job_arrays.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/05-job_arrays.md b/05-job_arrays.md index 214ef62..1c509cf 100644 --- a/05-job_arrays.md +++ b/05-job_arrays.md @@ -53,7 +53,7 @@ This means that you only need to submit one "master" job, making it easier to ma Job arrays are created with the *-J* option `-J arrayName[start-finish]` where *arrayName* becomes the Job Name and *start* and *finish* are integers defining the range of array numbers created by LSF. For example, setting `-J testJob[1-3]` would result in three jobs sent: `testJob[1]`, `testJob[2]`, and `testJob[3]`. -For some unclear reason (which could be a bug! the `-J` option specified within the script header with `#BSUB` needs to be one of the first arguments listed. We recommend placing it as the third, below -G and -q options. +If you'd like to specify the `-J` option within the script header with `#BSUB`, it needs to be one of the first arguments listed. We recommend placing it as the third, below -G and -q options. With this array list option within `-J`, LSF then creates a special shell variable `$LSB_JOBINDEX`, which contains the array number for the job being processed. Later in this section we will see how we can use some tricks with this variable to automate our analysis.