From 77b4551ba9ebaaddbb7fcc3a77e5e024bc9bf0f2 Mon Sep 17 00:00:00 2001 From: "William F. Broderick" Date: Tue, 26 Oct 2021 17:10:09 -0400 Subject: [PATCH] updates singularity_env.sh no longer edit data dir, we'll mount it in the same place (so that sbatch can find it) --- README.md | 29 ++++++++++++++--------------- singularity_env.sh | 4 ---- 2 files changed, 14 insertions(+), 19 deletions(-) diff --git a/README.md b/README.md index 42e96bd..4305607 100644 --- a/README.md +++ b/README.md @@ -406,13 +406,13 @@ analysis, only the first of which must be set: /home/billbrod or /Users/billbrod) and that the name of your directory cannot have capital letters in it (i.e., it should be sfp_data, not SFP_data; this causes an issue on Macs) -- Preprocessing-related: these two only need to be set if you're re-running the - pre-processing steps **and** doing so without using the - [container](#singularity-image). - - `MRI_TOOLS`: path to the Winawer lab MRI tools repo, commit - [8508652bd9e6b5d843d70be0910da413bbee432e](https://github.com/WinawerLab/MRI_tools/tree/8508652bd9e6b5d843d70be0910da413bbee432e). - - `WORKING_DIR`: working directory for preprocessing, stores some temporary - outputs. +- `MRI_TOOLS`: path to the Winawer lab MRI tools repo, commit + [8508652bd9e6b5d843d70be0910da413bbee432e](https://github.com/WinawerLab/MRI_tools/tree/8508652bd9e6b5d843d70be0910da413bbee432e). + this only needs to be set if you're re-running the pre-processing steps + **and** doing so without using the [container](#singularity-image). +- `WORKING_DIR`: working directory for preprocessing, stores some temporary + outputs. Needs to be set if you're re-running pre-processing, regardless of + whether you're using the container or not. - GLMdenoise-related: these two only need to be set if you're re-running the GLMdenoise steps **and** doing so without using the [container](#singularity-image). @@ -420,14 +420,13 @@ analysis, only the first of which must be set: - `VISTASOFT_PATH`: Path to the Vistasoft MATLAB toolbox. - Container-related: these only need to be set if you're using the [container](#singularity-image) **and** running preprocessing and/or - GLMdenoise (you don't need to edit the `MRI_TOOLS`, etc paths as well). Note - the current paths should be correct if you're on NYU Greene. They're the paths - to the install locations for the additional dependencies required for - preprocessing and GLMdenoise. To find their path on the cluster, make sure - they're on your path (probably by using `module load`) and then run e.g., - `which matlab` (or `which mri_convert`, etc.) to find where they're installed. - Note that we want the root directory of the install (not the `bin/` folder - containing the binary executables so that if `which matlab` returns + GLMdenoise. Note the current paths should be correct if you're on NYU Greene. + They're the paths to the install locations for the additional dependencies + required for preprocessing and GLMdenoise. To find their path on the cluster, + make sure they're on your path (probably by using `module load`) and then run + e.g., `which matlab` (or `which mri_convert`, etc.) to find where they're + installed. Note that we want the root directory of the install (not the `bin/` + folder containing the binary executables so that if `which matlab` returns `/share/apps/matlab/2020b/bin/matlab`, we just want `/share/apps/matlab/2020b`). - `MATLAB_PATH`: directory containing the matlab install. diff --git a/singularity_env.sh b/singularity_env.sh index db1c7ba..b432280 100644 --- a/singularity_env.sh +++ b/singularity_env.sh @@ -12,11 +12,7 @@ export PATH=$FSLDIR/bin:$PATH if [ -f /home/sfp_user/spatial-frequency-preferences/config.json ]; then cp /home/sfp_user/spatial-frequency-preferences/config.json /home/sfp_user/sfp_config.json - sed -i 's|"DATA_DIR":.*|"DATA_DIR": "/home/sfp_user/sfp_data",|g' /home/sfp_user/sfp_config.json sed -i 's|"MRI_TOOLS":.*|"MRI_TOOLS": "/home/sfp_user/MRI_tools",|g' /home/sfp_user/sfp_config.json sed -i 's|"GLMDENOISE_PATH":.*|"GLMDENOISE_PATH": "/home/sfp_user/GLMdenoise",|g' /home/sfp_user/sfp_config.json sed -i 's|"VISTASOFT_PATH":.*|"VISTASOFT_PATH": "/home/sfp_user/vistasoft",|g' /home/sfp_user/sfp_config.json - sed -i 's|"WORKING_DIR":.*|"WORKING_DIR": "/home/sfp_user/sfp_data/preproc_tmp_dir",|g' /home/sfp_user/sfp_config.json - mkdir -p /home/sfp_user/sfp_data/preproc_tmp_dir - echo "this is a temporary directory created for preprocessing, and can be deleted" > /home/sfp_user/sfp_data/preproc_tmp_dir/delete_me.txt fi