From a0857e7bc1966c28c6d8e1627bfd65ff16e043ab Mon Sep 17 00:00:00 2001
From: Steven Meisler <smeisler@g.harvard.edu>
Date: Mon, 23 Aug 2021 14:52:01 -0400
Subject: [PATCH 1/3] change srun to sbatch; add tmpdir

---
 scripts/mit_slurm/bootstrap_fmriprep.sh | 21 +++++++++++++++------
 1 file changed, 15 insertions(+), 6 deletions(-)
 mode change 100755 => 100644 scripts/mit_slurm/bootstrap_fmriprep.sh

diff --git a/scripts/mit_slurm/bootstrap_fmriprep.sh b/scripts/mit_slurm/bootstrap_fmriprep.sh
old mode 100755
new mode 100644
index e30e9a0..da61b80
--- a/scripts/mit_slurm/bootstrap_fmriprep.sh
+++ b/scripts/mit_slurm/bootstrap_fmriprep.sh
@@ -41,10 +41,18 @@ fi
 BIDSINPUT=$1
 if [[ -z ${BIDSINPUT} ]]
 then
-    echo "Required argument is an identifier of the BIDS source"
+    echo "First required argument is an identifier of the BIDS source"
     # exit 1
 fi
 
+TMPDIR=$2
+if [[ -z ${TMPDIR} ]]
+then
+    echo "Second required argument is a path to temporary working directory"
+    # exit 1
+fi
+mkdir -p "${TMPDIR}"
+
 # Is it a directory on the filesystem?
 BIDS_INPUT_METHOD=clone
 if [[ -d "${BIDSINPUT}" ]]
@@ -111,7 +119,7 @@ pushgitremote="$2"
 subid="$3"
 # change into the cluster-assigned temp directory. Not done by default in SGE
 # TODO: change to local tempdir assigned by SLURM
-cd ${CBICA_TMPDIR}
+cd ${TMPDIR}
 # OR Run it on a shared network drive
 # cd /cbica/comp_space/$(basename $HOME)
 # Used for the branch names and the temp dir
@@ -202,7 +210,8 @@ rm -rf prep .git/tmp/wkdir
 EOT
 
 chmod +x code/fmriprep_zip.sh
-cp ${FREESURFER_HOME}/license.txt code/license.txt
+#cp ${FREESURFER_HOME}/license.txt code/license.txt
+cp /om2/user/smeisler/TheWay/scripts/mit_slurm/license.txt code/license.txt #REMOVE THIS LATER
 
 mkdir logs
 echo .SLURM_datalad_lock >> .gitignore
@@ -226,14 +235,14 @@ wget -qO- ${MERGE_POSTSCRIPT} >> code/merge_outputs.sh
 # SLURM SETUP START - remove or adjust to your needs
 ################################################################################
 env_flags="--export=DSLOCKFILE=${PWD}/.SLURM_datalad_lock"
-echo '#!/bin/bash' > code/srun_calls.sh
+echo '#!/bin/bash' > code/sbatch_calls.sh
 dssource="${input_store}#$(datalad -f '{infos[dataset][id]}' wtf -S dataset)"
 pushgitremote=$(git remote get-url --push output)
 eo_args="-e ${PWD}/logs -o ${PWD}/logs"
 for subject in ${SUBJECTS}; do
-  echo "srun ${env_flags} --job-name=fp${subject} ${eo_args} \
+  echo "sbatch ${env_flags} --job-name=fp${subject} ${eo_args} \
   ${PWD}/code/participant_job.sh \
-  ${dssource} ${pushgitremote} ${subject} " >> code/srun_calls.sh
+  ${dssource} ${pushgitremote} ${subject} " >> code/sbatch_calls.sh
 done
 datalad save -m "SLURM submission setup" code/ .gitignore
 

From 24deb1006c0fe1103aa9f0e4f9df1035be681db5 Mon Sep 17 00:00:00 2001
From: jsmentch <jsmentch@gmail.com>
Date: Mon, 23 Aug 2021 15:06:03 -0400
Subject: [PATCH 2/3] fix fmriprep container path

---
 scripts/mit_slurm/bootstrap_fmriprep.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/mit_slurm/bootstrap_fmriprep.sh b/scripts/mit_slurm/bootstrap_fmriprep.sh
index da61b80..08a64a2 100644
--- a/scripts/mit_slurm/bootstrap_fmriprep.sh
+++ b/scripts/mit_slurm/bootstrap_fmriprep.sh
@@ -159,7 +159,7 @@ datalad run \
     -i code/fmriprep_zip.sh \
     -i inputs/data/${subid} \
     -i inputs/data/*json \
-    -i containers/.datalad/environments/fmriprep-20-2-3/image \ # FIX!!
+    -i /om4/group/gablab/data/containers/images/bids/bids-fmriprep--20.2.3.sing
     --explicit \
     -o ${subid}_fmriprep-20.2.3.zip \
     -o ${subid}_freesurfer-20.2.3.zip \
@@ -189,7 +189,7 @@ subid="$1"
 mkdir -p ${PWD}/.git/tmp/wdir
 # TODO: fix path to singularity image
 singularity run --cleanenv -B ${PWD} \
-    containers/.datalad/environments/fmriprep-20-2-3/image \ # FIX!!
+    /om4/group/gablab/data/containers/images/bids/bids-fmriprep--20.2.3.sing
     inputs/data \
     prep \
     participant \

From a9315add42991c318a8a92a14dd8da2bab641c2b Mon Sep 17 00:00:00 2001
From: jsmentch <jsmentch@gmail.com>
Date: Mon, 23 Aug 2021 17:02:01 -0400
Subject: [PATCH 3/3] add datalad get singularity iamge

---
 scripts/mit_slurm/bootstrap_fmriprep.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/mit_slurm/bootstrap_fmriprep.sh b/scripts/mit_slurm/bootstrap_fmriprep.sh
index 08a64a2..f5abc7f 100644
--- a/scripts/mit_slurm/bootstrap_fmriprep.sh
+++ b/scripts/mit_slurm/bootstrap_fmriprep.sh
@@ -102,6 +102,7 @@ fi
 
 CONTAINERDS=///repronim/containers
 datalad install -d . --source ${CONTAINERDS}
+datalad get containers/images/bids/bids-fmriprep--20.2.3.sing
 
 ## the actual compute job specification
 cat > code/participant_job.sh << "EOT"
@@ -159,7 +160,7 @@ datalad run \
     -i code/fmriprep_zip.sh \
     -i inputs/data/${subid} \
     -i inputs/data/*json \
-    -i /om4/group/gablab/data/containers/images/bids/bids-fmriprep--20.2.3.sing
+    -i containers/images/bids/bids-fmriprep--20.2.3.sing
     --explicit \
     -o ${subid}_fmriprep-20.2.3.zip \
     -o ${subid}_freesurfer-20.2.3.zip \
@@ -187,9 +188,8 @@ cat > code/fmriprep_zip.sh << "EOT"
 set -e -u -x
 subid="$1"
 mkdir -p ${PWD}/.git/tmp/wdir
-# TODO: fix path to singularity image
 singularity run --cleanenv -B ${PWD} \
-    /om4/group/gablab/data/containers/images/bids/bids-fmriprep--20.2.3.sing
+    containers/images/bids/bids-fmriprep--20.2.3.sing
     inputs/data \
     prep \
     participant \