sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
aaba6ad6ca37c27ac51a06f02401c2679770943faf1f9a7252501617e217da41 | Shell | 320 | 7 | LOCALDIR=/Users/akre96/Documents/github/rrbs_bismark/Trim_Reads
cd $LOCALDIR
## Run on cloud
#java -Dconfig.file=google.conf -jar ~/cromwell/cromwell-36.jar run RunBismark.wdl -i RunBismark_inputs_GCloud.json
## Run locally (test)
java -jar ~/cromwell/cromwell-36.jar run trim_reads.wdl -i trim_reads_inputs_Local.json
|
6308d5dedb138320e55a548a3066fb2d84170880f75645d60ef497b1db01b8e9 | Shell | 321 | 6 | conda create -n GeoMPNN python=3.10 -y
conda activate GeoMPNN
pip install lips-benchmark[recommended] airfrans dill torch_geometric gpustat
pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.0.1+cu117.html
pip install tensorboard --upgrade
pip install -e .... |
eaf1f6bdf99736d43e7c3e3e0f1168e67f94e40ecbda6a4a0c4477db3cb16d1e | Shell | 323 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_mid
01_scripts/42_eval_t1.sh $R... |
cbd9e71f819e2bb6351a4984f8ff6cabded99003023a399e474ff220a08e2a19 | Shell | 324 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_apex
01_scripts/42_eval_t1.sh $... |
f8c9e568d007712b6f4dd23ab6dffdf5c69229649ac090da06c024a2c8b460b0 | Shell | 324 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_base
01_scripts/42_eval_t1.sh $... |
294140b16f9b2c3229d944b495bc9b910bb16d0f81ae140fb1af01e25b3633e4 | Shell | 325 | 6 | DATA_FOLDER=../../data
OUTPUT_FOLDER=../../outputs/provenance
(python --version && pip list && pip freeze) > $OUTPUT_FOLDER/environment.txt
python psd_by_trial_type.py $DATA_FOLDER/i140703-001.nix $DATA_FOLDER/l101210-001.nix --output_path=$OUTPUT_FOLDER --skip_channels="0;2,4" > $OUTPUT_FOLDER/psd_by_trial_type.out ... |
b1b57121ee9edff6db8811263bc86d870ace8c36e1a98b001871db2fe81f181e | Shell | 326 | 10 | python -m train \
experiment=hg38/chipseq \
wandb.mode=online \
wandb.group=Chipseq \
wandb.name=train_inf_gpt_small_gm12878 \
hydra.run.dir="./outputs/chipseq/train_inf_gpt_small_gm12878" \
model.config.n_layer=12 \
model.config.n_head=12 \
model.config.n_embd=768 \
dataset.batch_si... |
f726f1240dd73063d91c74f08f201b80d3dadb8de6e1d35db8460f8d2785f8c8 | Shell | 326 | 6 | # usage: source setup.sh
conda create -n GFNO python=3.8 -y
conda activate GFNO
conda install pytorch==1.12.1 torchvision==0.13.1 torchaudio==0.12.1 cudatoolkit=11.6 -c pytorch -c conda-forge -y
conda install scipy numpy h5py conda gfortran tensorboard gpustat -c anaconda -c conda-forge -y
pip install e2cnn escnn zarr ... |
40d45bab125f5ebc3aef81cf1350ca47ac7037c60170ee4530cec2a2b1088252 | Shell | 327 | 15 | #!/bin/bash
echo "MuTILs container is running..."
docker run \
--name Mutils \
--gpus '"device=0,1,2,3,4"' \
--rm \
-it \
-v /path/to/the/slides:/home/input \
-v /path/to/the/output:/home/output \
-v /path/to/the/mutils/models:/home/models \
--ulimit core=0 \
szolgyen/mutils:v2 \
... |
a6d6b0ef0f8c81d345b435e7de3a5894ba0649d73df327ea2f3e7a91110990da | Shell | 327 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0082_vis1
01_scripts/41_eval_rt.sh -s16 -... |
ff171d441d0e82f35b035f5004c5ab172ec748359c722e6f45795538eb5683c4 | Shell | 327 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0056_vis1
01_scripts/41_eval_rt.sh -s13 -... |
89b4c2b144499ed5dd67e0af23884e3e7f508d3e0e92c12199efc5b39c29ee98 | Shell | 328 | 6 | DATA_FOLDER=../../data
OUTPUT_FOLDER=../../outputs/no_provenance
(python --version && pip list && pip freeze) > $OUTPUT_FOLDER/environment.txt
python psd_by_trial_type.py $DATA_FOLDER/i140703-001.nix $DATA_FOLDER/l101210-001.nix --output_path=$OUTPUT_FOLDER --skip_channels="0;2,4" > $OUTPUT_FOLDER/psd_by_trial_type.o... |
d0e8cdf4289698854a4481ac020e2698af9df692791ce2963ed2892ae0988284 | Shell | 328 | 12 | #!/bin/sh
#SBATCH --account=theory
#SBATCH --cpus-per-task=2
#SBATCH --mem-per-cpu=16gb
#SBATCH --output=PlasticRecall_%x_R=%a.out
#SBATCH --array=1,2,5
echo $SLURM_ARRAY_TASK_ID
echo $SLURM_JOB_NAME
echo $SLURM_JOB_ID
stdbuf -oL python script_delayed_recall.py $SLURM_ARRAY_TASK_ID $SLURM_JO... |
8402a5150d482baefe3332fddf19f2beae35083fc3e6ce6bec50522c03ed5cc9 | Shell | 334 | 11 | #!/bin/bash
srun="srun --exclusive -N1 -n1"
mkdir -p logs
parallel="parallel --delay .2 -j $SLURM_NTASKS --joblog logs/parallel_${SLURM_JOB_ID}.log --resume"
$parallel "$srun scripts/sequencing_stats.sh {1} > logs/parallel.${SLURM_JOB_ID}_{1}.log" ::: $(eval echo -e {1..$(ls star/*.Aligned.sortedByCoord.out.bam | w... |
213102772c222b351303e94845eaa52053a6320a5786d2394507b9ff6d94431c | Shell | 335 | 18 | #!/bin/sh
python doCleanPDBs.py
ls -1 *.pdb | grep -v "Het" | cut -f1 -d"." > ids.lst
mv ppicket-frame.tzd ppicket-frame.pml
for i in `cat ids.lst`
do
echo $i
export theExpr="s/FRAME/$i/g"
echo $theExpr
cat ppicket-frame.pml | sed $theExpr > $i.pml
done
mv ppicket-frame.pml ppicket-frame.tzd
ls *.pml -1 | xargs -... |
2bc669fa0619e70d6fd277364f201c8524ad04182eb21206b168fa85ef74c40c | Shell | 335 | 10 | #!/bin/sh
mkdir -p "database/mirbase/hsapiens"
mkdir -p "database/mirbase/mmusculus"
export ftp_proxy=${http_proxy}
wget "ftp://mirbase.org/pub/mirbase/22.1/genomes/mmu.gff3" -O "database/mirbase/mmusculus/mirbase_mmu.gff3"
wget "ftp://mirbase.org/pub/mirbase/22.1/genomes/hsa.gff3" -O "database/mirbase/hsapiens/mir... |
8e85248b2533dd09fbccb8f41e9b2310b1c76cfb13e1884999b642a11c00bef1 | Shell | 338 | 6 | #!/bin/bash
#Generic script takes in one input.json file for a sample and runs the pipeline
#$1 is the input.json file
#Usage : for i in `cat ids3.txt`;do ./submit_rnaseq_pilot_generic.sh $i;done
java -Dconfig.file=google.conf -jar /Users/archanaraja/work/tools/cromwell-38.jar run rnaseq_pipeline_pilot.wdl -i "$1"
echo... |
9745b56ddea7a5c0353084233ba55a5f4c485445d513d12d9cd4effd78d301ce | Shell | 338 | 23 | module load afni
cd /project/4180000.19/multiRat/to_trim
ls ./ | while read line
do
echo $line
cd ${line}
cd anat
nii=$(ls *.nii.gz)
mv $nii tmp.nii.gz
3dWarp -oblique2card -prefix $nii tmp.nii.gz
rm tmp.nii.gz
cd ../func
nii=$(ls *.nii.gz)
mv $nii tmp.nii.gz
3dWarp -oblique2card -prefix $nii tmp.nii.gz
rm tmp.nii.... |
619c68fadb34fbf734c2d1a5e6ee7e74ebe20bcab9f360f3adb435f9c7827285 | Shell | 340 | 6 | URL1=https://people.eecs.berkeley.edu/~taesung_park/projects/CycleGAN/models/places_vgg.caffemodel
MODEL_FILE1=./models/places_vgg.caffemodel
URL2=https://people.eecs.berkeley.edu/~taesung_park/projects/CycleGAN/models/places_vgg.prototxt
MODEL_FILE2=./models/places_vgg.prototxt
wget -N $URL1 -O $MODEL_FILE1
wget -N $U... |
6af07c3baa9cf8b2bdbe81a66e759cb6a2ee6fbbd8f72ed219424b93e5c0e9f8 | Shell | 340 | 12 | runai submit \
--name sgospm12-abcd-p2 \
--image 10.202.67.207:5000/wds20:sgospm12 \
--backoff-limit 0 \
--gpu 0 \
--cpu 1 \
--large-shm \
--node-type dgx2-a \
--host-ipc \
--project wds20 \
--volume /nfs/home/wds20/sergio/project/data/ABCD/rawtovbm:/data \
--command -- /opt/spm12/spm12 batch /dat... |
e67b5781c3b655cf98b1f7a5db8f6766910d9ddec6b81633d3dfad671fc75550 | Shell | 341 | 12 | runai submit \
--name sgospm12-bhrcs-p2 \
--image 10.202.67.207:5000/wds20:sgospm12 \
--backoff-limit 0 \
--gpu 0 \
--cpu 1 \
--large-shm \
--node-type dgx2-a \
--host-ipc \
--project wds20 \
--volume /nfs/home/wds20/sergio/project/data/INPD/rawtovbm:/data \
--command -- /opt/spm12/spm12 batch /da... |
130ceb7c2664fd123342509a8bbab89e722164de644995e84ae06ed42916cc81 | Shell | 342 | 4 | wget https://github.com/patience111/ARGNet/releases/download/v1.0.1/AELS_tall.h5
wget https://github.com/patience111/ARGNet/releases/download/v1.0.1/AESS_tall.h5
wget https://github.com/patience111/ARGNet/releases/download/v1.0.1/classifier-ls_tall.h5
wget https://github.com/patience111/ARGNet/releases/download/v1.0.1/... |
8293540badbb67664e941768eb1ba62778e93e752c641b2ec9f81ef8957b2f03 | Shell | 342 | 5 | # lambda genome
java -Dconfig.file=../google_prod_PAPI.conf -jar ../../../tools/cromwell-40.jar run Bismark_IndexGenomes.wdl -i IndexGenomes_inputs_lambda_GCloud.json
#Rat (rn6 , v 96 annotations)
java -Dconfig.file=../google_prod_PAPI.conf -jar ../../../tools/cromwell-40.jar run Bismark_IndexGenomes.wdl -i IndexGenome... |
aab61ad79a71df7312459f3aea696c2a6c0e7f745bef5a6831f6c4e212119792 | Shell | 345 | 12 | runai submit \
--name sgospm12-abide2-p2 \
--image 10.202.67.207:5000/wds20:sgospm12 \
--backoff-limit 0 \
--gpu 0 \
--cpu 1 \
--large-shm \
--node-type dgx2-a \
--host-ipc \
--project wds20 \
--volume /nfs/home/wds20/sergio/project/data/ABIDE2/rawtovbm:/data \
--command -- /opt/spm12/spm12 batch ... |
1ea65db0937232f73c94add8532d4fdfa47ecb92d833845517c2713526884ae4 | Shell | 347 | 12 | runai submit \
--name sgospm12-adhd200-p2 \
--image 10.202.67.207:5000/wds20:sgospm12 \
--backoff-limit 0 \
--gpu 0 \
--cpu 1 \
--large-shm \
--node-type dgx2-a \
--host-ipc \
--project wds20 \
--volume /nfs/home/wds20/sergio/project/data/ADHD200/rawtovbm:/data \
--command -- /opt/spm12/spm12 batc... |
89090977b885f17cf62e54966566c7bb694b443ed3ac4960882a585fd9f0c15e | Shell | 351 | 6 | conda create -n DNA_Gen python=3.9
conda activate DNA_Gen
conda install pytorch==2.1.1 torchvision==0.16.1 torchaudio==2.1.1 pytorch-cuda=11.8 -c pytorch -c nvidia
pip install torch_geometric==2.5.2
pip install pytorch_lightning==1.8.6 wandb collections mamba-ssm==1.1.2 transformers scikit-learn torchmetrics
pip instal... |
e78b95072f2cf561c3861b6876717c7e37be7247e7e2acfd8f03a3d0cea1d375 | Shell | 351 | 6 | conda create -n GeneExp python=3.9
conda activate GeneExp
conda install pytorch==2.1.1 torchvision==0.16.1 torchaudio==2.1.1 pytorch-cuda=11.8 -c pytorch -c nvidia
pip install torch_geometric==2.5.2
pip install pytorch_lightning==1.8.6 wandb collections mamba-ssm==1.1.2 transformers scikit-learn torchmetrics
pip instal... |
716cd22a2ba631eff8d1f4b5c3c597a6dfd0a2337da2b825a7b228ac05dfa23e | Shell | 353 | 11 | #!/bin/bash
# to download references from igenomes awscli is needed
# conda create --name aws
# conda activate aws
# conda install -c conda-forge awscli
# conda activate aws
# from base dir run: bash bash/wes/00_download_igenomes.sh
aws s3 --no-sign-request --region eu-west-1 sync s3://ngi-igenomes/igenomes/Homo_sap... |
b59b28ff52086a1132583918e12ff5d61217c80aeb635249e7dd7dd5a35587dd | Shell | 353 | 12 | runai submit \
--name sgo-normativepsy-bash \
--image 10.202.67.207:5000/wds20:normativepsychiatry \
--backoff-limit 0 \
--gpu 0 \
--cpu 4 \
--large-shm \
--host-ipc \
--project wds20 \
--volume /nfs/home/wds20/sergio/normative_psychiatry:/project \
--volume /nfs/home/wds20/sergio/project/data/:/dat... |
26dad5598d48d0341e6f7505edefd38bc845eb66930901f8da8444b0de0d0524 | Shell | 354 | 8 | conda create -n pdearena python=3.8 -y
conda activate pdearena
pip install torch==1.12.1+cu113 torchvision==0.13.1+cu113 torchaudio==0.12.1 --extra-index-url https://download.pytorch.org/whl/cu113
pip install -e .
pip install pytorch-lightning==1.7.7 phiflow
pip install -U 'jsonargparse[signatures]'
pip install torchme... |
7e1b4c4ee15cb22b9754f3a3ae0c69112d3dd10a803b9e2bce8d596b1b1dd9b6 | Shell | 355 | 7 | LOCALDIR=/Users/akre96/Documents/github/rrbs_bismark/Trim_Reads/bash
cd $LOCALDIR
## Run on cloud
#java -Dconfig.file=../google.conf -jar ~/cromwell/cromwell-36.jar run ../tasks/fastQCe.wdl -i ../inputs/fastQC_inputs_GCloud.json
## Run locally (test)
java -jar ~/cromwell/cromwell-36.jar run ../wdl-tasks/fastQC.wdl -i ... |
981d4a2abb4ad0cb25bc4aa2b20a7871a44c7e18016ab3493c0bc52d40293700 | Shell | 355 | 26 | #!/usr/bin/bash
#load environment
source ~/.bashrc
#print user info
echo "$(id)"
# Define mlflow
export MLFLOW_TRACKING_URI=file:/project/mlruns
echo ${MLFLOW_TRACKING_URI}
# parse arguments
CMD=""
for i in $@; do
if [[ $i == *"="* ]]; then
ARG=${i//=/ }
CMD=$CMD"--$ARG "
else
CMD=$CMD"$i "
fi
don... |
06b588205dbd57afa934d572ee34d2a6afa4cbbcdb3b096b259e19b31e5e2497 | Shell | 356 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0082_vis1
01_scripts/41_eval_rt.sh -s16 -... |
80282d0e0aba709f9ee15d354fa8049f25509934d4f3555ead3a3889a07b18c8 | Shell | 356 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0056_vis1
01_scripts/41_eval_rt.sh -s13 -... |
bba91a0e5f4a1e31ee4c7f091638c430719970711e65c928d8ab71d111d8c44e | Shell | 356 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0056_vis1
01_scripts/41_eval_rt.sh -s13 -... |
db469d4af834f09dfe89430c02bddc5166ee17d23cacb68ba0901da4a1c44b11 | Shell | 356 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0082_vis1
01_scripts/41_eval_rt.sh -s16 -... |
ff863bf0af3a39fd0fa37945116669c4981534b61e706141d50e6e9623d8ba1e | Shell | 356 | 14 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=18.0G,h_vmem=20G,h_fsize=50G
#$ -N 'subset_genotypes'
#$ -o ./summary.out
#$ -e ./summary.out
GENOTYPE_DIR='../../../../../input/genotypes/subset_by_sex/shared_snps/_m'
module load plink/2.0
plink2 --bfile $GENOTYPE_DIR/LIBD_Brain_TopMed \
--keep ../../_m/keepFam.txt ... |
ebb55b2e997973ca99a403bc8bbe40744ebac149f1213538d9a746f93bfa4243 | Shell | 358 | 7 | LOCALDIR=/Users/akre96/Documents/github/rrbs_bismark/Trim_Reads/bash
cd $LOCALDIR
## Run on cloud
java -Dconfig.file=../google.conf -jar ~/cromwell/cromwell-36.jar run ../wdl-tasks/multiQC.wdl -i ../inputs/multiQC_inputs_GCloud.json
## Run locally (test)
#java -jar ~/cromwell/cromwell-36.jar run ../tasks/multiQC.wdl -... |
f435d09b6ea2b5069f001681fe93b49db3c70cde6b9bde6f78171b60f26a009b | Shell | 361 | 14 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_mid
NET=12_networks_t1/11_resne... |
23e4df457eb1d229ddd61c967a8a4497175568f10f040b2a6cb0c3f6d59f949a | Shell | 362 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0056_vis1
01_scripts/41_eval_rt.sh -s13 -... |
3b2bdb749eba265fcd02d562669a252b28ac5ae8acb2126cb076eabb2f25716a | Shell | 362 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0056_vis1
01_scripts/41_eval_rt.sh -s13 -... |
69bb6d4baaac5810c32c0c2eb6c78ded26a2410388f408a4f14f4858d442734d | Shell | 362 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0082_vis1
01_scripts/41_eval_rt.sh -s16 -... |
8b3a60bbbcdef270163cb0b521d732bb0ae551107b76c7b2dfb37055a95c7f21 | Shell | 362 | 14 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_base
NET=12_networks_t1/11_resn... |
9d1e20a71e84212b0a5857900dbe0556870a23e3d952dd7ee262fd0c85529419 | Shell | 362 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0082_vis1
01_scripts/41_eval_rt.sh -s16 -... |
a94aabcda2e887e74d510592843ddd8434821501eccede34d1dc7bd890fdafbc | Shell | 362 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0056_vis1
01_scripts/41_eval_rt.sh -s13 -... |
ab2bc57773aa5b59593151b27d1d67b0961d8fe6d0a0f130fe4c3acaa06c7743 | Shell | 362 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0082_vis1
01_scripts/41_eval_rt.sh -s16 -... |
b39eb0d2ba6774ecf4c31456aa5d4e99eeba18a77ced12281c0470e211212e84 | Shell | 362 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0082_vis1
01_scripts/41_eval_rt.sh -s16 -... |
eb1509cc24db539700ba8c40007310ec9bc66e5f7287c95ffc67315159df960f | Shell | 362 | 15 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_mid
NET=12_networks_t1/12_resne... |
f1ea9085e15e9f5cb516f9249667702dc09ec5a470d4ab2db1293b2707205cfd | Shell | 362 | 14 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_apex
NET=12_networks_t1/11_resn... |
febe359db7412f68f34f70a707b97f9c0d0dbb877835d874d818f50fa1613063 | Shell | 362 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0056_vis1
01_scripts/41_eval_rt.sh -s13 -... |
460efc8a22c7856163d97580c23f97de77260b1a6302bd106c072eb134938538 | Shell | 363 | 15 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_apex
NET=12_networks_t1/12_resn... |
c61a177a2ecf7f7f485bc7e2bbd17cb21f52dd441e72afe9b30c514d0d82ade3 | Shell | 363 | 8 | #!/bin/sh
#SBATCH --account=theory # The account name for the job.
#SBATCH -c 4 # The number of cpu cores to use.
#SBATCH --mem-per-cpu=8gb # The memory the job will use per cpu core.
#SBATCH --output=PlasticNet_R=%a_w2only_w1plusminus.out
#SBATCH --array=1-10,15,30
stdbuf -oL py... |
c930a3800e1755d70646032003ed1ab212029209c1718ed3157e8969bb5bfa30 | Shell | 363 | 15 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_base
NET=12_networks_t1/12_resn... |
6575173a7ee2e66d8e2010923a6a056da664f2d985a296e8e22ea39101beaf0b | Shell | 364 | 15 | #!/bin/bash
#
# Script to build the Docker image to train the models.
#
# $ create_dockerimage.sh
set -ex
TAG=normativepsychiatry
docker build --network=host --tag "10.202.67.207:5000/${USER}:${TAG}" -f ./Dockerfile . \
--build-arg USER_ID=$(id -u) \
--build-arg GROUP_ID=$(id -g) \
--build-arg USER=${USER}
doc... |
97c8c76b511ad339f79c7e104c043e808ae5c09f56d6415b607190e0586a18a6 | Shell | 366 | 7 | LOCALDIR=/Users/akre96/Documents/github/rrbs_bismark/Trim_Reads/bash
cd $LOCALDIR
## Run on cloud
#java -Dconfig.file=../google.conf -jar ~/cromwell/cromwell-36.jar run ../tasks/attachUMI.wdl -i ../inputs/attachUMI_inputs_GCloud.json
## Run locally (test)
java -jar ~/cromwell/cromwell-36.jar run ../wdl-tasks/attachUMI... |
0f842d9623f4099ed8f4f3e9538973770221b702d8bf6e3f05d0cf6f3adc4172 | Shell | 367 | 14 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_mid
NET=12_networks_t1/13_resne... |
6ff9520883d00c150a9eb473dca15354230c3c14de4dde0c4c8133f78e49cb0c | Shell | 367 | 15 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_mid
for NET in 12_networks_t1/*... |
8876731cab75583aad1720f33c506cf1ee43e13026802a829816e031f99cf2bc | Shell | 367 | 14 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_mid
NET=12_networks_t1/21_rovir... |
cb98f17b2b0fd86d48083bd3d4a2583551b541512a7668dd689898d7877cf1fa | Shell | 367 | 14 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_mid
NET=12_networks_t1/22_rovir... |
dc18d15df0f9f61761fa7a88dd11aac655f748c69c4a6f8bd8aee5b460f327ea | Shell | 367 | 13 | OUTPUT_FOLDER=../../../outputs/provenance_snakemake
(
cd workflow || exit
mkdir -p $OUTPUT_FOLDER
(python --version && pip list && pip freeze) > $OUTPUT_FOLDER/environment.txt
snakemake $1 --cores 2 > $OUTPUT_FOLDER/snakemake.out 2>&1
python ../generate_gexf_from_prov.py --source_path=$OUTPUT_FOLDER --ou... |
ea2b2dffc454de20a5eaa69d1f2d21827c76202173f84fb254c6bc887236fa26 | Shell | 367 | 14 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_mid
NET=12_networks_t1/14_resne... |
3cc9229752611b2efda69f36df546486381c8505efcaaefa6282e475e3fb0c88 | Shell | 368 | 14 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_base
NET=12_networks_t1/14_resn... |
409ff8d859cad0d44aa5bbbfa27d13a63700440e189e4731d82633d9cb05e8cc | Shell | 368 | 15 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_apex
for NET in 12_networks_t1/... |
4d5556976f6a115864377d25d3eb8a5137b9a5434d5694b2957c9914098a593f | Shell | 368 | 14 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_base
NET=12_networks_t1/22_rovi... |
5096a5f670953056c3dc31d073545b392966799834673274bc762d397ec6967a | Shell | 368 | 14 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_base
NET=12_networks_t1/21_rovi... |
555575a8c236df831683a72485d67a5120edfdf35357d9e29c7158ccedbd6647 | Shell | 368 | 14 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_apex
NET=12_networks_t1/21_rovi... |
5ff9e2743bef85e446dd3f4663cbb1e619affaa9fe4653e142a1ee8ad42ac8d0 | Shell | 368 | 14 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_base
NET=12_networks_t1/13_resn... |
7604e9c1276066c94de1b8ff10541287b061e62aa0de781bc5059ef24ec6f26e | Shell | 368 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0082_vis1
01_scripts/41_eval_rt.sh -s16 -... |
778e83a56089869f2fe68e2692b1801607206accbb1114704cce334d9129a822 | Shell | 368 | 14 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_apex
NET=12_networks_t1/13_resn... |
84c9e528adf1b4f19aafeb6f659ce2d6d5407b572136da318607ed082377fd58 | Shell | 368 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0082_vis1
01_scripts/41_eval_rt.sh -s16 -... |
ad6cdaead8eb462508c19d9bc6836ce55d93394281cd09ebe085288e46bacd00 | Shell | 368 | 15 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_base
for NET in 12_networks_t1/... |
b23196d8bbefb5f21209ee7928cd47bc87eb133481bce54aa127861fa93d68ed | Shell | 368 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0056_vis1
01_scripts/41_eval_rt.sh -s13 -... |
b4c5f8138ff9b694495408c270b6a3c22ba5fd0095fcce2a08606a89b8c88d2e | Shell | 368 | 14 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_apex
NET=12_networks_t1/14_resn... |
bddd706208cdc1309ac7f9a9f6080087055a801ef4747a71cda55968c3e083ae | Shell | 368 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0056_vis1
01_scripts/41_eval_rt.sh -s13 -... |
c6d9a0afef0f070c992bf2df957c330deea3db0eca077c0f0ddc6e38c604ac51 | Shell | 368 | 14 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_apex
NET=12_networks_t1/22_rovi... |
91b4facc266eb8d0a9fd67a4749442364eec53b90d928ec34e9f5280c6a9ba79 | Shell | 370 | 3 | python /mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/scripts/scripts_for_Feany_lab_omicsintegrator/parameter_select.py \
/mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/output/Glia/Glia_randomization_results.pkl W_6.00_B_10.00_G_5.00 \ "{}.augmented_forest.graphml" \
"/mnt/data0/projects/bio... |
c4c7a7b6d19bc49c02031946126aae32c4880ba847134eaf17a610a97d0a8b79 | Shell | 370 | 6 | #!/bin/sh
# まずはヘッダーを作成
echo 'sample\tgroup\tpath' > sample2condition.txt
# サンプル名はRun、群はdiseasestatusの項目、パスはSRR IDに.genes.resultsを足したものなので、それらを記述したファイルを作成する。
tail -n+2 $1 | awk 'BEGIN{FS="\t";OFS="\t"}{print $7,$14,$7".genes.results"}' >> sample2condition.txt
|
6a78a351596d42de24ca2aa3fc775400863bad568809e9e9a7f759e0f5d0e75d | Shell | 371 | 18 | #!/usr/bin/env bash
# definitions
origDir=/vols/Scratch/preclinicalMPM_scripts
workDir=/vols/Scratch/comparative_scripts/mouse_MPM_results
maptype="MT R1 R2"
template=/vols/Scratch/comparative_scripts/registrations/QBI_atlas_2mm_v6.nii
for map in $maptype; do
echo "$map"
fslmerge -t $workDir/all_"$map" $workDir/"$... |
3f7b6e5ae3c2ba48566534743057d1a900abe1b2822bb9353ea557efc107f8df | Shell | 373 | 14 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_mid
NET=12_networks_t1/23_rovir... |
993096898c47f7e2c435669d87217998e54c33f20a7324590e0d1df6e3e0bc77 | Shell | 373 | 14 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_mid
NET=12_networks_t1/24_rovir... |
20a6bdea65a452e1c328f7cab5f6e5b731c176ae7a5103646002f369fb84a4b0 | Shell | 374 | 14 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_base
NET=12_networks_t1/23_rovi... |
4effe814cea8fffc02de990398645956e80b50a0c2f2af877af27d7f75c57444 | Shell | 374 | 14 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_apex
NET=12_networks_t1/23_rovi... |
8c599852402d20bcc3258e388eb45f0a93b033026d15da893f5748042cfeed73 | Shell | 374 | 14 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_apex
NET=12_networks_t1/24_rovi... |
8f02e7f70c0dcda308dbbfd2805dd22f5d3415839518cd1691fe92cea0a88d04 | Shell | 374 | 14 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/t1_sa/vol0084_vis1_base
NET=12_networks_t1/24_rovi... |
1dca4b566427f87b4a0db7348adc40bf2197da8cca3839e18b9a802d7e2dd58c | Shell | 375 | 14 | #!/bin/bash
chr=$(echo {1..20} | cut -d ' ' -f $SLURM_ARRAY_TASK_ID)
genome=genomes/Mmul_10.dna.fa
mkdir -p vcf
gatk --java-options '-Xmx64g' HaplotypeCaller \
--reference ${genome} \
$(ls bam/*.recalibrated.chr${chr}.bam | sed 's/^/--input /g') \
--standard-min-confidence-threshold-for-calling 20.0 \
--output ... |
9d3f0152e44f6e372fbca8a6ff775964c7c87f11670e331ab046b15d14bcaaaf | Shell | 375 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0056_vis1
01_scripts/41_eval_rt.sh -s13 -... |
e4568d37a450a022e9a6b00b36e8fe126210de4dca0d8ba1aecc071ed521fc12 | Shell | 375 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0082_vis1
01_scripts/41_eval_rt.sh -s16 -... |
3ee9dd8e4c2004094b5c727f0d38195e840fece9aa5991d10e19f36669b92f52 | Shell | 376 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0082_vis1
01_scripts/41_eval_rt.sh -s16 -... |
ab09bc59950fe99a9859d1e8be145f9a8d4263300fa7e4448ac8dad62edf3a64 | Shell | 376 | 7 | #!/bin/bash
# Here, we're making some unconditional designs
# We specify the path for the outputs
# We tell RFdiffusion that designs should be 100-200 residues in length (randomly sampled each design)
# We generate 10 such designs
../scripts/run_inference.py inference.output_prefix=example_outputs/design_unconditional... |
bb988ea15af3d8095acc11cd48810793a17792812c6c06540345fbb22980e7dd | Shell | 376 | 13 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0056_vis1
01_scripts/41_eval_rt.sh -s13 -... |
8967631b83a066f61a0383c5566b8aac9a5509f1efc9a49edd8ab79140eb6c20 | Shell | 377 | 18 | #!/usr/bin/env bash
[[ ! -d .git ]] && echo "You need to be in the root directory of the repo" && exit
changed=0
for f in $(find Intern -name "*.cpp" -or -name "*.h")
do
oldhash=$(md5sum "$f")
clang-format -i "$f"
newhash=$(md5sum "$f")
if [[ ! "$oldhash" == "$newhash" ]]; then
echo Formattin... |
9ec174f83577c252baa2fe04d0a842a0b5e951b71362c722cfdcc90a60a3a696 | Shell | 377 | 8 | conda create -n shockCast python==3.10 -y
conda activate shockCast
conda install -c conda-forge ffmpeg -y
# pip install torch==1.12.1+cu116 torchvision==0.13.1+cu116 torchaudio==0.12.1 --extra-index-url https://download.pytorch.org/whl/cu116
# https://stackoverflow.com/a/56889729/10965084
python -m pip install -r ../... |
539eddf2edd03aebab18ea21fc8b4c542666d1cb0e1dac7f6a4cabac48cdbde2 | Shell | 379 | 15 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0082_vis1
for NET in 11_networks_rt/{3,4,... |
5e9d8aa4712ab18cfff89f133f6da9e5def6ef09f414e3d5bac28f4ac3e18661 | Shell | 379 | 7 | LOCALDIR=/Users/akre96/Documents/github/rrbs_bismark/Align_Trimmed
cd $LOCALDIR
## Run on cloud
#java -Dconfig.file=/Users/akre96/Documents/github/rrbs_bismark/google.conf -jar ~/cromwell/cromwell-36.jar run align_trimmed.wdl -i align_trimmed_inputs_GCloud.json
## Run locally (test)
java -jar ~/cromwell/cromwell-36.ja... |
eb984888e9d6008d4b30eb136ab50f1d59be5ab3642efa20a581ce47222c66c9 | Shell | 379 | 15 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR/..
RAWDIR=${RAWDIR:-$SCRIPT_DIR/../00_data/10_raw_data}
RAW=$RAWDIR/rt_sa/vol0056_vis1
for NET in 11_networks_rt/{3,4,... |
59058a95427b09d2651db057e6bb07a96d98e4b7ec5fe3cf0c3a81537f734e58 | Shell | 381 | 15 | #!/bin/bash
#SBATCH -p gpu
#SBATCH --mem=128g
#SBATCH --gres=gpu:a100:1
#SBATCH -c 12
#SBATCH -t 7-00:00:00
#SBATCH --output=exp_020.out
source activate mlfold-test
python ./training.py \
--path_for_outputs "./exp_020" \
--path_for_training_data "path_to/pdb_2021aug02" \
--num_example... |
b73898c5d6af98ad24e60327e9f817b9ed96588a8d28ef43dd18f23e5d82b87e | Shell | 383 | 1 | python /mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/scripts/scripts_for_Feany_lab_omicsintegrator/parameter_select.py /mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/output/Glia_OL_CB/Glia_OL_CB_randomization_results.pkl W_6.00_B_10.00_G_5.00 "{}.augmented_forest.graphml" "/mnt/data0/projec... |
d27a6a4e8ced4b487a99da38e2ff70edea0cf250c2fed532452c49f9d4c93b1d | Shell | 383 | 14 | # gpt
ROOT_PATH=""
model_path="$ROOT_PATH/outputs/promoter/train_inf_gpt/checkpoints/val/sei_promoter.ckpt"
python -m train \
experiment=hg38/promoter \
wandb.mode=online \
wandb.group=PromoterGen \
wandb.name=gen_gpt \
hydra.run.dir=./outputs/promoter/gen_gpt \
dataset.batch_size=16 \
tra... |
7f21819709950e4659a43cb7f8e8155ad68906c1ed0a648d371b98345d8a1e33 | Shell | 385 | 16 | #!/bin/bash
#$ -l tmem=7G
#$ -l h_vmem=7G
#$ -l h_rt=40:00:00
#$ -l scratch0free=10G
#$ -l tscratch=10G
#$ -S /bin/bash
#$ -N chsaw-ss_mod
#$ -e ./logs
#$ -o ./logs
#$ -j y
#$ -t 1 #1-18892:1000
#$ -wd /SAN/cath/cath_v4_3_0/alphafold/chainsaw_on_alphafold/chainsaw
cat "$0"
cd /SAN/cath/cath_v4_3_0/alphafold/chainsaw_on... |
95a2ac30e0ac0e84a966006de4d1e38bff45fb8ec9376de0894f1401a69abd31 | Shell | 385 | 23 | #$ -cwd
#$ -R y
#$ -l h_fsize=50G
#$ -N 'go_enrichment'
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date -Is
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
module list
echo "**** Run GO plotting ****"
python... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.