sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
678a1e7c0428647a2fa916883854068fc5c6115425df24c9eb212aa77be0f450 | Shell | 482 | 7 | #$ -N partherit
#$ -cwd
#$ -q multi15.q
#$ -S /bin/bash
# Genomic SEM common factor results
/data/workspaces/lag/workspaces/lg-genlang/Working/SCRIPTS/23andMe/clap-beat_dyslexia/pleiotropyevo/ldsc/partherit_baseline.sh /data/clusterfs/lag/users/gokala/beat-dyslexiaevol/data/munged/GenomicSEM_multivarGWAS_CPM_dys_rhyim... |
788573e38988793575ffbf62403bf679d53bd65b9c0c8a1a6f63d1800f96c8c0 | Shell | 482 | 7 | #$ -N partherit
#$ -cwd
#$ -q multi15.q
#$ -S /bin/bash
# Genomic SEM common factor results
/data/workspaces/lag/workspaces/lg-genlang/Working/SCRIPTS/23andMe/clap-beat_dyslexia/pleiotropyevo/ldsc/partherit_baseline.sh /data/clusterfs/lag/users/gokala/beat-dyslexiaevol/data/munged/GenomicSEM_multivarGWAS_CPM_dys_rhyim... |
e27fb079eb74f3d854748b0d874c44d40e6858c0198cab354ffafdea601c4140 | Shell | 482 | 1 | python3 train.py --train_valid_path train_sequences.txt --foldify --delimiter tab --seed 42 --train_batch_size 1024 --train_workers 8 --valid_batch_size 4098 --valid_workers 8 --epoch_num 80 --batch_per_epoch 1000 --weights uniform --seqsize 150 --temp .TEMPDIR --use_single_channel --singleton_definition integer --gpu ... |
42f3d07bb819d6929291bbae00dfcda0e6505425c5dbe5d6e99431beb0b6e643 | Shell | 483 | 19 | #!/bin/bash
email=a.alemany@hubrecht.eu
Dt=15:00:00
Dmem=10G
threads=1
if [ $# -ne 2 ]
then
echo "Please, give these following inputs:"
echo "1) input root to fastq files"
echo "2) protocol [celseq1, celseq2, scscar]"
exit
fi
infq=$1
protocol=$2
echo "/hpc/hub_oudenaarden/aalemany/bin/mapandgo2/extr... |
6493c9dabdfda39c0d469933bd2173b61b6d4df132b8851c9376b184d5e9ba2f | Shell | 484 | 14 | #Cell Ranger to generate filtered feature-barcode matrices
#In linux terminal (not R)
#!/bin/sh
#SBATCH --account=humbio
#SBATCH --partition=ada
#SBATCH --nodes=1 --ntasks=40
#SBATCH --time=10:00:00
#SBATCH --job-name='sample_id'
#SBATCH --mail-user=...@....ac.za
#SBATCH --mail-type=BEGIN,END,FAIL
cellranger count -... |
6c5ac67a7e1d4357def09444288d81312735622da1975cb34f92c6c76dec9124 | Shell | 484 | 7 | #$ -N partherit
#$ -cwd
#$ -q multi15.q
#$ -S /bin/bash
# Genomic SEM common factor results
/data/workspaces/lag/workspaces/lg-genlang/Working/SCRIPTS/23andMe/clap-beat_dyslexia/pleiotropyevo/ldsc/partherit_baseline.sh /data/clusterfs/lag/users/gokala/beat-dyslexiaevol/data/munged/GenomicSEM_multivarGWAS_CPM_dys_rhyim... |
84c131b868b670885dd0e6110a4ae0d94d710c98be2c901619e105e7e1f6ad75 | Shell | 484 | 7 | #$ -N partherit
#$ -cwd
#$ -q multi15.q
#$ -S /bin/bash
# Genomic SEM common factor results
/data/workspaces/lag/workspaces/lg-genlang/Working/SCRIPTS/23andMe/clap-beat_dyslexia/pleiotropyevo/ldsc/partherit_baseline.sh /data/clusterfs/lag/users/gokala/beat-dyslexiaevol/data/munged/GenomicSEM_multivarGWAS_CPM_dys_rhyim... |
d91ce02d9aa9cfff4d61f23bcf1c7a30e784ec0b81935c782701c6ca689ca7a3 | Shell | 484 | 20 | viewpoint=V11O2
for viewpoint in train1_80k
do
python3 ../train_barlowTwins.py \
--max_epochs 100 \
--batch_size 512 \
--data_dir /data/lpandey/UT_Austin_EgocentricDataset/output_64x64Squished/${viewpoint} \
--seed_val 40 \
--dataset_size 80000 \
--backbone resnet_2blocks \... |
fbb5ac62038477adcc45dd2638e11e969a61ab7652042524a6f57df2bedc03f2 | Shell | 484 | 16 | #!/bin/bash
# File: run_Milnes_sensitivity.sh
# Author: Kelly Chang
# Date: Oct 2017
# Version: 1.0
#
# Description: Bash script to perform sensitivity analysis with bootstrap
# samples.
#
DRUGNAMES=(dofetilide bepridil sotalol quinidine cisapride terfenadine ondansetron chl... |
9276bdcafca8e3c964fca34f52825a837f957df22259f88f2815fffd3d02eedb | Shell | 486 | 16 | #!/bin/bash
echo ">> Loading ligand files from PDBBind"
wget http://pdbbind.org.cn/download/PDBbind_v2020_sdf.tar.gz
tar -xf PDBbind_v2020_sdf.tar.gz -C data/
rm PDBbind_v2020_sdf.tar.gz
echo ">> Loading similarity file from UniProt"
cd data/annotations/
wget https://ftp.uniprot.org/pub/databases/uniprot/current_rele... |
a6c1b4f71e867f5097b8f1df8ca9a81bdb6b0c12272ee6a7ffae9da831897374 | Shell | 487 | 13 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo "# Running ./ap_SequenceWeightingProtocol ./test_inputs/ferrodoxins.fasta"
./ap_SequenceWeightingProtocol ./test_inputs/ferrodoxins.fasta
echo "# Running ./ap_SequenceWeightingProtocol ./test_inputs/identical.fasta"
./ap_SequenceWeightingProtocol ./test... |
1208b4d26df690b62d3c26e639e50d7345e28266ce3b75f4a2755eae090d46a6 | Shell | 488 | 15 | #!/bin/sh
# test Open Babel with roundtripping if the test suite exists
# (just un-tar into this folder as "test-set" and it'll run)
echo
if [ -d test-set ]; then
echo "# Testing molecule file roundtripping..."
echo "# This test will take quite some time!"
echo "# and it currently always passes, so check... |
80253b99c947e562ae45f8b6c05543d2729244b31c88a6d375a9883946025eed | Shell | 488 | 14 | #!/bin/bash
echo "# Running ./polymer -polymer::n_beads=20 -sample:t_start=1.0 -sample:t_steps=1-sample:mc_inner_cycles=500 -sample:mc_outer_cycles=10 -sample::perturb::range=0.3 -sample:seed=82345 -v=INFO"
./polymer -polymer::n_beads=20 \
-sample:t_start=1.0 \
-sample:t_steps=1 \
-sample:mc_inner_cycles=500 \
-sa... |
8a2f8ddfa4bc688df7db8911aa8d12e4cd33c7ad7bf016edc843ec3bb51d5b74 | Shell | 490 | 14 | #!/bin/sh
DATADIR=/Users/ctsu0221/data/asl/fsl_course/
#DEBUG=--debug
oxasl -i ${DATADIR}/mpld_asltc --casl --iaf=tc --ibf=tis --slicedt=0.0452 \
--tis=1.65,1.9,2.15,2.4,2.65,2.9 --bolus=1.4 \
--fslanat=${DATADIR}/T1.anat --senscorr \
-c ${DATADIR}/aslcalib --tr=4.8 --cmethod=single --csf=${DATADIR}... |
9f267909a8ff388a87ae5a09299580dc9c7500e4f8b553c7d1b8701042310974 | Shell | 490 | 11 | #!/bin/sh
RES_DIR_ML="/home/webermau/rey-figure/lukas-final/final-aug_01/rey-multilabel-classifier/"
RES_DIR_REG="/home/webermau/rey-figure/lukas-final/final-reg_01/rey-regressor-v2"
angle=0
while [ $angle -le 45 ]; do
python eval_multilabel_semantic.py --results-dir $RES_DIR_ML --transform "rotation" --angles $ang... |
3645709d858c37f3e6a99541f36009b8450c7355222959ec7c6ec6602437bc76 | Shell | 491 | 26 | #!/bin/bash --login
#SBATCH --nodes=10
#SBATCH --ntasks-per-node=40
#SBATCH --time=10:00:00
#SBATCH --job-name='Multirun LFPy Circuit'
#SBATCH --account=rrg-etayhay
#SBATCH --mail-type=ALL
#SBATCH --mail-user=agmccrei@gmail.com
#SBATCH -o output1.out
#SBATCH -e error1.out
module load NiaEnv/2018a
module load intel/20... |
767f58c69ac01d22861d609a53b3a1f96e6a081a11c1f2c70f3bbe142194a870 | Shell | 491 | 19 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
mkdir -p outputs_from_test
echo -e "#Running ./ex_Quaternion test_inputs/2gb1.pdb"
./ex_Quaternion test_inputs/2gb1.pdb
./strc -in:pdb=test_inputs/2kwi.pdb -select:chains=B -out:pdb=peptide.pdb
echo "" > peptide_rot.pdb
for i in `seq 1 1 10`
do
echo "MOD... |
b5a311079d5cc6a329d70d623f6cef4a27a8060bc831d19960acbe812d9251e2 | Shell | 491 | 19 | #!/bin/bash
email=a.alemany@hubrecht.eu
Dt=15:00:00
Dmem=10G
threads=1
if [ $# -ne 2 ]
then
echo "Please, give these following inputs:"
echo "1) input root to fastq files"
echo "2) protocol [celseq1, celseq2, scscar, nla]"
exit
fi
infq=$1
protocol=$2
echo "/hpc/hub_oudenaarden/aalemany/bin/mapandgo2... |
ab04882e1c14456a30fa7530a5880d6713df46ad0486d34c700779d9a3528b89 | Shell | 492 | 19 | #!/bin/sh
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
progressFile=${1}
fullList=${2}
# Do not return until all jobs are finished
noJobs=`cat ${fullList} | wc -l`
noJobsDone=0
noJobsDonePrev=-1
while [ ${noJobsDone} -lt ${noJobs} ]; do
if [ ! ${... |
d5c1870c3b983d5455fa5ed8e339045c3c5948a0e4f55acb7303a86b0f33c7ae | Shell | 492 | 15 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "#Running ./ex_SelectChainBreaks test_inputs/4mcb.pdb"
./ex_SelectChainBreaks test_inputs/4mcb.pdb
echo -e "#Running ./ex_SelectChainBreaks test_inputs/5edw.pdb"
./ex_SelectChainBreaks test_inputs/5edw.pdb
echo -e "#Running ./ex_SelectChainBreaks te... |
1e3155c2bcc2e97627b1e34a974304e56fe8c4cf6ba3e78af3af73bb1b51cbed | Shell | 493 | 20 | sudo yum update -y
sudo yum install git
git clone https://github.com/caticoa3/malaria_hero.git
#transfer trained models
scp -i ~carlos/Desktop/AWS\ self\ guided\ tutorial/learning.pem -r models/ ec2-user@ec2-18-188-29-9.us-east-2.compute.amazonaws.com:~/malaria/models
sudo yum install docker -y
sudo service start doc... |
80408a63ad9d7b3c558f932d2b9f62e5fd48e5757a1087b3c0859e1a0ce25484 | Shell | 494 | 21 | #!/bin/bash -ex
. /usr/sbin/get_hive_home.sh
echo 'Determine hive version'
if [ "$HIVE_HOME" = "" ]
then
HIVE=hive
else
HIVE="$HIVE_HOME/bin/hive"
fi
export HIVE_VERSION_MAJOR=$($HIVE --version | grep -E '^Hive' | sed -E 's/Hive ([0-9])\..*/\1/')
if [ "$HIVE_VERSION_MAJOR" = "2" ] || [ "$HIVE_VERSION_MAJOR" ... |
e9f3a6dae8c4a8058b92f8e0355605b54ce779b76389485191df0573b2b78954 | Shell | 494 | 17 | #!/bin/bash
# File: run_IC50_mcmc.sh
# Author: Kelly Chang
# Date: Oct 2017
# Version: 1.0
#
# Description: Bash script to run Markov-chain Monte Carlo simulations for
# the 12 CiPA training drugs.
#
DRUGNAMES=(dofetilide bepridil sotalol quinidine cisapride terfenadine onda... |
118c575739cb8d5dee3b4d7ec818b7a505ca5bba7148db3bf8ccf92becd1395b | Shell | 496 | 12 | #!/bin/bash
### 1. configure the conda enviroment ###
source /opt/miniconda3/bin/activate WGS_analysis
### 2. set parameters ###
rscript=/home/siyuan/jobs/suzukii_WGS/genetic_diff/window_diversity/plot/plot_win_diversity.R
wd=/home/siyuan/jobs/suzukii_WGS/genetic_diff/window_diversity/plot
dd=/home/siyuan/jobs/suzuki... |
927bf852c7a00455fcf23faf346a2799459db7cb383f13bfc5a51797d927d716 | Shell | 496 | 15 | #!/bin/bash
#Purpose: This script loops through each output file and looks for phrase "without error" to indicate that freesurfer completed successfully. Returns a list of subjects that failed.
#PATHS
CODE_DIR=/fslgroup/fslg_spec_networks/compute/code/HCP_analysis/freesurfer
#LOOP
for file in ${CODE_DIR}/logfiles/*.... |
113085c2ffff672684e48934ff698be82c7e8e78dfab5af773df5c8853361aa6 | Shell | 499 | 40 | #!/bin/bash
G_SYNOPSIS="
NAME
pypi.sh
SYNOPSIS
pypi.sh <ver>
ARGS
<ver>
A version string to upload. Typically something like '0.20.22'.
DESCRIPTION
pypi.sh is a simple helper script to tag and upload a new version of pypi.sh
"
if (( $# != 1 )) ; then
echo "$G_SYNOPSIS"
exit 1
fi
VER=$1
g... |
440fa8db40baec337633f43e106937e8579203a56219b8c5e242d90162d3338a | Shell | 500 | 6 | #! /usr/bin/env bash
python /opt/elephant/script/convert_to_2d_labels.py /workspace/datasets/ISBI2021/Fluo-C3DH-A549
python /opt/elephant/script/convert_to_2d_labels.py /workspace/datasets/ISBI2021/Fluo-C3DH-H157
python /opt/elephant/script/convert_to_2d_labels.py /workspace/datasets/ISBI2021/Fluo-C3DL-MDA231
python /o... |
98175da10f8cf6e6b4a28f96c062712f995ed321f822ead6c47f5019e582ccde | Shell | 504 | 20 | #!/bin/bash
set -ex
# Mirror jenkins user in container
echo "jenkins:x:1014:1014::/var/lib/jenkins:" >> /etc/passwd
echo "jenkins:x:1014:" >> /etc/group
# Create $HOME
mkdir -p /var/lib/jenkins
chown jenkins:jenkins /var/lib/jenkins
mkdir -p /var/lib/jenkins/.ccache
chown jenkins:jenkins /var/lib/jenkins/.ccache
# ... |
85d1aaa4f07839a64f94803db0e4e5bec7109694492083347b82f13abb356ec4 | Shell | 505 | 20 | #!/bin/bash
#SBATCH --partition a100_short,a100_long
#SBATCH -t 03-00:00:00
#SBATCH --mem=40G
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=10
#SBATCH --gres=gpu:1
#SBATCH --job-name=TrainNN
#SBATCH --mail-type=FAIL
export JULIA_BIN=/gpfs/scratch/asslaj01/julia-1.10.0/bin/julia
set -Eeo pipefail
echo ... |
38955e7d686c29c83ce73311264700b2c1abd6779af78c206939c1a374e1c2f7 | Shell | 506 | 25 | #!/bin/bash
subj_ids=$1
ses=1
sample=MLS
task=reward
inp_path=/oak/stanford/groups/russpold/data/${sample}
if [ -z "$1" ]; then
echo
echo "Error: Missing list. Provide subject list w/o 'sub-' prefix in positon 1."
echo
exit 1
fi
n=0
cat $subj_ids | while read line ; do
sed -e "s|SUBJECT|${line}|g; s|SESSION|${... |
bec4ba81f5e67ee8a4b77acb024a7c738cd84f1c6b530eef23028ab4956757ba | Shell | 507 | 21 | viewpoint=V11O2
for viewpoint in train1_80k
do
python3 ../train_byol.py \
--max_epochs 100 \
--batch_size 512 \
--data_dir /data/lpandey/UT_Austin_EgocentricDataset/output_64x64Squished/${viewpoint} \
--seed_val 0 \
--dataset_size 80000 \
--backbone resnet_2blocks \
... |
a91e99335c03bb8ba3ccc47933069f9224044cf9be2a358a074a3763f92521ab | Shell | 508 | 19 | #!/bin/bash
# get transcript IDS for rRNA hits.
blastn=$1
fasta=$2
output_qseqid=$3
#output_fasta=$4
# Check if the pattern is present in the blastn file
if grep -q -E "rRNA,|, rRNA" $blastn; then
# If the pattern is found, extract the sequences
cat $blastn | grep -E "rRNA,|, rRNA" | cut -f 1 | sort | uniq >... |
385b9760c60fe24dbda38e6028808a68324541cbd4bf52312e16d28a2e213dd7 | Shell | 510 | 13 | #!/bin/bash
file_lift=$(ls | grep _lift.bed$)
for i in $file_lift
do
filename="${i%_lift.bed}"
bedtools intersect -a $filename"_t2t.bed" -b $filename"_lift.bed" -v > output/${filename}_t2t_specific.bed
awk -F '\t' -v OFS='\t' '{$2 = $2-1}1' output/${filename}_t2t_specific.bed > output/${filename}_t2t_spec... |
75837d7c726ef60fb609cb7c4574d7a2573fac07f98439d8f323d9b1c8073b11 | Shell | 510 | 9 | #!/bin/bash
#SBATCH --time=4-00:00:00
#SBATCH --mem=40G
#SBATCH --array=1
#SBATCH --output=/m/cs/scratch/networks-pm/fmriprep_sub30-%j.out
#SBATCH --cpus-per-task=4
module load singularity-fmriprep/22.1.0
singularity_wrapper exec fmriprep /m/cs/scratch/networks-pm/pm/ /m/cs/scratch/networks-pm/pm_preprocessed/ -w /m... |
75f56d477c725bb330a5ddc74ecb754663243cf5f36265365d3b81865baf78b6 | Shell | 510 | 20 | #!/bin/bash
# Set output directory
output_dir="nr"
mkdir -p "$output_dir"
# URL to the metadata file
nr_url="https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz"
# Fetch the nr file
file_name=$(basename "$nr_url")
echo "Downloading $file_name..."
curl -L -o "$output_dir/$file_name" "${nr_url}"
# Extract the... |
6e2d956e7f7b82822acd614a7eb59f6ec0a995da0815fe0a76ff0a13ddccf954 | Shell | 511 | 6 | python3 -W ignore scperb.py --model_name CD4T --exclude_celltype CD4T --data study
python3 -W ignore scperb.py --model_name CD14+Mono --exclude_celltype CD14+Mono --data study
python3 -W ignore scperb.py --model_name B --exclude_celltype B --data study
python3 -W ignore scperb.py --model_name CD8T --exclude_celltype CD... |
92f4ed88640e76570fba5431d78e6ca47e8e21e8aa073245ae40a8e6bf70a95a | Shell | 513 | 11 | #!/bin/sh
./bin2hex.pl atomtyp.txt AtomTypeData >atomtyp.h
./bin2hex.pl bondtyp.txt BondTypeData >bondtyp.h
./bin2hex.pl phmodel.txt PhModelData PHMODELDATA >phmodeldata.h
./bin2hex.pl resdata.txt ResidueData >resdata.h
./bin2hex.pl torlib.txt TorsionDefaults >torlib.h
./bin2hex.pl types.txt TypesData >types.h
./bin2h... |
eef9c4292f8d6b13485bf2a33178655d0193892bd6a2fc78f940f9bf95d80fe6 | Shell | 516 | 21 | #!/usr/bin/env bash
# Halt on error
set -e
echo "SCRIPT NOT READY"
exit 1
OUTDIR="./results-the-nn-way-v1"
# Iterate over different seeds here
for SEED in 20000; do
echo "Seed: $SEED"
for LEXP in data/LearningExp_*.txt; do
echo "Starting run with experiment data: $LEXP"
python3 train.py "$LEXP" --seed "$SEE... |
4f07c676b243ddd2521d69635179150027dfca469d2c6d2adada33e7c98176da | Shell | 517 | 13 | #!/bin/bash
mkdir -p ../testdata/bmdata
wget ftp://ftp.ensembl.org/pub/release-101/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz -O ../testdata/bmdata/human.fa.gz
gunzip --force ../testdata/bmdata/human.fa.gz
wget ftp://ftp.ensemblgenomes.org/pub/plants/release-48/fasta/arabidopsis_thaliana/dna/Arabidops... |
ae77a303ffd8213ed339069720649762f31602f4f6a9aebed25ef963e2f86d4e | Shell | 517 | 14 | #!/bin/bash -xe
apt-get install -y ${HIVE_PACKAGE} ${HIVE_PACKAGE}-server2
source /usr/sbin/get_hive_home.sh
find $HIVE_HOME/lib | grep '.jar' | \
grep -E 'hive-jdbc|hive-common|hive-exec|hive-service|hive-metastore|libfb303|libthrift' | \
tr '\n' ':' > /opt/hive-jdbc-cp
# hack for missing xerces classes in... |
e43f7b2176b1070724e0f523a3a12f884acbd07d102b64401aee12e7c9bea1ad | Shell | 517 | 24 | #!/usr/bin/env bash
# Check status of Slurm job
jobid="$1"
if [[ "$jobid" == Submitted ]]
then
echo smk-simple-slurm: Invalid job ID: "$jobid" >&2
echo smk-simple-slurm: Did you remember to add the flag --parsable to your sbatch call? >&2
exit 1
fi
output=`sacct -j "$jobid" --format State --noheader | head -n... |
467d63276f189decf1fb290fc835cc26261269eb6169543c3e40356f0d6bb7ce | Shell | 519 | 10 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo -e "#Running python3 ./superimpose_by_fragment.py test_inputs/2gb1.pdb test_inputs/2gb1-model1.pdb test_inputs/2gb1-model2.pdb test_inputs/2gb1-model3.pdb test_inputs/2gb1-model4.pdb"
python3 ./superimpose_by_fragm... |
d52d552184b70501ba08ac23885fde171f4a5813645cdc5ce0c2b57354716e06 | Shell | 519 | 17 | PDIR=`pwd`
cd $PDIR/geo1/WORK
${OVDIR}/scripts/read_civfl.py 2 0.998001 > prep.out
cd $PDIR/geo2/WORK
${OVDIR}/scripts/read_civfl.py 2 0.998001 >> prep.out
cd $PDIR/geo1.6-31g/WORK
${OVDIR}/scripts/read_civfl.py 4 0.99 >> prep.out
cd $PDIR
rm -f ONEINT RUNFILE
${OVDIR}/scripts/seward_double-mol.py geo1 geo2 run >> p... |
38d73b8ef985229d272366bd1c7c84432672889518d8bd75186a035c86330e13 | Shell | 522 | 16 | #!/bin/bash
# File: run_AP_fixed.sh
# Author: Kelly Chang
# Date: Oct 2017
# Version: 1.0
#
# Description: Bash script to run AP simulations for the 12 CiPA training
# drugs using fixed inputs (i.e. optimal drug parameters).
#
DRUGNAMES=(dofetilide bepridil sotalol quinidine... |
3ee664d78dccfcce57a442759272644ab2aacbbc792648ee0d21b94a4d2484e9 | Shell | 522 | 15 | #!/bin/bash
# Convert Jupyter notebooks to Python scripts
jupyter nbconvert --to script Models_02.ipynb
jupyter nbconvert --to script Preprocessing_01.ipynb
jupyter nbconvert --to script Utils_00.ipynb
jupyter nbconvert --to script Training_03.ipynb
# List of converted Python scripts
python_scripts=("Models_02.py" "P... |
dcedc3b4121de6be9f7b6536cf1604938cbe8637b93c4d872e191ade1390ac9e | Shell | 522 | 14 | VAA3D=/PBshare/SEU-ALLEN/Users/zuohan/vaa3d/start_vaa3d.sh
timeLim=300s
[ -f all.txt ] || find ../stage1/out -name *pbd > all.txt
find out -name *swc | awk '{print "../stage1/"$0}' | sed 's/.swc//' > done.txt
sort all.txt done.txt done.txt | uniq -u > unfinished.txt
cat unfinished.txt | xargs -n 1 -P 50 -I {} bash -... |
e1d05a9fb4af7455381a15f0bbe9802da603c8285942bf86e2f638eb084adcae | Shell | 522 | 28 | #! /bin/bash
set -e
NC='\033[0m'
RED='\033[91m'
if [[ -d /startup && $(ls /startup) ]]; then
cd /startup
echo
echo "###### Adding custom startup scripts ######"
for x in $(ls); do
echo -e "\tAdding startup script ${RED}${x}${NC}"
cp ${x} /etc/startup
chmod 700 /etc/startup/${x}
done
sync
ec... |
50f56a28203c61d202bdd79780fdda87b10dc4571526fbddccc83154b9634acf | Shell | 525 | 24 | #!/bin/bash
#SBATCH -N 1
#SBATCH --mem 350G
#SBATCH --time=6:00:00
#SBATCH --exclusive
#SBATCH --job-name=correlations
#SBATCH --account=proj9
#SBATCH --partition=prod
#SBATCH --output=logs/dimension_computation
source /gpfs/bbp.cscs.ch/home/egassant/connalysis/bin/activate
declare -a
configs=("activity_dim_from_s... |
3bece55ad932dd6e15fda940bc5ba3afd68772737ef5b9d7475d6c23ebda3fbf | Shell | 526 | 20 | #!/bin/bash
#SBATCH --job-name=Shallow_Grid_1_N_Link_Mid_Inference_Stage
#SBATCH --partition=general1
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=40
#SBATCH --mem-per-cpu=4400
#SBATCH --extra-node-info=2:20:1
#SBATCH --time=24:00:00
#SBATCH --mail-type=FAIL
#SBATCH --array=0
#SBATCH --output=%x_%A_%a... |
f0085c1cc39b0a82674e8f0043712a50c5fecb85436205f950ef5923b0597c40 | Shell | 526 | 15 | img_dir=/home/vkzohj/public/projects/230k_valid/crop/out
mkdir -p out
find $img_dir -name *v3dpbd > all.txt
find out -name *pbd | sed 's/out//' | awk "{print \"$img_dir/\"\$0}" > done.txt
sort all.txt done.txt done.txt | uniq -u > unfinished.txt
VAA3D=/PBshare/SEU-ALLEN/Users/zuohan/vaa3d/start_vaa3d.sh
cat unfinish... |
dbca0a58dbcd19b007afb43fdec9b763ac5439d25d06df0015a13d4b1bebb040 | Shell | 527 | 12 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo -e "#Running python3 ./crmsd_on_c-alpha.py test_inputs/1cey.pdb"
python3 ./crmsd_on_c-alpha.py test_inputs/1cey.pdb
echo -e "#Running python3 ./crmsd_on_c-alpha.py test_inputs/2gb1-model1.pdb test_inputs/2gb1-model... |
751412f4e22b6545e1d038f5c24a94a7870a607115809b97caab80a55cbeaff5 | Shell | 530 | 17 | #! /usr/bin/bash
SCRIPT_FILE_NAME="$0"
SCRIPT_FILE_PATH=$(realpath "${SCRIPT_FILE_NAME}")
SCRIPT_FOLDER_PATH=$(dirname "${SCRIPT_FILE_PATH}")
ARG_COUNT=$#
if [ $ARG_COUNT -lt 2 ]
then
RUN_INDEX="00"
else
RUN_INDEX="$1"
fi
cd "${SCRIPT_FOLDER_PATH}"
SCRIPT_NAME=run-coco-from-apt-training-with-db-with-train-tf-... |
1124a937ca998276775994217356fd4412e58b06a7dee904548610448fa0cd81 | Shell | 531 | 22 | #!/bin/sh
#SBATCH --job-name=scCoAnnotate
#SBATCH --account=rrg-kleinman
#SBATCH --output=logs/%x.out
#SBATCH --error=logs/%x.err
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=5
#SBATCH --time=24:00:00
#SBATCH --mem-per-cpu=60GB
module load scCoAnnotate/2.0
# path to snakefile and config
snakefile=<path to snakefile>... |
dfaf8620a61142df92900868b9567eb7588c4bd0792d4f2ac88c60be683bdae6 | Shell | 532 | 21 | #!/usr/bin/env bash
# Halt on error
set -e
NUM_ITER=1000
SEED=42000
OUTDIR="./results_ll_tied_weights_effect"
# Iterate over different seeds here
for LEXP in data/LearningExp_*.txt; do
for TIED_WEIGHTS in "all" "within" "between" "none"; do
echo "Learning experiment: $LEXP // TIED WEIGHTS: $TIED_WEIGHTS";
py... |
7740e44095efa8f7573408bbd40ec9a6f7c70178fe0d669f4659aafd053d5870 | Shell | 533 | 8 | # # Dendritic spine model
echo "Run dendritic spine example"
python3 main.py --submit-tscc --ntasks 1 dendritic-spine --mesh-file /root/scratch/meshes/spine_mesh.h5 --outdir /root/scratch/dendritic-spine-results
# # Run cru example with vs. without serca
python3 main.py --submit-tscc --ntasks 2 cru --mesh-file /root/s... |
9576765e802b9adb16ba8116316578680e49dae7f7d00bb52e1427f583d35d2f | Shell | 533 | 8 | # # Dendritic spine model
echo "Run dendritic spine example"
python3 main.py --submit-tscc --ntasks 1 dendritic-spine --mesh-file /root/scratch/meshes/spine_mesh.h5 --outdir /root/scratch/dendritic-spine-results
# # Run cru example with vs. without serca
python3 main.py --submit-tscc --ntasks 1 cru --mesh-file /root/s... |
8bb834318f03227d4179e9b9cc7409388ec89bcdb085f9930e34f25146c7b12f | Shell | 534 | 11 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
export PYTHONPATH="../../../../../bin"
echo -e "#Running python3 ./validate_saturated_ring6.py test_inputs/pdb6bge.ent.gz EPE _N1_ _C2_ _C3_ _N4_ _C5_ _C6_"
python3 ./validate_saturated_ring6.py test_inputs/pdb6bge.ent.gz EPE _N1_ _C2_ _C3_ _N4_ _C5_ _C6... |
108a227441c8e284e94cf8dc18565d897a3eab17f6dd32fc956e11ec24c71bca | Shell | 535 | 12 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ap_scorefile_columns test_inputs/1pgxA-abinitio.fsc"
./ap_scorefile_columns test_inputs/1pgxA-abinitio.fsc
echo -e "Running ./ap_scorefile_columns test_inputs/1pgxA-abinitio.fsc rms ss_pair rsigma"
./ap_scorefile_columns test_inputs/1pgxA-... |
9b07bc7f31296a8e0f2d11c67576a7f79d590096e261a68a566b363ebd6b8641 | Shell | 535 | 20 | #!/usr/bin/env bash
# Halt on error
set -e
NUM_ITER=1000
SEED=42000
OUTDIR="./results_ll_con_loss_effect"
# Iterate over different seeds here
for CON_WEIGHT in "0.0" "0.1" "0.2" "0.3" "0.4" "0.5" "0.6" "0.7" "0.8" "0.9" "1.0"; do
for LEXP in data/LearningExp_*.txt; do
python3 train.py "$LE... |
ce048b39e31cba6ccb4049669b21fc480f8d9033c62bcde41d2f4b8ac143318b | Shell | 536 | 29 | #!/bin/bash
TEST_DIR=$1
RIGHT_DATA_DIR=$2
F1=($(\ls $TEST_DIR/*.tif))
F2=($(\ls $RIGHT_DATA_DIR/*.tif))
if [ ${#F1[*]} -ne ${#F2[*]} ]; then
echo "# of tiffs in TEST_DIR = ${#F1[*]}"
echo "# of tiffs in RIGHT_DATA_DIR = ${#F2[*]}"
exit 1
fi
for((i=0; i<${#F1[*]}; i++)); do
# echo ${F1[$i]} ${F2... |
8292cad2d70b02b85160c808bcad17e25b2d31a835b9d9df7a8b5b89af73135e | Shell | 539 | 29 | #!/bin/bash
inputDir="${1}"
finalReport="${2}"
set -e
set -u
inputReports=("${inputDir}/"*)
tmpFinalReport="${finalReport}.tmp"
first="true"
for i in "${inputReports[@]}"
do
if [[ ${first} == "true" ]]
then
cat ${i} > ${tmpFinalReport}
first='false'
headerNumber=$(( $(head -30 "${i}" |grep -n "\[Data\]" |... |
0742205be70d81b9e9d6d68460312d8afed4cb06f4fd6d93852d0e677b52620d | Shell | 542 | 23 | #!/bin/sh
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
progressFile=${1}
fullList=${2}
# Do not return until all jobs are finished
if [ -z ${fullList} ]; then
noJobs=1
else
noJobs=`grep -c "^" ${fullList}`
fi
noJobsDone=0
noJobsDonePrev=-1
wh... |
29be547b25c4f786e30ef017d530b313e8f8f8b4b890c5d79b37038929976468 | Shell | 543 | 27 | #!/bin/bash
# remove ROSMAP participants that are duplicates of ADC
plink \
--bfile tmp/rosmap_2 \
--keep data/rosmap/ids_qced.txt \
--make-bed \
--out tmp/rosmap_3
# merge adc and rosmap filesets
python code/prep/merge_plink_filesets.py \
-b tmp/rosmap_3 \
-b1 data/adc/adc_np \
-o tmp/rosmap_adc_merge... |
7d3178c4859d35767fc46f421f7e6eaf5ff874040123e57dc1aa28a1df0feec7 | Shell | 543 | 21 |
# (c) Coraline Rinn Iordan 07/2017, 10/2017, 10/2019
# Process prototype
# $1: PARAMS.NIFTIDIR
# $2: PARAMS.PROTOTYPE.NIFTIFILE
# $3: PARAMS.TEMPLATEDIR
# $4: PARAMS.CURRENTANAT
/opt/AFNI/5-23-17-openmp/afni_proc.py -script AFNIprocess \
-out_dir "$1"/PrototypeProcessed \
-scr_overwrite \
-dsets "$1"/"$2... |
b6f9d367dd71fe3a938eb9df87742fc89ae340d3274363df7c35cf74acdece57 | Shell | 543 | 16 |
############################################################################################
# Compilation file
#
############################################################################################
# path to boost library : TO BE MODIFIED BY USER
path=... |
330ef05f7080e577095569eb3537a2d29db8a40aed0cac4164d03d52f12a0b88 | Shell | 546 | 17 | #!/bin/bash
HOME=/fslgroup/fslg_spec_networks/compute
code_DIR=${HOME}/code/HCPD_analysis/CBIG2016_preproc
output_DIR=/fslgroup/fslg_HBN_preproc/compute/HCPD_analysis/CBIG2016_preproc_FS6
##Change this first line to your code_DIR pointing to the subjids file
#for subj in `cat $code_DIR/subjids/ids.txt`;do
for subj in... |
50b87b4f572d6dfc030474fec6255e14945346af8368e856b4c1013ebaaf6349 | Shell | 549 | 21 | #!/bin/sh
# executables
BABEL=$1
CONVERT=$2
COMPARE=$3
# files
OBFILE=$4
IMAGEDIR=$5
IMAGEFILE=$6
REF_IMAGE=$7
echo $BABEL ${OBFILE} ${IMAGEDIR}/${IMAGEFILE}.svg
$BABEL ${OBFILE} ${IMAGEDIR}/${IMAGEFILE}.svg
echo $CONVERT ${IMAGEDIR}/${IMAGEFILE}.svg ${IMAGEDIR}/${IMAGEFILE}.png
$CONVERT ${IMAGEDIR}/${IMAGEFILE}.sv... |
678f4199eb142866283a4a5a72c244fedb0c394dc69ff5fd37d02e98080e5e20 | Shell | 549 | 10 | NCellsList=("5000" "10000" "15000" "20000" "25000" "30000")
iterationList=({1..10})
for iteration in ${iterationList[@]}; do
echo $iteration
for NCells in ${NCellsList[@]}; do
echo $NCells
Rscript singleDeep/PrepareData.R --inputPath SLE/data/Science/science_processed.h5ad --fileType scanpy --sampleColumn ind_co... |
e0ac5c43edb0f162afc356eeec93a0875f814f7a30a84e1ef360b58d5b7d4852 | Shell | 549 | 26 | #!/bin/bash
set -e
if [ -z ${AWS_SSH_PRIVATE_KEY_FILE} ]
then
echo "ERROR: You must set AWS_SSH_PRIVATE_KEY_FILE in the environment."
exit 1
fi
flatfileName=flatfile.txt
rm -f ${flatfileName}
for privateIp in $(cat nodes-private)
do
echo ${privateIp}:54321 >> ${flatfileName}
done
i=0
for publicDnsName i... |
b663507448d5e689354cb5944cfe5d4720ef75a360715940b222e89ec25532cd | Shell | 551 | 13 | #!/bin/bash
# Written by Jianzhong Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
id_list=$1
if [ -z "${id_list}" ];then
id_list=$CBIG_REPDATA_DIR/stable_projects/predict_phenotypes/ChenTam2020_TRBPC/lists/release2_subjects_with_rs_and_t1.txt
fi
# job limit = 100 so we... |
0a1684d1077b9070987dd416005b7a4e87efad8d6a193cc15c8beddf7fb70ecd | Shell | 553 | 17 | #!/bin/bash
#SBATCH --ntasks 1
#SBATCH --mem-per-cpu 8G
#SBATCH --cpus-per-task 1
#SBATCH --time 3:00:00
#SBATCH --output=logs/%j.%x.out
cd /scratch/n.tan/extended-event-modeling/ || echo "cd failed.."
source activate sem-viz-jupyter
input=`head -n $SLURM_ARRAY_TASK_ID $1 | tail -n 1`
echo $input
export OMP_NUM_THR... |
8d332b5f60de85cf7a9693058603916ae469f94c36058a84d044cb0e6c3e108f | Shell | 555 | 22 | #!/bin/bash
# Use this pipeline to merge replicated encode files.
# acc_id.txt should be a tab separated file with the first column containing accession numbers
# The second column should be the relative concatenated ID
# i.e. <accession1> read1
# <accession2> read1
# This file will be used in f... |
cc4c2b3bdf17ab9256eb438ad57756259256b34c0c49934376b36d9db2b5859f | Shell | 561 | 23 |
for pheno in diffuse_abeta
do
n=$(./code/magma/count_non_missing_values.R shared/nacc_rosmap_act_np.pheno $pheno)
echo $n
magma_input=tmp/"$pheno"_magma_input.csv
./code/magma/extract_markername_pvalue.R \
-i output/gwas/metal/results/"$pheno"1.csv \
-o "$magma_input"
... |
3bf120401f6dd92319c150cde721ff389a410676168bf053be37f7e9db85e505 | Shell | 562 | 17 | #!/bin/bash
HOME=/fslgroup/fslg_spec_networks/compute
code_DIR=${HOME}/code/NSD_analysis/CBIG2016_preproc
output_DIR=/fslgroup/fslg_fun_conn/compute/NSD_analysis/CBIG2016_preproc_FS6_TASK
mkdir -p $output_DIR
##Change this first line to your code_DIR pointing to the subjids file
for subj in `cat $code_DIR/subjids/sub... |
27abf83f0c9b3c58ad464389ed4dc39f2f5994498b58e17715e86b3b0349f2d5 | Shell | 563 | 22 | #!/bin/bash
# Use this pipeline to merge replicated internally produced files.
# acc_id.txt should be a tab separated file with the first column containing accession numbers
# The second column should be the relative concatenated ID
# i.e. <path/to/file1> read1
# <path/to/file2> read1
# This fil... |
86281297245c5795f8a35b0d8d187df89282c92cb80d4a22727635ae5790d89e | Shell | 564 | 18 | #!/bin/bash
HOME=/fslgroup/fslg_spec_networks/compute
code_DIR=${HOME}/code/NSD_analysis/CBIG2016_preproc
output_DIR=/fslgroup/fslg_fun_conn/compute/NSD_analysis/CBIG2016_preproc_FS6_REST
mkdir -p $output_DIR
##Change this first line to your code_DIR pointing to the subjids file
#for subj in `cat $code_DIR/subjids/su... |
08aa84cacb4519ef1f780653b174ea8ac9a8494497d174ce400fda8a74636622 | Shell | 565 | 10 | NCellsList=("5000" "10000" "15000" "20000" "25000" "30000")
iterationList=({1..10})
for iteration in ${iterationList[@]}; do
echo $iteration
for NCells in ${NCellsList[@]}; do
echo $NCells
python singleDeep/singleDeep.py --inPath "cell_types_performance/ablation/SLE_Science_N"$NCells"_"$iteration"/" --samp... |
f4a380528e742980779359a1e84c1a7fd688a4192e8b5461b686f65767350a4a | Shell | 565 | 13 | #!/bin/bash
# run the job
bash parallel_by_chr.sh \
-w /home/siyuan/jobs/suzukii_WGS/reannotate/in_parallel \
-s /home/siyuan/jobs/suzukii_WGS/reannotate/in_parallel/genome_reannotate.py \
-b /opt/miniconda3/envs/play_with_genome/bin/bedtools \
-a /home/siyuan/reference/WT3-2.0/refseq/annotation/GCF_013340165.1_LBDM_D... |
beb665b491de6de5211442ba9a6aae87ab4a07518e3472ab671f838c58c89c23 | Shell | 567 | 21 |
# (c) Coraline Rinn Iordan 07/2017, 10/2017, 10/2019
# Process prototype without skull stripping
# $1: PARAMS.NIFTIDIR
# $2: PARAMS.PROTOTYPE.NIFTIFILE
# $3: PARAMS.TEMPLATEDIR
# $4: PARAMS.CURRENTANAT
/opt/AFNI/5-23-17-openmp/afni_proc.py -script AFNIprocess \
-out_dir "$1"/PrototypeProcessed \
-scr_overwri... |
ec2dad98a5697c37bc7b53b884f122abe8394d56f3db228247d1aa650d645f28 | Shell | 568 | 19 | #!/bin/bash
if [ $# -ne 4 ]
then
echo "Please, give: "
echo "1) sorted bam file (output from STAR mapping)"
echo "2) bed file with annotated introns (from reference genome)"
echo "3) bed file with annotated exons (from reference genome)"
echo "4) root for name of output files"
fi
email=a.alemany@hubrecht.eu... |
083bd41977aca7283152fcab5e3ef95d514b8139798618d3afd23d0aefd5ea6c | Shell | 569 | 23 | trap '
trap "
kill -9 0
wait
" INT TERM KILL
mail -s "lyf workstation jobs done" vkzohj@seu.edu.cn <<< "prune on 230k enhanced 512x512x256 blocks done. There are $(find out -name *swc | wc -l) swc."
cd ../stage5_consensus_weak
bash run.sh
' EXIT
# interrupt
trap '
trap " " INT TERM EXIT KILL
kill -9 0
wait
sleep 10s
m... |
854b4c2cfa0f36ab64a5ceaf634741c073f27456106b43536a9267322412ad80 | Shell | 569 | 11 | #!/bin/bash
# Written by Peng Wang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ~/storage
rsync -a --exclude .git CBIG/* Standalone_Wang2018_MFMem
# remove useless stable projects
rm -r Standalone_Wang2018_MFMem/stable_projects/brain_parcellation
rm -r Standalone_Wang2018_... |
1a70d9579910554bd5f8a263e2059fc750d2095bac159cf16399603567df910c | Shell | 571 | 22 | #!/bin/sh
# Written by Gia H. Ngo and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
K=12
for SEED in `seq 1 100`; do
ALPHA=100
ETA=0.01
JOB=`/apps/sysapps/TORQUE/bin/qsub -l nodes=1:ppn=1,mem=2... |
a78826eec0f21aa73c162dd09fd49e2494953352cb2bfbc89ab7ed9e9c117265 | Shell | 571 | 19 | #!/bin/bash
# File: run_hERG_fit_drug.sh
# Author: Kelly Chang
# Date: Oct 2017
# Version: 1.0
#
# Description: Bash script to fit hERG model to Milnes protocol data.
#
# change CMA-ES default hyperparameters
POP_SIZE="80"
STOPTOL="0.001"
DRUGNAMES=(dofetilide bepridil sotalol quinidine ... |
ea7f0da1f4c8b6ac6790ef2c314af04d22609c0cf4ff720ae44f23e27189ee5e | Shell | 571 | 27 | #!/bin/bash
function run {
IsMinikube=$1
IMAGE_NAME=$2
if [ "${IsMinikube}" = True ]; then
eval "$(minikube docker-env)"
fi
# Build Docker Image
echo "Building Docker Image ${IMAGE_NAME} \n"
docker image build -t "${IMAGE_NAME}" .
# Push docker image to proper container registry if using cloud p... |
d97776f85736ee39224cd3be8b3e7d7c40b1d896b45f40e66e3fec15205fa00b | Shell | 573 | 21 |
# (c) Coraline Rinn Iordan 07/2017, 10/2017, 10/2019
# Process prototype after skull stripping
# $1: PARAMS.NIFTIDIR
# $2: PARAMS.PROTOTYPE.NIFTIFILE
# $3: PARAMS.TEMPLATEDIR
# $4: PARAMS.CURRENTANAT
/opt/AFNI/5-23-17-openmp/afni_proc.py -script AFNIprocess \
-out_dir "$1"/PrototypeProcessed \
-scr_overwrite... |
16dbcd7eb45518e39c3ea7f33595483084902253d9edf9d68d37945ef70e57ec | Shell | 575 | 18 | # Check arguments and usage guide
if [ "$#" -lt 1 ]; then
echo "Usage: $0 <path_swconfig_json> <debug_mode> <print_swconfig> <sweep_progress>"
echo " path_swconfig_json: [*/swconfig*.json]"
echo " debug_mode: [true|false]"
echo " print_swconfig: [true|false]"
echo " sweep_pro... |
6595276b30c9a83ddc80904fb9b0e76e33543474c8d05070b4d9278964584f12 | Shell | 575 | 15 | #!/bin/bash
# Install NMRPipe. Add --no-certificate to the wget commands when behind
# a proxy that decrypts the SSL connection devalidates the certificate.
mkdir bin
cd bin
mkdir NMRPipe
cd NMRPipe
wget https://www.ibbr.umd.edu/nmrpipe/install.com
wget https://www.ibbr.umd.edu/nmrpipe/binval.com
wget https://www.ibbr.... |
3bbe08f41ba06ca79b1d2b8303b69dc750b03d74bbba8d5ae12f3e4a97d83091 | Shell | 579 | 28 | #!/bin/bash
set -ex
## Installing Ubuntu APT packages (required sudo privileges)
sudo apt-get update \
&& sudo apt-get install -y --no-install-recommends \
"build-essential" \
"bzip2" \
"cmake" \
"gcc" \
"libboost-all-dev" \
"libboost-python-dev" \
"libcairomm-1.0-dev" \
... |
fa48154bd02100c681fa58859103f200aabe03cf9e37c25f4c2bf5b488a90795 | Shell | 579 | 24 | #!/bin/bash
set -e
### Set venv directory
SCRIPT_DIR="$(dirname "$(realpath "$0")")"
VENV_DIR="${SCRIPT_DIR}/../venv"
### Install dependencies
sudo apt-get install -y python3-venv
### Set up venv
python3 -m venv "${VENV_DIR}"
### Install python dependencies and package
source "${VENV_DIR}/bin/activate"
pip install... |
ece1ac18f8797874d074b970dfb93caedde24e581df2ff70bd7205708c361777 | Shell | 581 | 20 | #!/bin/bash
# Activate environment
source activate sampl6_logP
# Update requirements
conda list --export > requirements.txt
# Run first step of analysis and create collection file
python logP_analysis.py
python logP_analysis2.py
# Compile LaTeX statistic table twice for better rendering
pdflatex ./analysis_outputs_... |
b0e3532899600e9f92242992d4fb89944ea9a9aa3355bd6abc340a1d0fe0dfd0 | Shell | 584 | 21 | trap '
trap "
kill -9 0
wait
" INT TERM KILL
mail -s "lyf workstation jobs done" vkzohj@seu.edu.cn, yufeng_liu@seu.edu.cn <<< "consensus on 230k enhanced 512x512x256 blocks done.
Result located at $(pwd)/out. There are $(find out -name *swc | wc -l) swc."
' EXIT
# interrupt
trap '
trap " " INT TERM EXIT KILL
kill -9 ... |
7409d6a9b73b36b2f1c73e19b5906a334737a7ccccf4a3434c0595fd406cc216 | Shell | 585 | 24 | #!/bin/bash
set -ex
if [ -n "$VERIFICARLO_VERSION" ]; then
sudo apt-get update
sudo apt-get install -y --no-install-recommends libmpfr-dev libtool
pip install bigfloat
git clone https://github.com/verificarlo/verificarlo
cd verificarlo
git checkout 09b24e04797dcf849ca1080d8d06e6d89a14dc65
export PATH="... |
72cf8498f392379202d642e8f4e731f09a381f4ccfda09f91ddaad1dc65f612e | Shell | 587 | 19 | #!/bin/bash
# get transcript IDS for mitochondrial hits of the organism of interest.
blastn=$1
organism=$2
fasta=$3
output_qseqid=$4
#output_fasta=$5
# Check if the pattern is present in the blastn file
if grep -q -E "; mitochondrial|mitochondrion" $blastn; then
# If the pattern is found, extract the sequences
... |
48b169edb5dc0994ba5ab0111b891bdb6ee8c71a5a0747d98aa69388ce508ca7 | Shell | 588 | 18 | #!/bin/bash
# This script makes nice plots for Ramachandran map variants, as desired.
# Let's say the output file from str_calc is named RAMA_RAW
grep -v "#" RAMA_RAM | awk '{print $3,$5,$6}' | cut -c 3,6- Rama-2 > Rama-3
for i in A B C D E F G H I K L M N P Q R S T V W
do
grep $i Rama-3 | cut -c 2- > Rama-3-$i
... |
cfe2d49d9509129b087cb621c6339310e54e90fd89a72a4ba4a18c0bb9b10d82 | Shell | 590 | 17 | #!/bin/sh
#PBS -l walltime=01:00:0
#PBS -l mem=6gb
# Will come into play only if this script is qsub'ed
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
fast -R 0.3 -H 0.1 -o ${outDir}${filename} ${brain}
# Generate the partial GM list for template c... |
07d664b3690cfee48d3436286895e3a16dea1fd5b554c41020dd09ff2fd4e66f | Shell | 592 | 14 | #!/bin/bash
#SBATCH --time=00:10:00
#SBATCH --mem=16G
#SBATCH --array=1-12
#SBATCH --output=/m/cs/scratch/networks-pm/jobs/H3regress-%j.out
#SBATCH --cpus-per-task=4
n=$SLURM_ARRAY_TASK_ID
variants=`sed "${n}q;d" options.txt`
module load r
Rscript /m/cs/scratch/networks-pm/effects_externalfactors_on_functionalconnect... |
1b959679912c4b9b8027c2fd446377b4c9966bd213a990dac56a92404ffeda5a | Shell | 592 | 14 | #!/bin/bash
#SBATCH --time=00:10:00
#SBATCH --mem=16G
#SBATCH --array=1-12
#SBATCH --output=/m/cs/scratch/networks-pm/jobs/H1regress-%j.out
#SBATCH --cpus-per-task=4
n=$SLURM_ARRAY_TASK_ID
variants=`sed "${n}q;d" options.txt`
module load r
Rscript /m/cs/scratch/networks-pm/effects_externalfactors_on_functionalconnect... |
e53745411d58b80113ad68089e501b7a0335dfc9bf1e170f8918afa7f1d84e29 | Shell | 592 | 14 | #!/bin/bash
#SBATCH --time=00:10:00
#SBATCH --mem=16G
#SBATCH --array=1-12
#SBATCH --output=/m/cs/scratch/networks-pm/jobs/H2regress-%j.out
#SBATCH --cpus-per-task=4
n=$SLURM_ARRAY_TASK_ID
variants=`sed "${n}q;d" options.txt`
module load r
Rscript /m/cs/scratch/networks-pm/effects_externalfactors_on_functionalconnect... |
acf5101fd9fc4afb5b56fe44540fad3dbca9b3bfaf5dcfe0ab6a959d3b04b37b | Shell | 593 | 27 | #! /usr/bin/env bash
set -e
USER_ID=${LOCAL_UID:-0}
GROUP_ID=${LOCAL_GID:-0}
NVIDIA_GID=${NVIDIA_GID:-0}
echo "Starting with UID : $USER_ID, GID: $GROUP_ID, NVIDIA GID: ${NVIDIA_GID:-0}"
useradd -u $USER_ID -o -m user
if [ $GROUP_ID -ne 0 ]; then
groupmod -o -g $GROUP_ID user
fi
if [ $NVIDIA_GID -ne 0 ]; then
gro... |
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