sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
7fd1587b380fb51548fd2bb2611cae5fa85952f5e7a965224afcd6eafd3dd9d0 | Shell | 860 | 17 | #!/bin/bash
python collect_retrain_summary.py results_retrain/exp_aids/ 0 75 1 10
python collect_retrain_summary.py results_retrain/wb_aids/ 0 75 1 10
python collect_retrain_summary.py results_retrain/deepsurv_aids/ 0 75 1 10
python collect_retrain_summary.py results_retrain/exp_gbcs/ 0 75 1 6
python collect_retrain_... |
39093f7d90ee77c24ad7197c2ef8ec21865ddc261e162ea21943a0504a272299 | Shell | 862 | 27 | #! /bin/bash
filepath=/Users/wang/Desktop/Research_projects/BBSC/Functional/fmri/derivatives/freesurfer-v7.2.0
cd $filepath
ls | grep -i sub- >$filepath/subjList.txt # command grep is trying to filter the input with 'sub-'. -i ignore the high or low cases
for sub in $(cat $filepath/subjList.txt); do
export SUB... |
fbae01f0a9ad31714f487ba1df97bf73eb07890a26d2ff4d6942980e383d6b05 | Shell | 862 | 43 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
nodever=$1
if [ -z "${nodever}" ]; then
echo "No node version given, aborting."
exit 1
fi;
bitrate=$2
set_ldc_sample_filename "${bitrate}"
model_source=${DEEPSPEECH_TEST_MODEL//.pb/.tflite}
model_name=$(basename "${model_source}")
model_name_mma... |
20d42a72dcb55698c5f681272bb33e47374760bcbaba3eea343e06e3adec6c4d | Shell | 864 | 21 | #!/bin/bash
#SBATCH --job-name=met_alexnet
#SBATCH --output=output/standard%A_%a.out
#SBATCH --error=output/standard%A_%a.err
#SBATCH --mem=4000
#SBATCH --time=3:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=0-399
#SBATCH --dependency=after:19718639
#SBATCH --constraint=high-capacity
#SBATCH --exclude=node093,node037,node... |
b34f0888f2bbaecf8b5b9b184c358a741bccd331626798150959691713dbb7ae | Shell | 864 | 35 | #!/bin/bash
case "${OMPI_COMM_WORLD_LOCAL_RANK}" in
0)
exec numactl --physcpubind=0-5,48-53 --membind=0 "${@}"
;;
1)
exec numactl --physcpubind=6-11,54-59 --membind=0 "${@}"
;;
2)
exec numactl --physcpubind=12-17,60-65 --membind=0 "${@}"
;;
3)
exec numactl --physcpubind=18-23,66-71 --membin... |
5a4feb6218791ee31eb222b5a65c0796a634499e451773a7ba8df0898a891f27 | Shell | 866 | 26 | #!/bin/bash
# Usage: bash download_bfd.sh /path/to/download/directory
set -e
if [[ $# -eq 0 ]]; then
echo "Error: download directory must be provided as an input argument."
exit 1
fi
if ! command -v aria2c &> /dev/null ; then
echo "Error: aria2c could not be found. Please install aria2c (sudo apt install ... |
1359e33f3d5ff5074a031840755d67b8d2008fca46f123249250704b6a6eb5fa | Shell | 867 | 26 | #!/bin/sh
# This script analyzes subject data in ~/MATLAB/DATA/Avgusta for each task
# The SGE_TASK variable specifies the data sets, as in $HOME/test.qsub
cd /home/knight/hoycw/PRJ_Error/scripts/
# define where the datasets are located
#PRCSDATADIR="/home/knight/hoycw/PRJ_Error/data/"
# don't change this variable
#... |
4ccee194f7ef8cd60938b9e5d2124d3cc2c427179fe2b06b332d666a0d4e2cc5 | Shell | 869 | 32 | #!/bin/sh
# script for execution of deployed applications
#
# Sets up the MATLAB Runtime environment for the current $ARCH and executes
# the specified command.
#
exe_name=$0
exe_dir=`dirname "$0"`
echo "------------------------------------------"
if [ "x$1" = "x" ]; then
echo Usage:
echo $0 \<deployedMCRroot\>... |
cfa49cab9ace9ddf9d4a413bbb85b933c4ce1c9ec51b040a587ca46bcbdeb8b9 | Shell | 869 | 26 | #!/bin/bash
# Resource monitoring tool for Cromwell.
# This script is for GCP backend only.
INTERVAL=$1
if [[ -z "$INTERVAL" ]]; then
INTERVAL=20
fi
printf 'time\tmem\tdisk\tcpu_pct\n'
while true; do
# Seconds since epoch.
TIME=$(date +%s)
# -b for size in bytes.
MEM=$(free -b | awk 'NR==2{print $3}')
# ... |
03df057e1f0b6063bc302e5a18fc62769d4b2032ed3abea5d70d0c75db696050 | Shell | 870 | 20 | source venv/bin/activate
export BIOHOME=/home/bb/valejose/valejose/revisions/
export PYTHONPATH=$BIOHOME/bioseq2seq
export CHKPT_DIR="$BIOHOME/bioseq2seq/experiments/checkpoints/coding_noncoding/"
readarray -t weighted_models < "weighted_models.txt"
for m in "${weighted_models[@]}"
do
a="${m//\//}"
b="${a//\.pt/}"
pyt... |
bc9e5c8eb00e228ffecb21a5248ff8487a7a6acef7974718820347e21c7ae42c | Shell | 870 | 22 | #!/bin/bash
#step1 get biallelic SNVs and calculate frequency
for i in $(seq 1 22) X
do
vcftools --gzvcf {file_pathway}/1kGP_high_coverage_Illumina.chr$i.filtered.SNV_INDEL_SV_phased_panel.vcf.gz \
--remove-indels \
--max-alleles 2 \
--min-alleles 2 \
--freq \
--out {file_pathway}/1kGP_high_coverage_Illumina.chr... |
8da904b814cdfd7b8877114d3f8a52fe87a3ea14b43469db2b47cdcdf23cc357 | Shell | 871 | 21 | #export BIOHOME=/nfs/stak/users/valejose/hpc-share
export BIOHOME=/home/bb/valejose/valejose/
export PYTHONPATH=$BIOHOME/bioseq2seq
export CHKPT_DIR="$BIOHOME/bioseq2seq/experiments/checkpoints/final"
echo $CHKPT_DIR
source experiments/scripts/templates.sh
readarray -t models < lncPEP_models.txt
for m in ${models[@]}
... |
d642d5851734efb8006a7a812d267131caa85c1ccdee278ae70a49afd9464021 | Shell | 871 | 24 | #!/usr/bin/env bash
# Checkout LLVM sources
git clone --depth=1 https://github.com/llvm/llvm-project.git llvm-project
# Setup libc++ options
if [ -z "$BUILD_32_BITS" ]; then
export BUILD_32_BITS=OFF && echo disabling 32 bit build
fi
# Build and install libc++ (Use unstable ABI for better sanitizer coverage)
cd ./l... |
96eebc84d68d39a788caa732ae306b11a7f2c19f2211cfa9edaf6cc7d3fec6c9 | Shell | 872 | 49 | #!/bin/bash
if [ "$1" != "" ]; then
LAMBDA=$1
else
LAMBDA=1
fi
if [ "$2" != "" ]; then
PHI=$2
else
PHI=1
fi
if [ "$3" != "" ]; then
TAU=$3
else
TAU=600
fi
if [ "$4" != "" ]; then
SEED=$4
else
SEED=123
fi
make
EXPNAME='spiking_augmented_grad'
SIMTIME=10000
ETA=1e-2
ZETA=1e-3
KAPPA=10
WEE=0.0
WEI=0.5
WIE=0... |
4fdb6b089430b3c252b60cd750b5166660db97c998dfb0e2cdd8be0afb82c8c0 | Shell | 874 | 28 | #!/bin/sh
# Move to scripts directory
root_dir="/Volumes/hoycw_clust/PRJ_Error/"
cd $root_dir/scripts/
# Load the correct SBJ list
echo "Please enter the desired SBJ list:"
read list_name
declare -a SBJs
SBJs=(`cat "${root_dir}scripts/SBJ_lists/${list_name}.sbj"`)
# Run BHV scripts for these SBJs
for sbj in "${SBJ... |
f88a3f10f1b239fc7529adc3978e5a7ecf05e91bc9cbc1968ce3bbc612af2d1f | Shell | 876 | 19 | #!/bin/bash -ve
## include sense and antisense versions of the target transcripts
../../util/fasta_write_sense_n_anti.pl trinity_out_dir/Trinity.fasta > trinity_out_dir/Trinity.sense_n_anti.fasta
## align reads back to the transcripts
../../util/alignReads.pl --left reads.left.fq.gz --right reads.right.fq.gz --tar... |
5f3c1f927c5838a188481dc8121481903dae3b17ccaab00e2f526bc3a1bfa511 | Shell | 878 | 26 | #!/bin/sh
# This script analyzes subject data in ~/MATLAB/DATA/Avgusta for each task
# The SGE_TASK variable specifies the data sets, as in $HOME/test.qsub
cd /home/knight/hoycw/PRJ_Error/scripts/
# define where the datasets are located
#PRCSDATADIR="/home/knight/hoycw/PRJ_Error/data/"
# don't change this variable
#... |
aac606f8bc1b7afe89dd3b4e8e0f4c2eddd5bcdc510c02c682e709b4ec4c623f | Shell | 880 | 25 | #!/bin/bash
export MRTRIX_NTHREADS=$2
bblid=$1
#Convert files
mrconvert -grad \
/work/data/qsiprep_outputs/sub-${bblid}/ses-PNC1/dwi/sub-${bblid}_*dwi.b \
/work/data/qsiprep_outputs/sub-${bblid}/ses-PNC1/dwi/sub-${bblid}_*dwi.nii.gz \
/work/data/MRtrix_recon/sub-${bblid}/ses-PNC1/dwi/sub-${bblid}_ses-PNC1.mif \
-f... |
1e577d693683cd6c92b344989771ff180e58aec71716f8268648cc0e0f65d2ee | Shell | 882 | 12 | #!/bin/bash
singularity exec \
--writable-tmpfs \
--bind $PWD:/pnet_robustness \
--bind $PWD/pnet_data/mounted/mutations.csv:/app/pnet_prostate_paper/_database/prostate/processed/P1000_final_analysis_set_cross_important_only.csv \
--bind $PWD/pnet_data/mounted/cnvs.csv:/app/pnet_prostate_paper/_database/prosta... |
a87266ae7474e32315cdb57fad99d2e57a596b40ab7ff7063ac0fd5b2e9ac5b1 | Shell | 882 | 51 | #!/bin/bash
if [[ $# -lt 1 ]]; then
echo "Usage: ./2b_sweep.sh s1 [s2 ...]"
exit 1
fi
ss=${@:1}
cue_types=( "sparse" "dense" "both" )
target_types=( "sparse" "category" )
args=()
for cue in "${cue_types[@]}"; do
for target in "${target_types[@]}"; do
root="${cue:0:1}${target:0:1}"
case "$target" in
... |
7755b54eff17a4acc56f8af61deb9c06cdd5288f649bc1232931e286265bea22 | Shell | 884 | 26 | #!/bin/sh
# This script analyzes subject data in ~/MATLAB/DATA/Avgusta for each task
# The SGE_TASK variable specifies the data sets, as in $HOME/test.qsub
cd /home/knight/hoycw/PRJ_Error/scripts/
# define where the datasets are located
#PRCSDATADIR="/home/knight/hoycw/PRJ_Error/data/"
# don't change this variable
#... |
a10054df58fa97522f449275f63422c813192e59c739af497d3935891efd06e4 | Shell | 884 | 25 | #!/bin/bash
export MRTRIX_NTHREADS=$1
#Subjects
readarray -t template < /work/scripts/MRtrix_recon/subject_lists/template.txt;
#Create directories necessary for population template
mkdir /work/data/MRtrix_recon/template/fod_input_new
mkdir /work/data/MRtrix_recon/template/mask_input_new
#Copy mask and FODs to new di... |
19c9e68c8abd8c594a21707d59f24c1785fc7d3c50503056060256bab909d1db | Shell | 887 | 32 | set -ex
# models
RESULTS_DIR='./results/edges2shoes'
G_PATH='./pretrained_models/edges2shoes_net_G.pth'
E_PATH='./pretrained_models/edges2shoes_net_E.pth'
# dataset
CLASS='edges2shoes'
DIRECTION='AtoB' # from domain A to domain B
LOAD_SIZE=256 # scale images to this size
CROP_SIZE=256 # then crop to this size
INPUT_NC... |
652180cde003f1aa576dc825ce86de9e516125e7fe9f92c8818f4741ee1efc9a | Shell | 887 | 27 | #! /bin/bash
filepath=/Users/wang/Desktop/Research_projects/BBSC/Functional/fmri/derivatives/freesurfer-v7.2.0
cd $filepath
ls | grep -i sub- >$filepath/subjList.txt # command grep is trying to filter the input with 'sub-'. -i ignore the high or low cases
for sub in $(cat $filepath/subjList.txt); do
export SUB... |
0889c6163862b9ff670d693259374ee14bc7c81709a2191517d736f02c1f686e | Shell | 888 | 18 | #!/bin/bash
#SBATCH --cluster=beef # Don't change
#SBATCH --partition=long # Don't change
#SBATCH --account=researcher # Don't change
#SBATCH --job-name=aav5_ann
#SBATCH --output=aav5_ann_slurm.out
#SBATCH --gres=gpu:1 # Number of GPU(s) per node.
#SBATCH --cpus-per-task=8 ... |
5796b02a56fb581b297e9cca072ddf64399f9c22297d558a1b52fb346f5b60af | Shell | 890 | 20 | #!/bin/bash
#SBATCH --job-name=met_resnet50l23
#SBATCH --output=output/standard%A_%a.out
#SBATCH --error=output/standard%A_%a.err
#SBATCH --mem=4000
#SBATCH --time=4:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=1-5
#SBATCH --constraint=high-capacity
#SBATCH --exclude=node093,node040
#SBATCH --partition=mcdermott
module ... |
c1b5e81082d414b53937ddae0f71714317374643edd3352562b436c63f5623a8 | Shell | 890 | 32 | #!/bin/bash -l
# Request wallclock time (format hours:minutes:seconds).
#$ -l h_rt=5:0:0
# Request RAM.
#$ -l mem=10G
# Request TMPDIR space (default is 10 GB).
#$ -l tmpfs=10G
# Select the number of threads.
#$ -pe mpi 8
# Set the name of the task.
#$ -N BLAST_lf_vs_pdom
# Set working directory
#$ -wd /home/ucfa... |
2f24a02dbc04ee3724c4640180f4ebeb4fe3f4489fc4eac84bb31ab610002d7f | Shell | 892 | 28 | #!/bin/bash -ve
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
if [ -z ${TRINITY_HOME} ]; then
echo "Must set env var TRINITY_HOME"
exit 1
fi
${TRINITY_HOME}/Trinity --seqType fq --max_me... |
963e5761362732d38558d99df4f71f0682ef78aac46c251f1739baea34cfb9d5 | Shell | 894 | 22 | #!/bin/bash
set -e
set -u
set -x
echo "#cell num_read_pairs num_raw_contacts ratio"
for cell_type in z1OMP z5OMP; do
for cell_num in $(seq 1 48); do
#echo "testing $cell_type.$cell_num"
R1_fastq_file="fastq_merged/dipc.merged.$cell_type.$cell_num.R1.fastq.gz"
contacts_seg_file="merged.$cell_type.$cell_num.ca.f... |
7bce747b35732f0f53594175d4ca260f76e029934141fee92895f5d7eccfe839 | Shell | 899 | 32 | set -ex
# models
RESULTS_DIR='./results/edges2handbags'
G_PATH='./pretrained_models/edges2handbags_net_G.pth'
E_PATH='./pretrained_models/edges2handbags_net_E.pth'
# dataset
CLASS='edges2handbags'
DIRECTION='AtoB' # from domain A to domain B
LOAD_SIZE=256 # scale images to this size
CROP_SIZE=256 # then crop to this s... |
eebc1428eea97c0e61f41e505fd9dfc4f37cf8ffe139dfc9948eab36a7e935f9 | Shell | 900 | 33 | #!/bin/bash -l
# Request wallclock time (format hours:minutes:seconds).
#$ -l h_rt=5:0:0
# Request RAM.
#$ -l mem=10G
# Request TMPDIR space (default is 10 GB).
#$ -l tmpfs=10G
# Select the number of threads.
#$ -pe mpi 8
# Set the name of the task.
#$ -N BLAST_vvul_vs_lf
# Set working directory
#$ -wd /home/ucfa... |
04f421fa19603908342c47e0e0a95d225653a56c87b3dd5d17a9da3ed5c2387b | Shell | 901 | 50 | #!/bin/bash
set +x
ROOT="."
MRIVOL="$ROOT/mri/crop/mri.crop.mgz"
OCTVOL="$ROOT/oct/pool3x3x3/oct.win33.nii"
OCTMSK="$ROOT/oct/pool3x3x3/mask.nii"
MODEL=affine
do_register()
{
KERNEL="$1"
LOSS_IMAGE=(\
@loss lcc --patch $KERNEL % \
@@mov $MRIVOL \
@@fix $OCTVOL --mask $OCTMSK \
)
OUT_DIR="$ROOT/mri2oct/${MODEL}... |
cba84676df63302ed4b60761b0add565b45276e3969c8c7184a7d644854a43e0 | Shell | 901 | 33 | #!/bin/bash -l
# Request wallclock time (format hours:minutes:seconds).
#$ -l h_rt=5:0:0
# Request RAM.
#$ -l mem=10G
# Request TMPDIR space (default is 10 GB).
#$ -l tmpfs=10G
# Select the number of threads.
#$ -pe mpi 8
# Set the name of the task.
#$ -N BLAST_lf_vs_Vvul
# Set working directory
#$ -wd /home/ucfa... |
610e5eaa3a2383ad23db6ad389d8aefde0aacd52dd8cc81605aa20ab5533d5f7 | Shell | 903 | 33 | #!/bin/bash -l
# Request wallclock time (format hours:minutes:seconds).
#$ -l h_rt=5:0:0
# Request RAM.
#$ -l mem=10G
# Request TMPDIR space (default is 10 GB).
#$ -l tmpfs=10G
# Select the number of threads.
#$ -pe mpi 8
# Set the name of the task.
#$ -N BLAST_lf_vs_pdom
# Set working directory
#$ -wd /home/ucfa... |
c22221e5a26b34bfe282a6fd0252156b00592f9415c358bf74b252fb051f251d | Shell | 905 | 20 | #!/bin/bash
#$ -cwd
#$ -o /gladstone/bioinformatics/projects/mn-1318-maxine-nelson-yadong-huang-snrnaseq-mm10-aug-2022/tmp/
#$ -e /gladstone/bioinformatics/projects/mn-1318-maxine-nelson-yadong-huang-snrnaseq-mm10-aug-2022/tmp
#$ -pe smp 1
#$ -l mem_free=50G
#$ -l scratch=50G
#$ -l h_rt=01:00:00
#$ -j yes
data_dir=/gl... |
2da067e4d325f3c1cccab33a3e05900a210a86b4d7368c8dfaeb10a7120df2b3 | Shell | 909 | 33 | #!/bin/bash -l
# Request wallclock time (format hours:minutes:seconds).
#$ -l h_rt=5:0:0
# Request RAM.
#$ -l mem=10G
# Request TMPDIR space (default is 10 GB).
#$ -l tmpfs=10G
# Select the number of threads.
#$ -pe mpi 8
# Set the name of the task.
#$ -N BLAST_dmel_vs_lf
# Set working directory
#$ -wd /home/ucfa... |
428c2a1dd1a96d0706edf024cce124c16b386d54dd3833262471a316f1005511 | Shell | 910 | 33 | #!/bin/bash -l
# Request wallclock time (format hours:minutes:seconds).
#$ -l h_rt=5:0:0
# Request RAM.
#$ -l mem=10G
# Request TMPDIR space (default is 10 GB).
#$ -l tmpfs=10G
# Select the number of threads.
#$ -pe mpi 8
# Set the name of the task.
#$ -N BLAST_lf_vs_dmel
# Set working directory
#$ -wd /home/ucfa... |
fc69e2b08f3a1b29bfc9c2548547e38246ce08aa917308634678a3970c08adad | Shell | 912 | 35 | #!/bin/bash
### Run fmriprep for specific sub
subj=$1
# fmriprep container
fmrip_con=/mnt/lustre/working/lab_lucac/shared/x_fmriprep_versions/fmriprep-20.2.1.simg
# paths
project_dir=/mnt/lustre/working/lab_lucac/lukeH/projects/OCDbaseline/
bids_dir=${project_dir}data/bids/
out_dir=${project_dir}data/derivatives/fmr... |
d307e3e13190853a87397ce668cca7e490bbd4b4f42bee7099f22bc2d86bb200 | Shell | 914 | 29 | #!/bin/sh
# Based on Deno installer: Copyright 2019 the Deno authors. All rights reserved. MIT license.
set -e
case $(uname -sm) in
"Darwin x86_64") target="Darwin_x86_64" ;;
"Darwin arm64") target="Darwin_arm64" ;;
"Linux aarch64") target="Linux_arm64" ;;
*) target="Linux_i386" ;;
esac
version=${1}
if [ $# -eq 0 ]... |
14ecfb02920f2bd128d0a1c35280ad09a5a462ab405511530b1ce08288131686 | Shell | 915 | 32 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
extract_python_versions "$1" "pyver" "pyver_pkg" "py_unicode_type" "pyconf" "pyalias"
bitrate=$2
set_ldc_sample_filename "${bitrate}"
model_source=${DEEPSPEECH_PROD_MODEL//.pb/.tflite}
model_name=$(basename "${model_source}")
model_name_mmap=$(basename "... |
8c9bbaac4c9e1e1903fe633e3b02365de1b6efdd9fa13e0086dc06b0d028a09f | Shell | 915 | 31 | set -ex
# models
RESULTS_DIR='results/combined_SEN1_2_10%_fall'
# dataset
CLASS='combined_SEN1_2_10%_fall_bicycle_gan'
DIRECTION='AtoB' # from domain A to domain B
LOAD_SIZE=286 # scale images to this size
CROP_SIZE=256 # then crop to this size
INPUT_NC=3 # number of channels in the input image
# misc
GPU_ID=0 # g... |
0429b077afab8d32ff9394d2b064e8f999ca4da6c9e6606b3d117c93ba908927 | Shell | 916 | 43 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
nodever=$1
if [ -z "${nodever}" ]; then
echo "No node version given, aborting."
exit 1
fi;
bitrate=$2
set_ldc_sample_filename "${bitrate}"
model_source=${DEEPSPEECH_PROD_MODEL}
model_name=$(basename "${model_source}")
model_source_mmap=${DEEPSP... |
dff0948de4e61f383b16467b03ccf002fb54a3e0db87b66d9e1b2404533ae4e2 | Shell | 917 | 36 | #!/bin/bash
#$ -q iblm.q
#$ -V
#$ -cwd
#$ -o /iblm/netapp/data1/jezhou/out
#$ -e /iblm/netapp/data1/jezhou/err
reference_genome=/iblm/netapp/data1/jezhou/cellranger/rn6
fastqs_dir=/iblm/netapp/data1/jezhou/Telese_Rat_Amygdala/snATAC/fastq
outdir=/iblm/netapp/data1/jezhou/Telese_Rat_Amygdala/snATAC/realigned_outputs
r... |
f2c2ee64009f8a97283386c76dffeccca317f62bc2af66bdad4b39d7810338fe | Shell | 917 | 36 | #!/bin/bash
#$ -q iblm.q
#$ -V
#$ -cwd
#$ -o /iblm/netapp/data1/jezhou/out
#$ -e /iblm/netapp/data1/jezhou/err
reference_genome=/iblm/netapp/data1/jezhou/cellranger/rn6
fastqs_dir=/iblm/netapp/data1/jezhou/Telese_Rat_Amygdala/snATAC/fastq
outdir=/iblm/netapp/data1/jezhou/Telese_Rat_Amygdala/snATAC/realigned_outputs
r... |
e2976dff77d1ea2f5b5674302b7267c6726a8abbc8e6f507e7435b323e24ab60 | Shell | 920 | 21 | #!/bin/bash
set -u
set -e
echo "#cell number_of_contacts percent_duplicates number_of_contacts_corrected"
for cell_type in z1OMP z5OMP; do
for cell_num in $(seq 1 48); do
fraction=$(grep "$cell_type\.$cell_num " determine_sex.txt | cut -d ' ' -f 2)
is_female=$(echo "$fraction > 0.03" | bc -l)
if [ $is_female =... |
21582e30e0865e5298f2106a3eabf0eb3dc077b1b3ec0ca7cbdcd7d50e929863 | Shell | 922 | 10 | #PBS -l walltime=7:59:00
#PBS -l select=1:ncpus=32:mem=256gb
PBS_ARRAY_INDEX=12
#$ python3 gnomix.py <query_file> <output_folder> <chr_nr> <phase> <genetic_map_file> <reference_file> <sample_map_file>
module load anaconda3/personal
path_genetic_map="/rds/general/project/human-popgen-datasets/live/HGDP_1000g/gnomix"
pat... |
0c784a7014d8792dd9384f84a471ce588143fc4852eaf9b5bb20b42757d5fdf8 | Shell | 923 | 31 | set -ex
# models
RESULTS_DIR='results/combined_SEN1_2_10%_winter'
# dataset
CLASS='combined_SEN1_2_10%_winter_bicycle_gan'
DIRECTION='AtoB' # from domain A to domain B
LOAD_SIZE=286 # scale images to this size
CROP_SIZE=256 # then crop to this size
INPUT_NC=3 # number of channels in the input image
# misc
GPU_ID=0 ... |
17b700c6c0c01ddb48326e32fa7811b8182f609a3fac10ea16101dce8fc6c3d9 | Shell | 923 | 31 | set -ex
# models
RESULTS_DIR='results/combined_SEN1_2_10%_summer'
# dataset
CLASS='combined_SEN1_2_10%_summer_bicycle_gan'
DIRECTION='AtoB' # from domain A to domain B
LOAD_SIZE=286 # scale images to this size
CROP_SIZE=256 # then crop to this size
INPUT_NC=3 # number of channels in the input image
# misc
GPU_ID=0 ... |
95f82fbd45c6887f51165a4671c65b912b1e562aaa96c7bdc4362cfab7833b78 | Shell | 923 | 31 | set -ex
# models
RESULTS_DIR='results/combined_SEN1_2_10%_spring'
# dataset
CLASS='combined_SEN1_2_10%_spring_bicycle_gan'
DIRECTION='AtoB' # from domain A to domain B
LOAD_SIZE=286 # scale images to this size
CROP_SIZE=256 # then crop to this size
INPUT_NC=3 # number of channels in the input image
# misc
GPU_ID=0 ... |
a600dde1c6772aea145118b540f89b707717b39fd726cacefa910f1dcf7004b0 | Shell | 923 | 31 | set -ex
# models
RESULTS_DIR='results/combined_SEN1_2_20%_winter'
# dataset
CLASS='combined_SEN1_2_20%_winter_bicycle_gan'
DIRECTION='AtoB' # from domain A to domain B
LOAD_SIZE=286 # scale images to this size
CROP_SIZE=256 # then crop to this size
INPUT_NC=3 # number of channels in the input image
# misc
GPU_ID=0 ... |
bb5b9147ff8bdf00f9cccba3bd6ee38268bbec0b662882bf6ef8276b03c01bad | Shell | 923 | 31 | set -ex
# models
RESULTS_DIR='results/combined_SEN1_2_10%_spring'
# dataset
CLASS='combined_SEN1_2_10%_spring_bicycle_gan'
DIRECTION='AtoB' # from domain A to domain B
LOAD_SIZE=286 # scale images to this size
CROP_SIZE=256 # then crop to this size
INPUT_NC=3 # number of channels in the input image
# misc
GPU_ID=0 ... |
ec93dbaf8d327220daae21b7bf540d3ebf5fa009051814a8f0547b06815b5b36 | Shell | 923 | 31 | set -ex
# models
RESULTS_DIR='results/combined_SEN1_2_20%_summer'
# dataset
CLASS='combined_SEN1_2_20%_summer_bicycle_gan'
DIRECTION='AtoB' # from domain A to domain B
LOAD_SIZE=286 # scale images to this size
CROP_SIZE=256 # then crop to this size
INPUT_NC=3 # number of channels in the input image
# misc
GPU_ID=0 ... |
8ff7d6927b1e93bf57158042b9a02c627cb9cb83def03771754f68af0078a245 | Shell | 927 | 48 | #!/bin/bash
#SBATCH --time=0-00:40:00
#SBATCH --mem-per-cpu=4000
#SBATCH --array=0-7
#SBATCH --output=./slurm_logs/slurm-%A_%a.out
INPUT_DIR=/scratch/n/tbi/meg
OUTPUT_DIR=/scratch/n/tbi-meg/v/processed
echo "INPUT_DIR set as $INPUT_DIR"
echo "OUTPUT_DIR set as $OUTPUT_DIR"
SUBJECT=$1
ml purge
module load teflon
ml ... |
293063a3d90244feae354929f1b17d8ece248b68d6fbed5a96eda516084b14d2 | Shell | 929 | 35 | #!/bin/bash
set -xe
tc_tests_utils=$(dirname ${BASH_SOURCE[0]})
# This defines a set of variables used by others
source ${tc_tests_utils}/tc-all-vars.sh
# Useful functions for setup / generic re-use like downloading data
source ${tc_tests_utils}/tc-all-utils.sh
# Scoping of Android-related tooling
source ${tc_test... |
a53bfa865a4e42778cb7a4e8c4227781901af68afef7a446226298d61dc2495b | Shell | 930 | 36 | #!/bin/bash
if [ -z "$MODEL" ]; then
export MODEL=resnet18_v1
fi
if [ -z "$NUM_TRAINING_SAMPLES" ]; then
export NUM_TRAINING_SAMPLES=1281167
fi
if [ -z "$NUM_EPOCHS" ]; then
export NUM_EPOCHS=3
fi
if [ -z "$NUM_GPUS" ] || [ $NUM_GPUS '-lt' 0 ]; then
export NUM_GPUS=0
fi
if [ -z "$DATA_BACKEND" ]; then
ex... |
6622dbc479bc9360a1db6601d9263271adf46f0bfc0ef5621cea958001e46d23 | Shell | 931 | 21 | projroot="/projects/ps-renlab2/szu/projects/CEMBA2"
allpeakFile="${projroot}/supple.07.peakcalling.allinone/mba.whole.sa2.final.peak.srt.bed"
tssBed="${projroot}/meta/gencode.vM23.gene.tssUpDn1k.bed"
outdir="${projroot}/04.cCREgene/sa2.cicero/src/main/resource"
allpeakOvlpTssBed1="${outdir}/mba.whole.sa2.peakOvlpTSS.be... |
ea7150f730609a6f6acb29a8c0da4d78e707f794c1b7374ebd630551aa325c56 | Shell | 931 | 10 | #PBS -l walltime=71:59:00
#PBS -l select=1:ncpus=32:mem=124gb
#PBS -J 1-22
#$ python3 gnomix.py <query_file> <output_folder> <chr_nr> <phase> <genetic_map_file> <reference_file> <sample_map_file>
module load anaconda3/personal
path_genetic_map="/rds/general/project/human-popgen-datasets/live/HGDP_1000g/gnomix"
path_gno... |
7767a9bf5971c049168f7bda6bcb645c493cacd6454a7d83eea84c75ed99f43d | Shell | 935 | 44 | #!/bin/bash
TMPDIR=`mktemp -d`
mkdir -p $TMPDIR
OUTDIR=~/data/lpl/stdp
mkdir -p $OUTDIR
echo "Tempdir $TMPDIR"
trap 'rm -rf -- "$TMPDIR"' EXIT
# ln -s $TMPDIR/ out/
make
SIMTIME=200
LAMBDA=1
if [ "$1" != "" ]; then
MEAN=$1
else
MEAN=20
fi
if [ "$2" != "" ]; then
SIGMA2=$2
else
SIGMA2=0.1
fi
if [ "$3" != "" ... |
dbe9e949076dd097aa27d4b3e77be7f138b553fba9379c5ceb88944f7ab72fc4 | Shell | 937 | 19 | #!/bin/bash
# https://slurm.schedmd.com/sbatch.html
#SBATCH --partition=priority # Partition (queue)
#SBATCH --time=5:00:00 # Runtime in D-HH:MM format
#SBATCH --job-name=seurat # Job name
#SBATCH -c 1 # cores
#SBATCH --mem=50G # Memory needed per CPU or --mem
#SB... |
e98c9387d1bbdd3f53e53712af64836f6bdfca4ef09624b2494399d50f7a4e0a | Shell | 938 | 30 | # Brain extraction shell script (SGE)
# Author: Ma Da (d.ma.11@ucl.ac.uk)
# Version 0.8_2013.08.29
# to test parameters used for MLSTEPS
# usage: ./STEPS_optimisation_dice.sh $1 $2
# $1: atlas (in_vivo ex_vivo)
# $2: sample number
# echo "Bash version ${BASH_VERSION}"
export QSUB_CMD="qsub -l h_rt=10:00:00 -l h_vmem=3... |
a60843edde55e7a4da24406ef7577440c91cd2325877505cbfb541ba071954a2 | Shell | 939 | 26 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
mkdir -p ${TASKCLUSTER_ARTIFACTS} || true
cp ${DS_ROOT_TASK}/DeepSpeech/ds/tensorflow/bazel*.log ${TASKCLUSTER_ARTIFACTS}/
package_native_client "native_client.tar.xz"
package_libdeepspeech_as_zip "libdeepspeech.zip"
cp ${DS_ROOT_TASK}/DeepSpeech/ds/na... |
5fc8e60f38423a19100534dafb0ae69e575906def5a8944cbf4cfc1656ef735e | Shell | 950 | 26 | #!/bin/sh
# This script analyzes subject data in ~/MATLAB/DATA/Avgusta for each task
# The SGE_TASK variable specifies the data sets, as in $HOME/test.qsub
cd /home/knight/hoycw/PRJ_Error/scripts/
# define where the datasets are located
#PRCSDATADIR="/home/knight/hoycw/PRJ_Error/data/"
# don't change this variable
#... |
6d2881f9e3211214019f95335a4da6de7e35e8be8f7abebddaa67c19431f3a0c | Shell | 950 | 42 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
nodever=$1
if [ -z "${nodever}" ]; then
echo "No node version given, aborting."
exit 1
fi;
bitrate=$2
set_ldc_sample_filename "${bitrate}"
model_source=${DEEPSPEECH_PROD_MODEL//.pb/.tflite}
model_name=$(basename "${model_source}")
model_name_mma... |
b1903c2d8b97dd589ca0dab231cf555e92973f62000e2757922986be5f5842ad | Shell | 953 | 33 | #!/bin/bash
cd $(dirname $0)
cd ..
train_pcqm(){
mkdir -p log/$exp_name model/$exp_name
python3 train_gem2.py \
--inference \
--batch_size=$batch_size \
--num_workers=10 \
--max_epoch=150 \
--dataset_config=$dataset_config \
--data_cache_dir=$data_cache_dir \
... |
57302ccc3c52eea2e4949c2698f810b8d7805a64ede7c891bfd5e99275c89c15 | Shell | 962 | 31 | set -ex
# models
RESULTS_DIR='/workspace/Image_translation_codes/BicycleGAN/results/combined_SEN1_2_20%_fall'
# dataset
CLASS='combined_SEN1_2_20%_fall_bicycle_gan'
DIRECTION='AtoB' # from domain A to domain B
LOAD_SIZE=286 # scale images to this size
CROP_SIZE=256 # then crop to this size
INPUT_NC=3 # number of chan... |
1b7a4aca2c87eb84692ebf0cf35f31f43e3a0e92b906de7472a0c101e29879fc | Shell | 963 | 38 | #!/bin/bash
# Good molecules, unbiased dynamics.
for m in 00077329 00079729 00086442 00107550 00133435 00138607 00140610 00164361 00167648 00169358 01867000 06568023
do
for i in {1..10}
do
sbatch --export=ALL,name=${m},rand1=${i} dyna_mm.slurm
done
done
# Bad/ugly molecules, unbiased dynamics.
for m in 00061095 0... |
7427fb80257d20a5edbf3073ad6b7f4d27808af8ff3811b223ad7f95f4a755fb | Shell | 963 | 24 | #!/bin/sh
if [ -n "$ExternalData_OBJECT_STORES" -a -d "$ExternalData_OBJECT_STORES" ] ; then
extra_args="-v ${ExternalData_OBJECT_STORES}:/var/io/.ExternalData --env ExternalData_OBJECT_STORES=/var/io/.ExternalData"
fi
ARCHS=${ARCH:-"i686 x86_64"}
for ARCH in ${ARCHS}; do
docker build --pull=true --rm=true -... |
7d0ae3ef71a6bc69fbdf2105565a02f1939d01f66f272eb2337d1c8b0ea95e08 | Shell | 964 | 24 | #!/bin/bash -ve
#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################
# stop before inchworm (just in silico norm)
${TRINITY_HOME}/Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right read... |
b5526fdb0b5193746fe14d56a0504a07f5ee97cd341a53f2cb9cd41653629529 | Shell | 965 | 33 | #!/bin/bash
set -xe
source $(dirname "$0")/tc-tests-utils.sh
extract_python_versions "$1" "pyver" "pyver_pkg" "py_unicode_type" "pyconf" "pyalias"
bitrate=$2
set_ldc_sample_filename "${bitrate}"
download_data
virtualenv_activate "${pyalias}" "deepspeech"
deepspeech_pkg_url=$(get_python_pkg_url ${pyver_pkg} ${py_... |
33375ac1ae4c45d22a6b0526256ede18cc24e8103d5db254dfd154b5decf6b6d | Shell | 968 | 44 | #!/bin/bash
IDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
BDIR="$( cd ${IDIR}/../build && pwd )"
SRCDIR="$( cd ${BDIR}/.. && pwd )"
echo "_______________________________________________________________________"
echo "___ "
echo "___ Assembling python package"
echo "___ "
cd ${BDIR}/install
ORIG=${BDIR}/i... |
3b9074115b7cccb775b14ca8757d24fafadca9a6d43177391650f3efe99dc955 | Shell | 969 | 31 | set -ex
# models
RESULTS_DIR='/workspace/Image_translation_codes/BicycleGAN/results/combined_SEN1_2_20%_spring'
# dataset
CLASS='combined_SEN1_2_20%_spring_bicycle_gan'
DIRECTION='AtoB' # from domain A to domain B
LOAD_SIZE=286 # scale images to this size
CROP_SIZE=256 # then crop to this size
INPUT_NC=3 # number of ... |
26425ac71a8e69cb568ab92c2771042282e1bc10c1316106213f3915451aeb08 | Shell | 973 | 29 | #!/bin/bash
set -ex
# This script will be run bazel when building process starts to
# generate key-value information that represents the status of the
# workspace. The output should be like
#
# KEY1 VALUE1
# KEY2 VALUE2
#
# Keys starting with STABLE_ cause dependent rules to be re-run when their value
# changes.
#
# I... |
45701943e87aba8641c5aeab80910322f3a05300b62c75e94ff439b205b694a7 | Shell | 975 | 36 | set -ex
# models
RESULTS_DIR='./results/night2day'
G_PATH='./pretrained_models/night2day_net_G.pth'
E_PATH='./pretrained_models/night2day_net_E.pth'
# dataset
CLASS='night2day'
DIRECTION='AtoB' # from domain A to domain B
LOAD_SIZE=286 # scale images to this size
CROP_SIZE=256 # then crop to this size
INPUT_NC=3 # nu... |
1d6ff8883cc0a00e4f41816439acaf4fdac6e013ebb649d69ec21a77417fa9db | Shell | 976 | 42 | #!/bin/bash -ve
if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
gunzip -c reads.right.fq.gz > reads.right.fq
fi
if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
gunzip -c reads.left.fq.gz > reads.left.fq
fi
#######################################################
## Run Trinity to G... |
456af65e637daf0a71fac083541da05673aaeaf71d960613ab89384b66453c80 | Shell | 976 | 42 | #!/bin/bash -ve
if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
gunzip -c reads.right.fq.gz > reads.right.fq
fi
if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
gunzip -c reads.left.fq.gz > reads.left.fq
fi
#######################################################
## Run Trinity to G... |
beda564d69afaf38452a1c98ee7c603914d9199f408ff246e88551e2c9935471 | Shell | 978 | 21 | #!/bin/bash
export MRTRIX_NTHREADS=$2
bblid=$1
#Intensity normalisation
mtnormalise \
/work/data/MRtrix_recon/sub-${bblid}/ses-PNC1/dwi/sub-${bblid}_wmfod_new.mif \
/work/data/MRtrix_recon/sub-${bblid}/ses-PNC1/dwi/sub-${bblid}_wmfod_new_norm.mif \
/work/data/MRtrix_recon/sub-${bblid}/ses-PNC1/dwi/sub-${bblid}_gm_n... |
108a2c62f26ec4420e61dbb71300b6796a5b9cd2af675a9c0b468a8d6e047958 | Shell | 979 | 32 | #!/bin/bash
# This wrapper converts an Adaptive sequence file to an OLGA TSV, runs OLGA's
# Pgen computation, and puts the result in a file with the original data.
# The following is commented out because of a conda issue https://github.com/ContinuumIO/anaconda-issues/issues/8838
# set -eux
INFILE=$1
OUTFILE=$2
TMP... |
120e1635440dbdb50f31c0c6b09716e4736803a6dbdc07022f919e405f69d84a | Shell | 980 | 31 | #!/bin/sh
set -xe
if [ ! -f DeepSpeech.py ]; then
echo "Please make sure you run this from DeepSpeech's top level directory."
exit 1
fi;
if [ ! -f "data/ldc93s1/ldc93s1.csv" ]; then
echo "Downloading and preprocessing LDC93S1 example data, saving in ./data/ldc93s1."
python -u bin/import_ldc93s1.py ./da... |
a30fd6024d34f3b4797ce3b3ebf2c9b675af2c8e3fd2bbe17b44e95beac934c1 | Shell | 980 | 42 | #!/bin/bash -ve
if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
gunzip -c reads.right.fq.gz > reads.right.fq
fi
if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
gunzip -c reads.left.fq.gz > reads.left.fq
fi
#######################################################
## Run Trinity to G... |
53f81a0bb4434631f4d6d4c09d85270f5830932a8a8561f44a2d06211768065a | Shell | 982 | 18 | set -eux
mkdir -p _output_demo
# Preprocess an Adaptive sequence file.
python3 ../preprocess_adaptive.py --sample 1000 ../pipe_main/sample_data/02-0249_TCRB.4000.tsv.bz2 _output_demo/train.processed.csv
python3 ../preprocess_adaptive.py --sample 100 ../pipe_main/sample_data/02-0249_TCRB.4000.tsv.bz2 _output_demo/100.... |
7fde0b6660caa450819c758da01332f45444e824f40d23a26896070a74f8e83d | Shell | 983 | 37 | set -ex
# models
RESULTS_DIR='./results/maps'
G_PATH='./pretrained_models/map2aerial_net_G.pth'
E_PATH='./pretrained_models/map2aerial_net_E.pth'
# dataset
CLASS='maps'
DIRECTION='BtoA' # from domain A to domain B
LOAD_SIZE=512 # scale images to this size
CROP_SIZE=512 # then crop to this size
INPUT_NC=3 # number of ... |
976eb6476044b9281e6fff556257a3ed7e744dc01703b0b87812bb35086fd3b8 | Shell | 983 | 42 | #!/bin/bash -ve
if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
gunzip -c reads.right.fq.gz > reads.right.fq
fi
if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
gunzip -c reads.left.fq.gz > reads.left.fq
fi
#######################################################
## Run Trinity to G... |
b3153664e80eae478a7d75215b5e7a548bcbceb99e455b1e9ea280cbcaef20b3 | Shell | 983 | 16 | #! /bin/bash
source activate GloDyNE
mkdir bash/log
echo '......Chengbin HOU @SUSTech 2019 AS733 0.1 DynWalks bash......'
echo '------------ AS733_DynWalks_S4.txt-----------------------------------------'
echo '------------ AS733_DynWalks_S4.txt-----------------------------------------' > bash/log/AS733_DynWalks_S4.... |
dddc1c7bda4207387514b40ae23ed568bce8c911ef1e2ea938f3e5129d0e866e | Shell | 983 | 24 | # Brain extraction shell script (SGE)
# Author: Ma Da (d.ma.11@ucl.ac.uk)
# Version 0.8_2013.08.29
# for STEPS label fusion on foler of images with registration already done
# usage: ./labfusion_batch.sh atlas $1 $2 $3 $4
# $1: folder include all the images for label fusion
# $2: atlas (in_vivo ex_vivo)
ROOT_DIR=$(pwd... |
0c8efa1911dc1c66d5ff14212ad4f9847c5e6fddc08edb1983209ec23510a995 | Shell | 989 | 33 | #!/bin/bash
export MRTRIX_NTHREADS=$1
tckgen \
-angle 22.5 \
-maxlen 250 \
-minlen 10 \
-power 1.0 \
/work/data/MRtrix_recon/template/wmfod_template_new.mif \
-seed_image /work/data/MRtrix_recon/template/template_mask_new.mif \
-mask /work/data/MRtrix_recon/temp... |
965313d58087851953f22dcbf60ae7419b599129eb984fb0d9bac24bf2950ecd | Shell | 990 | 23 | #!/bin/bash
#SBATCH --job-name=met
#SBATCH --output=output/standard%A_%a.out
#SBATCH --error=output/standard%A_%a.err
#SBATCH --mem=16000
#SBATCH --time=30:00:00
#SBATCH --gres=gpu:1
#SBATCH --array=0-399
#SBATCH --dependency=after:19718639
#SBATCH --constraint=high-capacity
#SBATCH --exclude=node097,node094,node098,no... |
3b3c496ad3d5b17ad19b34136b6eaaf6958b1808a4c2f285d3bfc40c62ccad6a | Shell | 995 | 31 | #!/bin/sh
#PBS -V
#PBS -q a100
#PBS -N nma-2
#PBS -l nodes=1:ppn=8
#export CUDA_VISIBLE_DEVICES="4"
source /public/home/group_zyl/.bashrc
# conda environment
conda_env=pt200
export OMP_NUM_THREADS=8
#path to save the code
path="/public/home/group_zyl/zyl/program/EFREANN-EMA/reann/"
#Number of processes per node to lau... |
4cdc91a45dcbd036e7bf141607c80485333dc798c2611dd717180a400ede79bb | Shell | 995 | 31 | #!/bin/sh
#PBS -V
#PBS -q a100
#PBS -N water
#PBS -l nodes=1:ppn=8
#export CUDA_VISIBLE_DEVICES="4"
source /public/home/group_zyl/.bashrc
# conda environment
conda_env=pt200
export OMP_NUM_THREADS=8
#path to save the code
path="/public/home/group_zyl/zyl/program/EFREANN-EMA/reann/"
#Number of processes per node to lau... |
fdcb7c2a7763abb1a72187dc7e07e8bd93549e9fb44b4131db55d11e04b6abaf | Shell | 995 | 28 | #!/bin/bash
#$ -q iblm.q
#$ -V
#$ -cwd
#$ -t 1-10
#$ -o /iblm/netapp/data1/jezhou/out
#$ -e /iblm/netapp/data1/jezhou/err
wd=$HOME/rat_snatacseq_analysis/coembed
celltype=`awk -v line=$SGE_TASK_ID 'NR==line' $wd/fimo_celltypes.txt`
bfile=${wd}/fimo/${celltype}_peak_seqs/da_peak_seqs_markov_bg.txt
# motifs=${wd}/fimo/$... |
8f400f53c318be24fe1cd9662ebc138c99878c7b8ce9a51e167d85dbd1a6aff0 | Shell | 999 | 21 | #!/bin/bash
#set -x
NAME="deterministic mapping quality"
BIN="ngmlr-"`grep -o "set( NGM_VERSION_MAJOR [0-9]* )" CMakeLists.txt | cut -d " " -f 3`"."`grep -o "set( NGM_VERSION_MINOR [0-9]* )" CMakeLists.txt | cut -d " " -f 3`"."`grep -o "set( NGM_VERSION_BUILD [^ ]* )" CMakeLists.txt | grep -v debug | cut -d " " -f 3`... |
3ae35d431e94a95865f21022236be6006bd61ce425377100e3b9d5057ad5728f | Shell | 1,004 | 9 | #omp_flags= "-D PKG_USER-OMP=ON -D BUILD_OMP=ON"
#bulid_type="-D CMAKE_BUILD_TYPE=RELEASE "
#build_mpi="-D BUILD_MPI=ON"
#shared_flags="-D CMAKE_SHARED_LINKER_FLAGS='-O3 -DNDEBUG' "
#cmake -D BUILD_MPI=ON -D BUILD_OMP=ON -D CMAKE_SHARED_LINKER_FLAGS='-O3 -DNDEBUG' -D CMAKE_BUILD_TYPE=RELEASE ../cmake
#cmake -D LAMMPS... |
0e7fbf2d81d8b1fc56ad968ffce0815d77288aad11d3f0b964b5fb7212b6c128 | Shell | 1,005 | 35 |
# OBS, currently init is commented out, so numneurons not used
export numNeurons=1000
export simNamePart=1k_cluster_close
export PD_DATA_DIR="$HOME/HBP/BasalGangliaData/Parkinson/20220225"
######################
simName=networks/pd0_$simNamePart
# Note that we need to start ipcluster after the SNUDDA_DATA environ... |
573eb3552726796105e8889ee05f45d32cdf3a145250c344ae670ed6fae2034f | Shell | 1,008 | 31 | #!/bin/bash
#SBATCH -n 1
#SBATCH --partition=pfen1
#SBATCH --time 3:00:00
#SBATCH --job-name=aucell
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=45G
#SBATCH --error=logs/pyscenic_aucell_%A.txt
#SBATCH --output=logs/pyscenic_aucell_%A.txt
###################
## 1) set up paths
PROJDIR=/projects/... |
89f57e2a9e67dddaaca41a1fb23e2ff67727bfd7ebad768eb846501d4816e8da | Shell | 1,008 | 28 | #!/bin/bash
mkdir -p data/ plots/NMF/ results/ results/GSEA/lmmp results/GSEA/mens results/NMF/MENS results/NMF/lmmp results/MENS
#setwd to project home
#Run kallisto bustools workflow
#Requires building kallistobus.yml
#bash ./preprocessing/scripts/run_all.sh
R -e "rmarkdown::render('scripts/MES_6mo_LMMP_analysis.R... |
54ec8ba39a526ce28e454c05b1c7df1946f7a8bfb9729a31baaec9a1cc619639 | Shell | 1,012 | 16 | #! /bin/bash
set -eu
conda install -y -c anaconda glpk libgfortran libgfortran-ng libiconv r-base r-git2r
# I had to add the following line to get svglite to install. You may not need it.
conda install -y -c conda-forge r-gdtools
for PACKAGE in alakazam ape argparse cowplot CollessLike data.table devtools dplyr entrop... |
56f254acf5f9aad5730817c13002abde6074956f3450207a6a68a36c98bfa2f2 | Shell | 1,012 | 30 | #!/bin/bash
#$ -q iblm.q
#$ -V
#$ -cwd
#$ -t 1-12
#$ -tc 4
#$ -o /iblm/netapp/data1/jezhou/out
#$ -e /iblm/netapp/data1/jezhou/err
wd=$HOME/rat_snatacseq_analysis/dapeak_analysis_rn6
celltype=`awk -v line=$SGE_TASK_ID 'NR==line' $wd/data/rds/full_cocaine_dataset_with_naive_rn6/celltypes_list.txt`
outdir=${celltype}_am... |
70dec4e6a0b1e1429d88a388d86c007edd49b9c559fe7f8dbca15a5c49d4b0dc | Shell | 1,012 | 47 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=32G
#SBATCH --gres=gpu:1
#SBATCH --qos=medium
#SBATCH --partition=gpu
#SBATCH --time=1-12:00:00
#SBATCH --job-name=jupyter-notebook
#SBATCH --output=jupyter-notebook-%J.log
# ##SBATCH --nodelist=g010
# get tunneling info
XDG_RUNT... |
6d50bfc9246b653ba893af7055ee831ab2834d80881645442a677cd896f64064 | Shell | 1,018 | 24 | #!/bin/bash
#SBATCH --cluster=beef # Don't change
#SBATCH --partition=long # Don't change
#SBATCH --account=researcher # Don't change
#SBATCH --job-name=aav5_optimize
#SBATCH --output=aav5_post_pre_process.out
#SBATCH --gres=gpu:0 # Number of GPU(s) per node.
#SBATCH --cpus-per-tas... |
6ea2b5fbad65a7f773c8d5f9f75dc80d6457a908733d8f3168c911a9b896f7e8 | Shell | 1,018 | 29 | #!/bin/sh
set -xe
ldc93s1_dir="./data/smoke_test"
ldc93s1_csv="${ldc93s1_dir}/ldc93s1.csv"
epoch_count=$1
audio_sample_rate=$2
if [ ! -f "${ldc93s1_dir}/ldc93s1.csv" ]; then
echo "Downloading and preprocessing LDC93S1 example data, saving in ${ldc93s1_dir}."
python -u bin/import_ldc93s1.py ${ldc93s1_dir}
fi... |
11c95b8a1cdfdda236420fd7a0e40b38b3489fe71da2c23780b2563b0ea68d4d | Shell | 1,025 | 37 | #!/bin/bash
chemprop_dir=../../../chemprop # location of chemprop directory, CHANGE ME
results_dir=results_hiv
train_path=../data/hiv/train.csv
val_path=../data/hiv/val.csv
test_path=../data/hiv/test.csv
#Hyperparameter optimization
python $chemprop_dir/hyperparameter_optimization.py \
--dataset_type classification... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.