sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
c5bb5b36d2e7e45cadf97dc0ce45ead194ce9773ef9aa0577060fc3d90178ff7 | Shell | 385 | 14 | #!/bin/bash
dir=$1
num=1
Schaefer=Schaefer2018_116Parcels_7Networks_inclHippHarvardOxford_float.mnc
source /opt/minc/1.9.18/minc-toolkit-config.sh
for i in $(ls ${dir}/gradient*_template.txt); do
minclookup -clobber -discrete -lookup_table $i ${Schaefer} ${dir}/schaefer2dwi_grad$num.mnc;num=$(bc <<< "${num}+1")
d... |
f13cd9477fd20dcb9caf9690583c6dc759bfa154669f9d4d10925618f0a3bd43 | Shell | 387 | 10 | #!/bin/bash
#SBATCH --output slurm_outputs/dsq-joblist.out
#SBATCH --array 0-62
#SBATCH --job-name encoding
#SBATCH --time "05:59:00"
# DO NOT EDIT LINE BELOW
/mnt/cup/labs/griffiths/bert-brains/code/bert-brains/dsq/dSQBatch.py --job-file /mnt/cup/labs/griffiths/bert-brains/code/bert-brains/joblist.txt --status-dir /m... |
e3aa2aab2e0f786c18dabb348ce176f3c82864a6aec3c60673b5e528995a4455 | Shell | 388 | 7 | LOCALDIR=/Users/akre96/Documents/MoTrPAC/rrbs_bismark/MSSM_MuscleRRBS/Run_Bismark/bash
cd $LOCALDIR
## Run on cloud
#java -Dconfig.file=../google.conf -jar ~/cromwell/cromwell-36.jar run ../tasks/trimGalore.wdl -i ../inputs/trimGalore_inputs_GCloud.json
## Run locally (test)
java -jar ~/cromwell/cromwell-36.jar run ..... |
22a3569d9f7da35090ac2442a56e3a48922e24789695c0a931b7845b85403b44 | Shell | 389 | 21 | #!/bin/bash
# Sometimes the pipeline crashes because some R pkg has
# some memory corruption issues.
# Because the problem is random, retrying usually works
# This script runs `dvc repro` non-stop until it finishes
# successfully
echo `date -R`
while true; do
dvc repro
if [ "$?" = "0" ]; then
exit 0
fi
... |
343862806f4eb80f247d7e8fa188b9cdd254af5a35c786c1671b9f93e0663517 | Shell | 390 | 23 | #$ -cwd
#$ -R y
#$ -l h_fsize=50G
#$ -N 'auto_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: ${HOSTNAME}"
module list
echo "**** Run GO plotting ****"
p... |
80e6b057ed576752952425f513aa59fc07378fa507e5e45542366dc28dd2ede8 | Shell | 390 | 11 | NSAMPLES=500
OUTDIR=data/
DELTA=20
# NOTE we call the prepare script for each folder individually to make
# sure that they are equally represented in the validation split.
for DATA in "/datafolder"; do
python prepare_dataset.py --data_folder "$DATA" --label_folder "/targetfolder" --samples_per_stack $NSAMPLES --o... |
138687f3769ea2c5f1a0dce664cedade028295df0bc59160c77bc48046e7a738 | Shell | 392 | 18 | #!/bin/bash
cd ../../bin/nextflow
module load Nextflow
module load Singularity
nextflow run nf-core/nanoseq -r 2.0.1 \
--input samplesheet.csv \
--protocol cDNA \
--flowcell FLO-MIN106 \
--kit SQK-PCB109 \
--skip_basecalling \
--skip_demultiplexing \
--skip_differential_analysis \
-pr... |
1acf4e33231256c5beba298e41bf8bca627b3163d4fd4ea70327c1734fd137bd | Shell | 394 | 13 | #!/bin/bash
i=$(tail -n+2 data/cayo_brain_bulk_metadata_animals.tsv | cut -f 1 | sed -n ${SLURM_ARRAY_TASK_ID}p)
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/samtools_extract_chromosome.sh ... |
cc4e0d7cbf17863b4e222c19014310b45664faa918b01653d283c82ec74a8a8a | Shell | 394 | 14 | #!/bin/bash
# convert a single BAM to bigwig format
# usage: bash bam2bigwig.sh /path/to/90251015803.Aligned.sortedByCoord.out /path/to/bigwigs
# this command will generate /path/to/bigwigs/90251015803.bw
#
# dependencies: samtools, deeptools
bam=$1
outdir=$2
prefix=$(basename "${bam}" | sed "s/\.Aligned.*//")
samt... |
03a292215a6f8ad57049386a7c709c3909cd75ddd4538d094a24f930a33a05ab | Shell | 395 | 14 | #!/bin/bash
#SBATCH -J gridsearch
#SBATCH -o out_gridsearch.txt
#SBATCH -e err_gridsearch.txt
#SBATCH --time=24:00:00
#SBATCH --cpus-per-task=10
#SBATCH --mem-per-cpu=4G
config_file=$1
# small_search_space: 0 (default - extended parameter search space) or 1 (for debugging: shorter running time)
small_search_spac... |
40e1b6015b026c3ccfb6fc197323dd98a960793e3060596de4c614170a100203 | Shell | 397 | 1 | python /mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/scripts/scripts_for_Feany_lab_omicsintegrator/parameter_select.py /mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/output/Optic_Lobe/gr0.25/Optic_Lobe_randomization_results.pkl W_6.00_B_10.00_G_5.00 "{}.augmented_forest.graphml" "/mnt/data0... |
7a07edf79cef696606a742d53d5148a0f541d6baa8e26501af1c0eae7bc6bb92 | Shell | 399 | 29 | #! /bin/sh
rm config.status
rm aclocal.m4
rm configure
rm configure.status
rm depcomp
rm install-sh
rm Makefile.in
rm Makefile
rm man/Makefile.in
rm man/Makefile
rm src/Makefile.in
rm src/Makefile
rm src/*.o
rm bin/*.o
rm src/fpocket
rm src/dpocket
rm src/tpocket
rm -r autom4te.cache
rm config.log
rm config.h
rm confi... |
881e5c9f521912b4043bf8778ac3ed27c9862dc7c61617f0fcc97ec059b81d9a | Shell | 399 | 24 | #$ -cwd
#$ -R y
#$ -l h_fsize=50G
#$ -N 'go_plotting'
#$ -o ./plotting.out
#$ -e ./plotting.out
echo "**** Job starts ****"
date -Is
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
module load R/3.6.1
module list
echo "**** Run GO p... |
8a5691729d44ee6a67bde68d0fe1da751a196bfb9eb7a979910f53ddb8e4f6fa | Shell | 399 | 16 | #!/bin/sh
set -e
[ -z "${GITHUB_PAT}" ] && exit 0
[ "${TRAVIS_BRANCH}" != "main" ] && exit 0
git config --global user.email "Daniel Rodriguez"
git config --global user.name "danrodgar@gmail.com"
git clone -b gh-pages https://${GITHUB_PAT}@github.com/${TRAVIS_REPO_SLUG}.git book-output
cd book-output
cp -r ../docs/*... |
1558ca3d32e50595141f37c17002ae19104ceaff87be1d533938b9920346fec4 | Shell | 402 | 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/trimDiversityAdapt.wdl -i ../inputs/trimDiversityAdapt_inputs_GCloud.json
## Run locally (test)
java -jar ~/cromwell/cromwell-36.jar run ../w... |
3cd1930b0facfd3c94f7e97a7ce1af0c8ae121be1bf9480de81eb97c00b4b012 | Shell | 402 | 11 | mkdir data
cd data
echo 'Downloading SCOPe dataset ...'
wget https://scop.berkeley.edu/downloads/scopeseq-2.08/astral-scopedom-seqres-gd-sel-gs-bib-40-2.08.fa
wget https://scop.berkeley.edu/downloads/pdbstyle/pdbstyle-sel-gs-bib-40-2.08.tgz
tar -xf pdbstyle-sel-gs-bib-40-2.08.tgz
rm pdbstyle-sel-gs-bib-40-2.08.tgz
cd .... |
1ad02b8fbc0bba550a290c4b6b9fafd54a8d89f0ecff2778656037eb2b0573d6 | Shell | 403 | 4 | python /mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/scripts/scripts_for_Feany_lab_omicsintegrator/omicsIntegrator_launch.py \
/mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/input/drosophila_string_stitch_final.oi2 \
/mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/input/Glia_pr... |
562d3d3780896ba52e06a41e5b79ba0cb2c61ce3240c0eadcb7df598a86fdcda | Shell | 403 | 1 | python /mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/scripts/scripts_for_Feany_lab_omicsintegrator/oi_hyperparameter_evaluate.py /mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/output/Glia/Glia_randomization_results.pkl /mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/input/Glia_... |
ad97143a2b8881b7ac67df624f06981c9d12befe859249013898ab13ac1fe094 | Shell | 404 | 7 | #!/bin/bash
echo "Please enter the GPU address"
read GPU
echo "Sellected GPU: $GPU"
#train
CUDA_VISIBLE_DEVICES=$GPU nohup python train.py --data_path '' --separate_val_path '' --separate_test_path '' --metric mse --dataset_type regression --save_dir '' --target_columns label --epochs 150 --ensemble_size 2 --num_fold... |
f01a1c6a2cdab0a2c11ab77a1a43ccd51d1fe4e1b239b8a12433345c522fe3ac | Shell | 404 | 4 | 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/Central_Body/gr1/Central_Body_randomization_results.pkl \
W_6.00_B_10.00_G_5.00 \ "{}.augmented_forest.graphml" \
"/... |
c7edc4f07b6a946c285bece67547585ee98375394231b6cd078fee7f3c922dff | Shell | 408 | 13 | #!/bin/bash
# arg1: environment used to pick config file to use in /config.
set -e
source .env.local
# cd to project root directory
cd "$(dirname "$(dirname "$0")")"
# Set environment variable (used for config) to staging by default
[[ ! -z "$1" ]] && ENVIRONMENT="$1" || ENVIRONMENT=staging
#ln -sf config/config.${E... |
15af2b15ef819b8116feea3eae9653e32576369e1d9bf02827484fe4f7b357bc | Shell | 412 | 14 | #!/bin/bash
# To choose regularization_strength from the data instead of using the value in
# the config, replace `auto_regularization: null` in configs/phase_3d.yml with the
# commented-out block beneath it.
wo sim \
-c ./configs/phase_3d.yml \
-o ./phase_data.zarr
wo rec \
-i ./phase_data.zarr \
-c ./configs... |
0b8ad6cc80fa3e64f6eb2a497a7084f55d2d7317ca4664533e0e7ec90f217936 | Shell | 414 | 7 | LOCALDIR=/Users/akre96/Documents/github/rrbs_bismark/Quantify_Methylation
cd $LOCALDIR
## Run on cloud
java -Dconfig.file=/Users/akre96/Documents/github/rrbs_bismark/google.conf -jar ~/cromwell/cromwell-36.jar run quantify_methylation.wdl -i quantify_methylation_inputs_GCloud.json
## Run locally (test)
#java -jar ~/cr... |
e4db409fb70ecccd66317ab3887cb2ec693d12105ee723e804c4aaa35c52f54a | Shell | 415 | 15 | #!/usr/bin/env bash
# DWI-to-native-surface pipeline. Cache cleanup is on; postprocessing is opt-in.
set -euo pipefail
PROJECT_ROOT=$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)
ARGS=()
while (($#)); do
case "$1" in
-s) ARGS+=(--subject); shift ;;
-h) ARGS+=(--help); shift ;;
*) ARGS+=("$1"); shift ;;
... |
f41eae143a12d4cd07c2219d2f3bf4f453d494a825f7fb060384aa4e4fa04ed4 | Shell | 416 | 4 | python /mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/scripts/scripts_for_Feany_lab_omicsintegrator/omicsIntegrator_launch.py \
/mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/input/drosophila_string_stitch_final.oi2 \
/mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/input/OL_CB_G... |
ff7f9ce3e65e449fe666b6b84c2e74c9812fe0ba031cebfe71fdcbe9f938b17e | Shell | 417 | 25 | #$ -cwd
#$ -R y
#$ -l h_fsize=50G
#$ -N 'go_plotting'
#$ -o ./plotting.out
#$ -e ./plotting.out
echo "**** Job starts ****"
date -Is
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
module load R/3.6.1
module load python
module list
... |
a738ca2ad071397db5d29b5acc88b7f4168327f1b0a2bfe650b065523bb38a64 | Shell | 419 | 4 | python /mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/scripts/scripts_for_Feany_lab_omicsintegrator/omicsIntegrator_launch.py \
/mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/input/drosophila_string_stitch_final.oi2 \
/mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/input/OL_priz... |
5ca401b33e55c78302fd5aeb04045e673281d2948ee4b2c40097d62d1136a627 | Shell | 420 | 13 | #!/usr/bin/env bash
# Use WDLTools to lint and check the WDL
curl -LJO https://github.com/dnanexus/wdlTools/releases/download/0.17.4/wdlTools-0.17.4.jar
curl -LJO https://github.com/broadinstitute/cromwell/releases/download/65/womtool-65.jar
# Create a new virtual environment
python3 -m venv venv
source venv/bin/act... |
fecb5a4958ef8bf41b60e033b55e653c48362b0339fc54af5a2d4dd5582749c7 | Shell | 420 | 6 | PREFIX="/Volumes/BIOINFORMATICS/projects/hassan2022/output/merged/expectedCells/"
SUFFIX="/outs/filtered_feature_bc_matrix"
OUTS="/Volumes/BIOINFORMATICS/projects/hassan2022/output/merged/scrublet/"
SAMPLES=("control1" "CRN00224919" "CRN00224920" "P251L2merged" "CTRL2merged" "TauKO1merged" "LIB055588_CRN00233457" "LIB0... |
20e43716d59cd8bd6a06835936745495f6c66b7e2fdf8d006c82c9d8f46d2343 | Shell | 421 | 24 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=10.0G,h_vmem=10G,h_fsize=50G
#$ -N 'summarize_eqtl'
#$ -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
... |
093ad1ded377a1014502fec43ad2c83b64cfcf3332a0525a327edb71770c0e92 | Shell | 425 | 21 | #!/bin/bash
#
# grep all regexes used in the pipeline.ini file of pipeline_testing.py
#
# useful to debug pipeline_testing.py
#
if [ $# -ne 1 ] ; then
echo
echo " Usage: get_testing_regexes.sh /pipeline/testing/pipeline.ini"
echo
exit 1 ;
fi
egrep '^suffixes|^regex_linecount|^regex_exist' $1 \
| sed 's... |
1b0a7052011c60eea50c3857d1a41e496acef0976700af984526df1f476ef884 | Shell | 425 | 28 | VIEW_POS0=63
VIEW_POS1=75
VIEW_POS2=0
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VIEW_POS12=0
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VIEW_POS14=0
VIEW_POS15=0
VIEW_XDIM=1
VIEW_YDIM=0
VIEW_ZOOM=2.768750e+00
VIEW_ANISO=1.000000e+00
VIEW_FLIP=XO
VIEW_TRANSPOSE=1
VIEW_PLOT=0
VIEW_... |
1cbddee7e22e38f25642d1ecca9bb57804e540a9b21e9fbbd2e6d38d924f108a | Shell | 425 | 28 | VIEW_POS0=63
VIEW_POS1=75
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VIEW_POS14=0
VIEW_POS15=0
VIEW_XDIM=1
VIEW_YDIM=0
VIEW_ZOOM=2.768750e+00
VIEW_ANISO=1.000000e+00
VIEW_FLIP=XO
VIEW_TRANSPOSE=1
VIEW_PLOT=0
VIEW_... |
2d2c2e4b98e60bedcbe605f763b06a6fceb08e120cfe044933dcd3f1879b967f | Shell | 425 | 21 | #!/bin/bash
RUN_TIME_PROJECT=$(date '+%d/%m/%Y %H:%M:%S')
DIRECTORY_PROJECT='../Models'
echo -e "Script run on $RUN_TIME_PROJECT" >> info.txt
echo -e "\n\ngit info\n\n" >> info.txt
git status >> info.txt
git log -n 1 >> info.txt
if [ -d $DIRECTORY_PROJECT/ ]
then
git rm -rf $DIRECTORY_PROJECT/
fi
mkdir $DIREC... |
c7410ea8e1834796c33768f8f0d16a40dd87489a5701aff725fd2ee6b66750b7 | Shell | 425 | 28 | VIEW_POS0=63
VIEW_POS1=75
VIEW_POS2=0
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VIEW_POS7=0
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VIEW_POS10=17
VIEW_POS11=0
VIEW_POS12=0
VIEW_POS13=16
VIEW_POS14=0
VIEW_POS15=0
VIEW_XDIM=1
VIEW_YDIM=0
VIEW_ZOOM=2.768750e+00
VIEW_ANISO=1.000000e+00
VIEW_FLIP=XY
VIEW_TRANSPOSE=1
VIEW_PLOT=0
VIEW_... |
61b6a60920005e57c06fc550e0beac00e32da578c309d25ca2a0d172dc41945f | Shell | 426 | 4 | python /mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/scripts/scripts_for_Feany_lab_omicsintegrator/omicsIntegrator_launch.py \
/mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/input/drosophila_string_stitch_final.oi2 \
/mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/input/CB_priz... |
7e14179c14ffaf3290f4cf376093be47fa5f4e12a41552cc2f28389ce97f948c | Shell | 426 | 28 | VIEW_POS0=89
VIEW_POS1=67
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VIEW_POS3=0
VIEW_POS4=0
VIEW_POS5=0
VIEW_POS6=0
VIEW_POS7=0
VIEW_POS8=0
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VIEW_POS10=109
VIEW_POS11=0
VIEW_POS12=0
VIEW_POS13=13
VIEW_POS14=0
VIEW_POS15=0
VIEW_XDIM=1
VIEW_YDIM=0
VIEW_ZOOM=3.800000e+00
VIEW_ANISO=1.000000e+00
VIEW_FLIP=XY
VIEW_TRANSPOSE=1
VIEW_PLOT=0
VIEW... |
a32febe15a2ee0254be0adf3718c14e99af6a9cc1d6797809742ff3728558175 | Shell | 426 | 28 | VIEW_POS0=105
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VIEW_POS14=0
VIEW_POS15=0
VIEW_XDIM=10
VIEW_YDIM=1
VIEW_ZOOM=2.981250e+00
VIEW_ANISO=1.000000e+00
VIEW_FLIP=OO
VIEW_TRANSPOSE=1
VIEW_PLOT=0
VIEW... |
2fcd959e84ca7df852df01dc5bb49ffb2643e4b74dbf5b95a543c257d7326660 | Shell | 427 | 12 | #!/bin/bash
# NOTE: Work in progress. Pipeline runs end-to-end but physics still being validated.
wo sim \
-c ./configs/birefringence-and-phase_3d.yml \
-o ./birefringence_and_phase_data.zarr
wo rec \
-i ./birefringence_and_phase_data.zarr \
-c ./configs/birefringence-and-phase_3d.yml \
-o ./birefringence_an... |
7899dfd421aff01d756d5d1fa4bce8867bf12ac67d41ae352638c20de7e3a4b6 | Shell | 427 | 18 | #!/bin/bash
#SBATCH -o ckd-fast.out
#SBATCH --cpus-per-task=10
#SBATCH --mem-per-cpu=4G
#SBATCH --time=24:0:0
# Various Test runs
iterations=10
python __main__.py -c ../../conf/CKD_config.yaml -o CKD-fast -n 10 -i $iterations -f
#python __main__.py -c ../../conf/CKD_config.yaml -o CKD-et_rf -n 10 -i $iterations -... |
0e2460c9206967b47ba0208dc841365e3091457318ade9f76caa4e1fed352f45 | Shell | 428 | 28 | VIEW_POS0=63
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VIEW_POS14=0
VIEW_POS15=0
VIEW_XDIM=1
VIEW_YDIM=0
VIEW_ZOOM=2.768750e+00
VIEW_ANISO=1.000000e+00
VIEW_FLIP=XO
VIEW_TRANSPOSE=1
VIEW_PLOT=0
VIEW_... |
263fc368cb1f6ab6886dbe4c55cc80090e7ddb31b73e0168f0df5177c388203c | Shell | 428 | 28 | VIEW_POS0=89
VIEW_POS1=67
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VIEW_XDIM=1
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VIEW_ZOOM=3.800000e+00
VIEW_ANISO=1.000000e+00
VIEW_FLIP=XY
VIEW_TRANSPOSE=1
VIEW_PLOT=0
VIEW_... |
349f45810e5b06858f4436b81c515cf165e6fbc7a33537308eb3b3805018265f | Shell | 428 | 28 | VIEW_POS0=65
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VIEW_POS11=0
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VIEW_POS13=16
VIEW_POS14=0
VIEW_POS15=0
VIEW_XDIM=10
VIEW_YDIM=1
VIEW_ZOOM=2.981250e+00
VIEW_ANISO=1.000000e+00
VIEW_FLIP=OO
VIEW_TRANSPOSE=1
VIEW_PLOT=0
VIEW_... |
ae8174701e6bc9e29ba21b259bcf16d637698947d983268b2536647c39d98f64 | Shell | 429 | 28 | VIEW_POS0=89
VIEW_POS1=67
VIEW_POS2=0
VIEW_POS3=0
VIEW_POS4=0
VIEW_POS5=0
VIEW_POS6=0
VIEW_POS7=0
VIEW_POS8=0
VIEW_POS9=0
VIEW_POS10=111
VIEW_POS11=0
VIEW_POS12=0
VIEW_POS13=13
VIEW_POS14=0
VIEW_POS15=0
VIEW_XDIM=1
VIEW_YDIM=0
VIEW_ZOOM=3.800000e+00
VIEW_ANISO=1.000000e+00
VIEW_FLIP=XY
VIEW_TRANSPOSE=1
VIEW_PLOT=0
VIEW... |
b6686b5ba60c4226439595024597ff4d705da4e324b8a025d853597c111157e5 | Shell | 429 | 28 | VIEW_POS0=129
VIEW_POS1=107
VIEW_POS2=0
VIEW_POS3=0
VIEW_POS4=0
VIEW_POS5=0
VIEW_POS6=0
VIEW_POS7=0
VIEW_POS8=0
VIEW_POS9=0
VIEW_POS10=109
VIEW_POS11=0
VIEW_POS12=0
VIEW_POS13=13
VIEW_POS14=0
VIEW_POS15=0
VIEW_XDIM=10
VIEW_YDIM=1
VIEW_ZOOM=2.981250e+00
VIEW_ANISO=1.000000e+00
VIEW_FLIP=OO
VIEW_TRANSPOSE=1
VIEW_PLOT=0
V... |
c218a2adf8718484e0612df74c87d55659f4d3d29e2f907207c6f0f1d2171b6d | Shell | 429 | 1 | python /mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/scripts/scripts_for_Feany_lab_omicsintegrator/oi_hyperparameter_evaluate.py /mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/output/Glia_OL_CB/Glia_OL_CB_randomization_results.pkl /mnt/data0/projects/biohub/hassan2022/output/omicsintegrato... |
023fe9c1929b658fbe2180b0783e2d1664aef6b5fa417cd723d8195705470061 | Shell | 430 | 28 | VIEW_POS0=0
VIEW_POS1=0
VIEW_POS2=0
VIEW_POS3=0
VIEW_POS4=0
VIEW_POS5=0
VIEW_POS6=0
VIEW_POS7=0
VIEW_POS8=0
VIEW_POS9=0
VIEW_POS10=0
VIEW_POS11=0
VIEW_POS12=0
VIEW_POS13=0
VIEW_POS14=0
VIEW_POS15=0
VIEW_XDIM=1
VIEW_YDIM=0
VIEW_ZOOM=1.987500e+00
VIEW_ANISO=1.000000e+00
VIEW_FLIP=XY
VIEW_TRANSPOSE=1
VIEW_PLOT=0
VIEW_MODE... |
60bc8f3c4266b4c4cfe12fe594fc5d4bbe5aeddc42f3a30d7b86c56b2cf9b0bf | Shell | 430 | 28 | VIEW_POS0=0
VIEW_POS1=0
VIEW_POS2=0
VIEW_POS3=0
VIEW_POS4=0
VIEW_POS5=0
VIEW_POS6=0
VIEW_POS7=0
VIEW_POS8=0
VIEW_POS9=0
VIEW_POS10=0
VIEW_POS11=0
VIEW_POS12=0
VIEW_POS13=0
VIEW_POS14=0
VIEW_POS15=0
VIEW_XDIM=1
VIEW_YDIM=0
VIEW_ZOOM=1.863281e+00
VIEW_ANISO=1.000000e+00
VIEW_FLIP=XO
VIEW_TRANSPOSE=1
VIEW_PLOT=0
VIEW_MODE... |
b55b850c4d404097d629c1281c394fe908cf7d50f38545fb3ff1d5f0ec6b9fa2 | Shell | 430 | 28 | VIEW_POS0=89
VIEW_POS1=67
VIEW_POS2=0
VIEW_POS3=0
VIEW_POS4=0
VIEW_POS5=0
VIEW_POS6=0
VIEW_POS7=0
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VIEW_POS9=0
VIEW_POS10=111
VIEW_POS11=0
VIEW_POS12=0
VIEW_POS13=13
VIEW_POS14=0
VIEW_POS15=0
VIEW_XDIM=10
VIEW_YDIM=1
VIEW_ZOOM=2.981250e+00
VIEW_ANISO=1.000000e+00
VIEW_FLIP=OO
VIEW_TRANSPOSE=1
VIEW_PLOT=0
VIE... |
ee3e0700346aa1c10016453264b5b35ad74087d37ab229c51206bbe8d1e78df4 | Shell | 430 | 28 | VIEW_POS0=0
VIEW_POS1=0
VIEW_POS2=0
VIEW_POS3=0
VIEW_POS4=0
VIEW_POS5=0
VIEW_POS6=0
VIEW_POS7=0
VIEW_POS8=0
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VIEW_POS10=0
VIEW_POS11=0
VIEW_POS12=0
VIEW_POS13=0
VIEW_POS14=0
VIEW_POS15=0
VIEW_XDIM=1
VIEW_YDIM=0
VIEW_ZOOM=1.987500e+00
VIEW_ANISO=1.000000e+00
VIEW_FLIP=XY
VIEW_TRANSPOSE=1
VIEW_PLOT=0
VIEW_MODE... |
713d5e76ebcb41cba3b8992c38dbd3e6d73a23d762f20d724bcd87791061bd0e | Shell | 432 | 17 | #!/bin/bash
mkdir -p plots
mkdir -p vispdb
mkdir -p results
python ../scripts/compare_feature_distributions.py \
--ref_file_a traj/condition-a_receptor.gro \
--trj_file_a traj/condition-a_receptor.xtc \
--ref_file_b traj/condition-b_receptor.gro \
--trj_file_b traj/condition-b_receptor.xtc \
--out_plots plots/r... |
aed2c44f59047552f5216da9dafbf8597d22b020b63c6bd0004e5e9bb20cbc83 | Shell | 432 | 9 | #!/usr/bin/env bash
find leftImg8bit/train -maxdepth 3 -name "*_leftImg8bit.png" | sort > train_images.txt
find leftImg8bit/val -maxdepth 3 -name "*_leftImg8bit.png" | sort > val_images.txt
find leftImg8bit/test -maxdepth 3 -name "*_leftImg8bit.png" | sort > test_images.txt
find gtFine/train -maxdepth 3 -name "*_trai... |
72ee2bda83dc8979bba03b1356c107ffaf3a02d2c04c6677c310fa36195eed8c | Shell | 433 | 24 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=100.0G,h_vmem=100G,h_fsize=50G
#$ -N 'summarize_eqtl'
#$ -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: ${HOSTNAME}"
module list... |
9d9caa8fb91316d0b99e2b957616579e08a1dfc1ec1aba110365494ae7f3244e | Shell | 433 | 24 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=150.0G,h_vmem=150G,h_fsize=50G
#$ -N 'summarize_eqtl'
#$ -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: ${HOSTNAME}"
module list... |
26b172d6f50f47747a07451366b7c277c64564579f25c93247f77da3570e885a | Shell | 437 | 28 | VIEW_POS0=0
VIEW_POS1=0
VIEW_POS2=0
VIEW_POS3=0
VIEW_POS4=0
VIEW_POS5=0
VIEW_POS6=0
VIEW_POS7=0
VIEW_POS8=0
VIEW_POS9=0
VIEW_POS10=0
VIEW_POS11=0
VIEW_POS12=0
VIEW_POS13=0
VIEW_POS14=0
VIEW_POS15=0
VIEW_XDIM=1
VIEW_YDIM=0
VIEW_ZOOM=2.620879e+00
VIEW_ANISO=1.000000e+00
VIEW_FLIP=XO
VIEW_TRANSPOSE=1
VIEW_PLOT=0
VIEW_MODE... |
16d16bc48ead64134b1d4e149106a2e08f429a4cde0909887aa1f63571de6d46 | Shell | 439 | 1 | CUDA_VISIBLE_DEVICES=0 python experiments.py --seed=1 --data_path=../data/ns_V1e-4_N10000_T30.mat --results_path=./DEBUG --strategy=oneshot --T=20 --ntrain=10 --nvalid=10 --ntest=10 --model_type=FNO3d --modes=8 --width=20 --batch_size=10 --epochs=1 --suffix=seed1 --txt_suffix=ns_V1e-4_N10000_T30.mat_FNO3d_seed1 --learn... |
e15f31399dad60797a585dc940b5aa800c9fdc5d0f7aeb44e0559382fe5194d3 | Shell | 439 | 24 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=20G,h_vmem=20G,h_fsize=50G
#$ -N 'enrichment_fishers'
#$ -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: ${HOSTNAME}"
module list... |
f777a8f77235baca26cac8ce16628a7b78600fffdbf46416fa0294b3a258b7ff | Shell | 440 | 24 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=100.0G,h_vmem=100G,h_fsize=50G
#$ -N 'clinical_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... |
5c20c0afa3775013eff000297379b222a4ae556540e52ad6ab66965157d62c8c | Shell | 441 | 18 | #!/bin/bash
start=$1
end=$2
njobs=$3
folder=${4:-\$\{now:%H-%M-%S\}}
ntrials=$(((end-start+njobs-1) / njobs ))
for i in `seq 0 $((njobs-1))`;
do
curr_start=$((start+(i*ntrials)))
curr_end=$((start+((i+1)*ntrials)-1))
if [ $curr_end -gt $end ]
then
curr_end=$end
fi
time sh run_configs.sh $curr_s... |
02feafdf78bc00663e7fae83b9117a072dbf3df17fb7c3ffe15ee8ad732ba9a7 | Shell | 442 | 25 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=5G,h_vmem=5G,h_fsize=50G
#$ -N 'overlap_qin'
#$ -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 load pandoc
m... |
3cd90e2e1e7dba8fee25478b283882ff87cbbf153d1ecb1438a5d00ff78e321d | Shell | 443 | 15 | #!/bin/bash
# Note that in the example below the indices in the
# input_pdbs/7zkr_GABARAP.pdb file have been shifted
# by +2 in chain A relative to pdbID 7zkr.
../scripts/run_inference.py \
--config-name base \
inference.output_prefix=example_outputs/uncond_cycpep \
inference.num_designs=10 \
'contigmap.contigs=[12... |
a3ba8b05171695cf83b0c8105d00500cb74c75ad38d1177f03df374ca1fcc9fe | Shell | 444 | 8 | DATA_FOLDER=../../data
OUTPUT_FOLDER=../../outputs/smoothed_plot
(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" > $OUTPUT_FOLDER/psd_by_trial_type.o... |
6dca11aceb15432cf66b161d1061d78dd1dc6387b8b7fb403e3b06166d2aa23b | Shell | 447 | 15 | #!/bin/bash
genDir=/fslgroup/fslg_spec_networks/compute
codeDir=${genDir}/code/Utah_analysis/freesurfer
dataDir=/fslgroup/grp_proc/compute/Utah_analysis/Utah_BIDS
for subj in `cat ${codeDir}/ALL_subjids.txt`; do
mkdir -p ${codeDir}/logfiles
sbatch \
-o ${codeDir}/logfiles/output_sub-${subj}.txt \
... |
7bfb6443aa975f9483ad65a91daeaa4567443dec420a78096030d07624c92590 | Shell | 447 | 1 | python /mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/scripts/scripts_for_Feany_lab_omicsintegrator/oi_hyperparameter_evaluate.py /mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/output/Optic_Lobe/gr0.5/Optic_Lobe_randomization_results.pkl /mnt/data0/projects/biohub/hassan2022/output/omicsinte... |
038089c8b99bc7ea1743d50fc9d4fb7d104c31a0527c4b5b85b506d7aa793888 | Shell | 449 | 18 | # Some of the more detailed metrics require the barrel centers and depth files, so run those first.
echo 'extract barrel centers'
python extract_barrel_centers.py
echo 'extract depth'
python get_layer_shells.py
python shell_based_depth.py
python extract_shell_depth.py
echo 'extract other metrics'
python extract_volu... |
520b4bfbc53cdd26de0ccb4a54e2890336ab2efd1286392cd8558810245731fb | Shell | 449 | 8 | #!/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
#for i in input_json/harmony_test/stanford_working/* ;do ./submit_rnaseq_generic.sh $i;done >>jobs.sh
#chmod +x jobs.sh
echo... |
d74354d90367d0b6e7341d6302e766636eff83a21412fbe0cbc22a4a599ce06e | Shell | 451 | 10 | for df in packages/coinstac-images/coinstac-base/dockerfiles/*
do
BASEFILE=$(basename $df)
docker build -f $df -t \
coinstacteam/coinstac-base:${BASEFILE/Dockerfile-/} \
packages/coinstac-images/coinstac-base/ || exit $?
docker push coinstacteam/coinstac-base:${BASEFILE/Dockerfile-/} || exit $?
done
docker ta... |
848ddb31682ee331a9f351c9b7d1b7807f1cede3163ca4754a3871a7d8b7628c | Shell | 453 | 25 | #!/bin/bash
# Following FSL and CUDA Version need to be active
# CUDA --version 8.0
# FSL --version 5.0.11
# Load Local Variables
source ./SET_VARIABLES.sh
echo "Removing intermedidate calculation folders"
rm -rf \
${DIFF_DATA_N4_DIR} \
${EDDY_DIR} \
${EDDY_FIELDS_DIR} \
${EDDY_FIELDS_REL_DIR} \
... |
616ebb465ae8895bb73e4b0a308d9adb29718fb2c0b026cd0fa249d55cd03c60 | Shell | 455 | 26 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l h_fsize=50G
#$ -N 'plot_enrichment'
#$ -o ./summary.out
#$ -e ./summary.out
#$ -m e -M jade.benjamin@libd.org
echo "**** Job starts ****"
date -Is
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
modu... |
9735efc1e72e68362b3929e4bd6d293808e93a0030362847b2f6139d1355507b | Shell | 455 | 18 | if [[ $# -ne 1 ]]; then
echo " Invalid number of arguments (1 expected)!"
exit 2
fi
PARTN=$1
runai submit \
--name sgospm12-abcd-p1-$PARTN \
--image 10.202.67.207:5000/wds20:sgospm12 \
--backoff-limit 0 \
--gpu 0 \
--cpu 1 \
--large-shm \
--node-type dgx1-3 \
--host-ipc \
--project wds20 \
--v... |
ce087aeb27183f529c48d7352c0fd5b98421e7ec750762f7ce6c4a39da3b211e | Shell | 456 | 18 | if [[ $# -ne 1 ]]; then
echo " Invalid number of arguments (1 expected)!"
exit 2
fi
PARTN=$1
runai submit \
--name sgospm12-bhrcs-p1-$PARTN \
--image 10.202.67.207:5000/wds20:sgospm12 \
--backoff-limit 0 \
--gpu 0 \
--cpu 1 \
--large-shm \
--node-type dgx1-3 \
--host-ipc \
--project wds20 \
--... |
1e758879aa91504bba62990c596b63a254858ececdeb102bd9d8254db51f365b | Shell | 457 | 6 | set -e
docker build -f packages/coinstac-images/coinstac/dockerfiles/Dockerfile-ci -t coinstacteam/coinstac:ci .
docker build -f packages/coinstac-images/coinstac/dockerfiles/Dockerfile-ci-ui -t coinstacteam/coinstac-desktop-app:ci .
docker build -f packages/coinstac-images/coinstac/dockerfiles/Dockerfile-api -t coins... |
a86ee8a5b36f3f34d7a1c064be177b78e9d7dda401b0326e0f603a85fd61bce8 | Shell | 458 | 1 | python /mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/scripts/scripts_for_Feany_lab_omicsintegrator/oi_hyperparameter_evaluate.py /mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/output/Central_Body/gr1/Central_Body_randomization_results.pkl /mnt/data0/projects/biohub/hassan2022/output/omicsin... |
2f42f68a3df0a1a7c3335dd5746fd9a0f59643a7f8bb11067d9929b2fa99a19f | Shell | 460 | 17 | #!/bin/bash
config_file=$1
run_external_benchmark=$2
benchmark_tool=$3
top_ratio=0.05
python benchmarking_collapsing_hypergeom_enrichment.py $config_file $run_external_benchmark $benchmark_tool
# Get consensus novel and known genes from mantis-ml predictions
if [ $run_external_benchmark == "0" ]; then
python get... |
97f69f0991c01c00cb64ea523e3d6dd93186878e3092634eb5403457f018fe05 | Shell | 460 | 1 | python /mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/scripts/scripts_for_Feany_lab_omicsintegrator/filter_and_visualize_network.py /mnt/data0/projects/biohub/hassan2022/output/omicsintegrator/output/Central_Body/W_6.00_B_5.00_G_6.00.augmented_forest.graphml /mnt/data0/projects/biohub/hassan2022/output/om... |
b8a203f5a1152a63279d7c23fc9a29cb5a42dd3ca1720db25ca4671c2e60681b | Shell | 460 | 18 | if [[ $# -ne 1 ]]; then
echo " Invalid number of arguments (1 expected)!"
exit 2
fi
PARTN=$1
runai submit \
--name sgospm12-abide2-p1-$PARTN \
--image 10.202.67.207:5000/wds20:sgospm12 \
--backoff-limit 0 \
--gpu 0 \
--cpu 1 \
--large-shm \
--node-type dgx1-3 \
--host-ipc \
--project wds20 \
-... |
6aab37cef4579e965ed871c5dd56ab358d0a6125084de2513bbf07537aab7d21 | Shell | 462 | 18 | if [[ $# -ne 1 ]]; then
echo " Invalid number of arguments (1 expected)!"
exit 2
fi
PARTN=$1
runai submit \
--name sgospm12-adhd200-p1-$PARTN \
--image 10.202.67.207:5000/wds20:sgospm12 \
--backoff-limit 0 \
--gpu 0 \
--cpu 1 \
--large-shm \
--node-type dgx1-3 \
--host-ipc \
--project wds20 \
... |
8ec6e99078a50b71f037c1772f81cedba0d6c1adc33f2b16f43715d2e612afb5 | Shell | 462 | 6 | cd rcnn
mkdir results
mkdir records
# python program.py <dataset> <column_index_of_score> <result_location> <id_for_embeddings: 0=onehot, 1=a_c, 2=a_{ph}, 3=[a_c,a_{ph}]> <hidden_dim> <epochs_per_fold>
CUDA_VISIBLE_DEVICES=4 python rcnn.py ../../../mtb/preprocessed/SKEMPI_all_dg_avg.txt -1 results/mtb_wvctc_rcnn_25.txt... |
156689f277bf941ad3807000cd8e5959f436b2c9f440d474ba1fd693c76a8ff8 | Shell | 463 | 11 | conda create --name PDE python=3.8
conda activate PDE
conda install -c conda-forge tmux -y
conda install -c conda-forge gpustat -y
conda install -c conda-forge tqdm -y
conda install pytorch==1.12.1 torchvision==0.13.1 torchaudio==0.12.1 cudatoolkit=11.3 -c pytorch -y
conda install -c conda-forge tensorboard -y
conda in... |
6f5d03837d5f0983a43699b2181522a2683ce975642fc4d1dad2a8d593f8db6c | Shell | 463 | 17 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
export BART_COMPAT_VERSION="v0.9.00"
FSIZE=$1
INPUT=$(readlink -f $2)
OUTPUT=$(readlink -f $3)
WORKDIR=$(mktemp -d 2>/dev/null || mktemp -d -t 'mytmpdir')
trap 'rm -rf "$WORKDIR"' EXIT
PAD=$((FSIZE-1))
bart resize -c ... |
941e6474fbb065e8bda4fbf39652b298992cd72c0656abfc43957be2ca19506f | Shell | 464 | 14 | #!/bin/bash
# Reconstruct in overlapping YX tiles and blend them back into one volume.
# configs/tile-stitch_phase_3d.yml holds the tiling and the blend, plus a
# `recon` block with the same schema as configs/phase_3d.yml.
wo sim \
-c ./configs/phase_3d.yml \
-o ./phase_data.zarr
wo tile-stitch \
-i ./phase_data... |
9e564b4d6efa0453f98afacb6a52556b92bbfab065e021f42eccf1f42113f2b1 | Shell | 464 | 27 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l mem_free=10.0G,h_vmem=10G,h_fsize=50G
#$ -N 'correlation'
#$ -o ./summary.log
#$ -e ./summary.log
echo "**** Job starts ****"
date -Is
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
#### List module... |
10bc09006f45e28cea0d89eacfcdf8cd661b470db16db6517be0a17e3103eea6 | Shell | 469 | 28 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l h_fsize=50G
#$ -N 'plot_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 load conda_R/4.2.x
module load ... |
de7408536c0d05c943353bc592444767d45c611b03ed5979b63d2fbf02bbc7f4 | Shell | 473 | 9 | #!/bin/bash
for i in `seq $1 $2`;
do
echo -e "\n\n ******** started trial $i ******** \n\n"
time C:\\Users\\avivra\\PycharmProjects\\pythonProject\\venv\\Scripts\\python.exe main.py --config-name=config$i hydra.run.dir=\"outputs/$3/$i\"
#echo C:\\Users\\avivra\\PycharmProjects\\pythonProject\\venv\\Scripts\\... |
37204c7c7bacc8099217a2533f6619f77337d38555ec3d7b8b51c7de3ae4c3b0 | Shell | 474 | 27 | #$ -cwd
#$ -R y
#$ -l mem_free=50G,h_vmem=50G,h_fsize=50G
#$ -N 'pi1_analysis'
#$ -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: ${HOSTNAME}"
module load conda_R/4.2.x
mod... |
0360144005f3dd9582f2818556e3cb59cfe4a55176953329d8154fb0509652cb | Shell | 476 | 21 | #Installations needed:
#pip install sphinx
#pip install sphinx_rtd_theme
# Remove old docs
rm -r source/* _build
# Auto-generate API docs:
sphinx-apidoc -M -o ./source ../pensa
# Format the auto-generated API docs
sed -i 's/ package//g' source/*.rst
sed -i 's/ module//g' source/*.rst
sed -i -e '/Submodules/,+2d' sou... |
182fe393fb2d1a831981a006231fe1d45a4c63b1859b6cbd997a7785a246ddbf | Shell | 477 | 27 | #!/bin/bash
#$ -cwd
#$ -N corr_variables
#$ -o ./summary.log
#$ -e ./summary.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for reproducibility
module load conda_R/4.2.x
m... |
79e76425c1d8b87f401d101e5f74a7e9921c26007e42028450a2a92d56f9eb05 | Shell | 477 | 13 | #!/bin/sh
mkdir -p "database/uniprot"
export ftp_proxy=${http_proxy}
wget \
"https://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping_selected.tab.gz" \
-O "database/uniprot/uniprot_HUMAN_9606_idmapping_selected.tab.gz"
wget \
"https://ftp.uniprot.org/pub/database... |
f8796bb5a38ed057778564a41022066a6a213c093404d55fccdf5713b6429d4d | Shell | 477 | 7 | #!/bin/bash
wget -P ../../data/gencode_annotations https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M31/gencode.vM31.primary_assembly.annotation.gtf.gz
wget -P ../../data/gencode_annotations https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M31/GRCm39.primary_assembly.genome.fa.gz
gun... |
a9603e7d494ea5d474811209eb0e334267de9b2170e5b6849233bd9e65ab4649 | Shell | 480 | 10 | DATA_FOLDER=../../data
OUTPUT_FOLDER=../../outputs/provenance_mpi
mkdir -p $OUTPUT_FOLDER
(python --version && pip list && pip freeze) > $OUTPUT_FOLDER/environment.txt
mpirun -np 2 python psd_by_trial_type.py $DATA_FOLDER/i140703-001.nix $DATA_FOLDER/l101210-001.nix --output_path=$OUTPUT_FOLDER --skip_channels="0;2,... |
6ad3a2762778ded3506b064ff9aac422c208ab1b08cbbdb69c6dfc2dd2c9d358 | Shell | 481 | 26 | #!/bin/bash
#$ -cwd
#$ -l mem_free=5.0G,h_vmem=5G,h_fsize=50G
#$ -N xci_enrichment
#$ -o ./summary.log
#$ -e ./summary.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for r... |
0f7f8b1f33588b10d45bc1dd3a4a48354c5b78e4f5c6d0b2fbb040e1e122945b | Shell | 483 | 28 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l h_fsize=50G
#$ -N combine_data
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for reproducibility
mod... |
5eb835874b17813643ef8c258714f36a1555df32a900008afe689aef76dd6c39 | Shell | 483 | 28 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l h_fsize=50G
#$ -N extract_eGenes
#$ -o ./egenes.log
#$ -e ./egenes.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for reproducibility
mod... |
9cd91464b42b7b64d0b935d6cdff89804e4ecac71c64bd76ab12ea03f1cd2570 | Shell | 485 | 24 | #!/bin/bash
#
# Apply a method (md5sum, wc) on a file.
#
# If file ends with .gz, uncompress and compute
# from stream.
#
# In both cases, ignore any lines starting with "#"
#
suffix="${1##*.}"
fn=$1
printf "%s\t" "$fn"
shift
if [[ $suffix = 'gz' ]]; then
zcat $fn | grep -v '^#' | "$@"
elif [[ $suffix = 'bam' ]]... |
7c791e74c16359113c73f0d8f14c907c8693d5e1876d79ac75ebbe749436c29d | Shell | 486 | 12 | #!/usr/bin/env bash
# definitions
workDir=/vols/Scratch/comparative_scripts/m2_homologies/parcellations
parcellation=$workDir/tracer_parcellation/parcellation_3.nii.gz
# 1 is pM2, 2 is M1, 3 is aM2, 4 is ALM
fslmaths $parcellation -uthr 1 -thr 1 -bin $workDir/seeds/pM2.nii.gz
fslmaths $parcellation -uthr 3 -thr 3 -b... |
1812b80fbc14025900871b8fbc674b0c7dd22de2a99c1db1c9068097a7a23918 | Shell | 487 | 22 | #!/usr/bin/env bash
# Thanks to:
# https://unix.stackexchange.com/questions/27013/displaying-seconds-as-days-hours-mins-seconds
if [[ $# -ne 1 ]] ; then
echo
echo " ERROR: ./secs2hours.sh <seconds>"
echo
exit 1
fi
T=$1
D=$((T/60/60/24))
H=$((T/60/60%24))
M=$((T/60%60))
S=$((T%60))
(( $D > 0 )) && printf ... |
467566a6fcc7492356f487de8edb94d9d9f6a022bdc6adc0fba94a7e2bdf4a45 | Shell | 489 | 28 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l h_fsize=50G
#$ -N extract_eGenes
#$ -o ./summary.out
#$ -e ./summary.out
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for reproducibility
m... |
56242a804807f3fa45fae1eed249f3449105d82c777208d9c2c3a85aed0f8e8a | Shell | 489 | 28 | #!/bin/bash
#$ -cwd
#$ -R y
#$ -l h_fsize=50G
#$ -N extract_eGenes
#$ -o ./egenes.log
#$ -e ./egenes.log
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
## List current modules for reproducibility
mod... |
4e20329a1441a04ee22c5280c7142a25dc74fa62aedb7454c863cc9caca2e133 | Shell | 490 | 21 | #!/usr/bin/bash
start=`date +%s`
SRC_PATH=$1
RESULT_PATH=$2
declare -a cell_types=("hela-lclc-mcf7-mdamb231" "hela-lclc-mcf7-mdamb231-preo" "breastcancer-hela-lclc" "breastcancer-hela-lclc-preo" "breastcancer-hela" "hela-mcf7-mdamb231" "mcf7-mdamb231")
declare -a times=(30 60 90 120 150)
for i in "${cell_types[@]}... |
25ecaf9d2cb5575fb714cb5aa0df7c61111f358f7fab5d203ad6ff2920f8dc6c | Shell | 491 | 23 | echo "Creating data for Figure 2..."
python Figure2.py
echo "Figure 2 done."
echo "Creating data for Figure 3 and 4..."
python Figure3_4.py
echo "Figure 3 and 4 done."
echo "Creating data for Figure 5..."
python Figure5.py
echo "Figure 5 done."
echo "Creating data for Figure 6 and 7..."
python Figure6_7.py
echo "Fig... |
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