sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
f09b3b6a9257fceca4c59e7e1ba51af5b2f091886ec762e9e611a7d03a15ccb2 | Shell | 1,487 | 36 | #!/bin/bash
#SBATCH -n 1 # number of comands issued in batch script at any times
#SBATCH --cpus-per-task=8 # number of cores to allocate each task
#SBATCH -N 1 # Request 1 node
#SBATCH --time=12:00:00
#SBATCH --gres=gpu:1 ... |
5c4b63a4b3a401181740808a42a6689b9dc86b26286a487ae2209cd59935a7e0 | Shell | 1,488 | 49 | # ensure conda is properly initialised, such as by using the line below
# source /cm/shared/engaging/anaconda/2018.12/etc/profile.d/conda.sh
conda activate rxnebm
# for multi-GPU, choose any number (0-65535) for port
ebm_seed=$1
sym_seed=$2
python trainEBM.py \
--ddp \
--nodes 1 \
--gpus 4 \
--nr 0 \
--port ... |
6cb80b3edec74bcbc9d9a494562a20aaedc840a25b172cecbacbaafba00a7313 | Shell | 1,490 | 51 |
OLD_NET=/home/disk/database/data/scHIC/GSE130711_analysis/scATAC_loop.txt
NET=./ics_out/UNIQ_LOOP.txt
python ../src00_ics/step0_uniqNet.py $OLD_NET $NET
MAT=/home/disk/database/data/scHIC/GSE130711_analysis/scATAC_normalized_exp_clustered.txt
INDEX=/home/disk/database/data/ICS_scHIC/f01_frontalCortex/ics_out/this... |
474b956523795d218d503b38fdc7a095505e8481f99b46751f822111a21228a8 | Shell | 1,494 | 36 | #!/bin/bash
#SBATCH -n 1 # number of comands issued in batch script at any times
#SBATCH --cpus-per-task=8 # number of cores to allocate each task
#SBATCH -N 1 # Request 1 node
#SBATCH --time=24:00:00
#SBATCH --gres=gpu:1 ... |
63ee82a0dedfba118a89d4e5d37ea83a607001571ad340ce296fa307429e5c4e | Shell | 1,494 | 36 | #!/bin/bash
#SBATCH -n 1 # number of comands issued in batch script at any times
#SBATCH --cpus-per-task=8 # number of cores to allocate each task
#SBATCH -N 1 # Request 1 node
#SBATCH --time=24:00:00
#SBATCH --gres=gpu:1 ... |
f3a8e70e5b704db0e4993889f894c3bb78e4fd7e0e7e7bce263565526564eeee | Shell | 1,494 | 41 | #!/bin/bash
BMAP1=DLE1.cmap # DLE1.cmap
BMAP2=BSSSI.cmap # BSSSI.cmap
ENZYME1=DLE1 # DLE1
ENZYME2=BSSSI # BSSSI
ASM=asm.fasta # ln -s to the asm.fasta
mkdir -p output
module load python
#### Python 2.7.15 :: Anaconda custom (64-bit)
module load perl/5.18.2
#### Loading Perl 5.18.4 ...
module load R
#### Loading gc... |
45a4c0cfd75746ad5169634e9d634b17f0084559206fa0a71c6142e2daf6b7d4 | Shell | 1,500 | 37 | #!/bin/bash
#SBATCH -n 1 # number of comands issued in batch script at any times
#SBATCH --cpus-per-task=8 # number of cores to allocate each task
#SBATCH -N 1 # Request 1 node
#SBATCH --time=35:00:00
#SBATCH --gres=gpu:2 ... |
34e3aeff3dbb46863fe422060fc1fd2754213d762ca905d1d2ec310c0cb3d4f6 | Shell | 1,501 | 29 | #!/usr/bin/env bash
# Derive the release version from a tag and check it against the sources.
#
# packaging/release_version.sh [<tag>] # prints the version, e.g. 0.8.3
#
# The version is the tag with a leading "cpp-" and then "v" removed
# (cpp-0.8.3, cpp-v0.8.0 and v0.9.0 give 0.8.3, 0.8.0 and 0.9.0); without a
#... |
50fff169b338bc13b241120b6d91ed9abe237ab323b3e607d17b590fa3569daa | Shell | 1,501 | 37 | #!/bin/bash
#SBATCH -n 1 # number of comands issued in batch script at any times
#SBATCH --cpus-per-task=8 # number of cores to allocate each task
#SBATCH -N 1 # Request 1 node
#SBATCH --time=35:00:00
#SBATCH --gres=gpu:2 ... |
80c186290dca60296ee4194d28884fe355773d24cf9d142557c2e31d5ea1dfc6 | Shell | 1,502 | 52 | #!/bin/bash
# Discover the job ID to run, from either a grid environment variable and a
# command line offset, or directly from the command line.
#
if [ x$SLURM_ARRAY_TASK_ID = x -o x$SLURM_ARRAY_TASK_ID = xundefined -o x$SLURM_ARRAY_TASK_ID = x0 ]; then
baseid=$1
offset=0
else
baseid=$SLURM_ARRAY_TASK_ID
of... |
d31e83f721491c1f76d5a35e90c5ca44f7945b9a69b698ba5838cea8f3d31a3f | Shell | 1,502 | 37 | #!/bin/bash
#SBATCH -n 1 # number of comands issued in batch script at any times
#SBATCH --cpus-per-task=8 # number of cores to allocate each task
#SBATCH -N 1 # Request 1 node
#SBATCH --time=35:00:00
#SBATCH --gres=gpu:2 ... |
1144b1a50cf1c91a9ee51d15718587a24fd8082162036b6ff077cae98bd2f478 | Shell | 1,503 | 41 | #!/bin/bash
#
# Copyright 2022 DeepMind Technologies Ltd. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless re... |
68ca856df746c7752b2c7a93fd754ecd0fdd88fa05b756fb61ea7d8dfe9070f2 | Shell | 1,503 | 56 | #!/bin/bash
#simple script to pack up a precompiled binary package, with the boost thread
# library statically linked in; on x86_64 Linux, libstc++ and libgcc are linked statically also
if [[ -z "$2" ]]; then
echo -e "Usage:\n./make_bin.sh <package_base_name> <boost_prefix> [<bam_prefix> [<Eigen_prefix>]]"
exit 1
fi
... |
344aa97309bad3acc1a89c9e975245cf59e868d25f8d58a1a0768efd2c2dca1d | Shell | 1,505 | 34 | #!/bin/bash
#SBATCH -n 1 # number of comands issued in batch script at any times
#SBATCH --cpus-per-task=8 # number of cores to allocate each task
#SBATCH -N 1 # Request 1 node
#SBATCH --time=3:00:00
#SBATCH --gres=gpu:1 ... |
4d7a2c16c79686544be4f3bf0d875f0169f7815d197b757384f3a26c9fe0b4a6 | Shell | 1,505 | 34 | #!/bin/bash
#SBATCH -n 1 # number of comands issued in batch script at any times
#SBATCH --cpus-per-task=8 # number of cores to allocate each task
#SBATCH -N 1 # Request 1 node
#SBATCH --time=3:00:00
#SBATCH --gres=gpu:1 ... |
cb6507ee5030c0fcf8ec55054cdf5eae0dcb6a6f4f0e8f035aa7a7bf41fd57b3 | Shell | 1,507 | 49 | # ensure conda is properly initialised, such as by using the line below
# source /cm/shared/engaging/anaconda/2018.12/etc/profile.d/conda.sh
conda activate rxnebm
# for multi-GPU, choose any number (0-65535) for port
ebm_seed=$1
gln_seed=$2
python trainEBM.py \
--ddp \
--nodes 1 \
--gpus 4 \
--nr 0 \
--port ... |
9e1e99033f9f732aebe7889b9a6aea576cda144e05c26df15a479fc75b78886e | Shell | 1,508 | 67 | #!/bin/bash
if ! command -v ANTS &> /dev/null
then
echo "Cannot find the ANTS program. Please \(re\)define \$PATH in your environment."
exit 1
fi
NUMPARAMS=$#
if [ $NUMPARAMS -lt 3 ]
then
echo " USAGE :: "
echo " sh antsaffine.sh ImageDimension fixed.ext moving.ext OPTIONAL-OUTPREFIX PURELY-RIGID "
ec... |
a294a628c37e8f8ed4e524a98f3b1f2e8e02932387ff1bb1959e191f8ba82ab2 | Shell | 1,509 | 71 | #!/bin/bash
# concat_two_files 0.0.1
main() {
echo "Value of input1: '$input1'"
echo "Value of input2: '$input2'"
echo "Value of output_extension: '$output_extension'"
dx download "$input1" -o input1
dx download "$input2" -o input2
if ! [[ -z $mito_asm ]]; then
echo "Value of asm: '$mito_a... |
0120e479689b87902117dd6cd123400305a435435b4c5d8458ecbc8b5d5437dc | Shell | 1,522 | 42 | #first step is getting the protein restr files
#################
#USAGE genrestr_sequence grofile.gro topol.top pdbfile.pdb psffile.psf
#################
#make sure the pdb files contain the whole system. they don't need the right termini but they need all elements proteins ligands and lipids
#note weird sed delimiter... |
48e44203ec9a3c440ccdebb089cbee823505e12950529da136b5aaef95bf8f74 | Shell | 1,523 | 55 | #! /bin/bash
if [ -z $1 ]; then
echo "Usage: ./_submit_bionano.sh <ref.fasta>"
echo "Assumes input.fofn in the path."
exit -1
fi
input_fofn=input.fofn
LEN=`wc -l $input_fofn | awk '{print $1}'`
ref=$1
ref=`basename $ref`
ref=`echo $ref | sed 's/.fasta//g'`
# check if bnx bed files are already generated
num_bed=`... |
37de87672c29928ce7b83b922c222a26fc8636d26898de24db794f4778f04f09 | Shell | 1,526 | 50 | # ensure conda is properly initialised, such as by using the line below
# source /cm/shared/engaging/anaconda/2018.12/etc/profile.d/conda.sh
conda activate rxnebm
# for multi-GPU, choose any number (0-65535) for port
ebm_seed=$1
xpert_seed=$2
python trainEBM.py \
--ddp \
--nodes 1 \
--gpus 4 \
--nr 0 \
--por... |
7bd15e38568b13f9dbd82cc5063ed9b996909d2ad1421a50ab60bbe383a2c06c | Shell | 1,527 | 40 | CELLS="02 05 06 09 10 11 13 17 18 30"
DIR="/Users/pbmanis/Desktop/Python/VCN-SBEM-Data" # "/VCN_Cells/"
REMOTESYSTEM="pbmanis@lytle.med.unc.edu"
REMOTEDIR="pbmanis@lytle.med.unc.edu:"
FLAGS="-RDa0P -r -v" #" --dry-run"
EXC="--exclude=Z*"
# RS1="--files-from=<(ssh pbmanis@lytle.med.unc.edu find /Users/pbmanis/Desktop/Py... |
ec0add98f4ebafcf8e13752abe62a5f3089b90a5d8497501f72ff35e185ac68e | Shell | 1,536 | 49 | #!/bin/bash
##############################################
# modified by Emna Achouri on June 15th 2016 #
# version0.2: converted PBS to SLURM #
##############################################
SLURM_SCRIPT=$HOME/masque_submission.sh
#Check arguments
if [ $# -ne 7 ]
then
echo "Usage: $0 <reads_dir> <output... |
549e7b4824fc625b831d640c6d3608c8ccc657d784ed311b296c11872ea8d07f | Shell | 1,539 | 49 | #!/bin/bash
##############################################
# modified by Emna Achouri on June 15th 2016 #
# version0.2: converted PBS to SLURM #
##############################################
SLURM_SCRIPT=$HOME/masque_submission.sh
#Check arguments
if [ $# -ne 7 ]
then
echo "Usage: $0 <reads_dir> <output... |
c1dedb7664acd862c7d8324761e48baa0219e845b168457f31294a0461c360ac | Shell | 1,550 | 51 | # ensure conda is properly initialised, such as by using the line below
# source /cm/shared/engaging/anaconda/2018.12/etc/profile.d/conda.sh
conda activate rxnebm
# for multi-GPU, choose any number (0-65535) for port
ebm_seed=$1
gln_seed=$2
python trainEBM.py \
--ddp \
--nodes 1 \
--gpus 4 \
--nr 0 \
--port ... |
d2a7f4ed04d822edd4758bbde83eda8e09fe54f72f4d74ac4bcc64fe5fe68771 | Shell | 1,551 | 38 | #!/bin/bash
#SBATCH -n 1 # number of comands issued in batch script at any times
#SBATCH --cpus-per-task=8 # number of cores to allocate each task
#SBATCH -N 1 # Request 1 node
#SBATCH --time=12:00:00
#SBATCH --gres=gpu:1 ... |
e344fa623b641c28c727780e8394113fe63b3a995261265dc622f6b6be212658 | Shell | 1,577 | 47 | #!/bin/bash
# Prepare epigenomic tracks (.bw format)
# For each epigenomic track:
# --> download bam file
# --> merge bam replicates
# --> sort and index bam file
# --> normalize and create .bw file
#
# Usage example:
# screen
# bash /epiphany/data_preparation/bam2bw.sh \
# https://www.encodeproject.org/files/EN... |
1da5b5cba3db0e995b11b82e4d0145624dd36a546bbc54def0b47f5b2732d04f | Shell | 1,591 | 35 | #!/bin/bash
#BSUB -M 128000
#BSUB -W 12:00
#BSUB -n 12
#BSUB -R "rusage[mem=128000] span[hosts=1]"
#BSUB -J majiq_quantifier
#BSUB -o logging/majiq_quantifier.out
#BSUB -e logging/majiq_quantifier.err
module load anaconda3
source activate /data/aronow/Kang/py_envir/splice/
# build
input_folder='/data/aronow/Kang/ind... |
eb2a08ebe3dbc868a145d33f722d368be5b4ab05dbf0fbf2883c5d7ec4cc39be | Shell | 1,591 | 58 | #!/bin/bash
source ~/.bashrc
conda activate qiime2-2021.4
export TBB_CXX_TYPE=gcc
module load disBatch/2.0-beta
cd /mnt/home/jmorton/software/q2-matchmaker/q2_matchmaker/tests/stress/data/amplicon_comparison
BIOM_Z=zurita.biom
BIOM_D=dan.biom
BIOM_B=berding.biom
MD=sample_metadata.txt
TMP=~/ceph/scratch/q2-matchmake... |
376cde97a4ad2f6e6e275347cdcf9149d710010e124f0cf5a28f425b7edcc48b | Shell | 1,597 | 54 | #!/bin/sh
# Discover the job ID to run, from either a grid environment variable and a
# command line offset, or directly from the command line.
#
if [ x$SLURM_ARRAY_TASK_ID = x -o x$SLURM_ARRAY_TASK_ID = xundefined -o x$SLURM_ARRAY_TASK_ID = x0 ]; then
baseid=$1
offset=0
else
baseid=$SLURM_ARRAY_TASK_ID
offs... |
604bf7c0c5ac6741742ef9245e668605ee59cf7d658c30cfa4a31d732d11d453 | Shell | 1,607 | 43 | #!/usr/bin/env bash
# Copyright (C) 2019 Christoph Gorgulla
# Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
#
# This file is part of VirtualFlow.
#
# VirtualFlow is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Fre... |
26ebef6799cdda3e83b34b0f463b29d4e497682fa6588c54d87c3cd00fdd154e | Shell | 1,609 | 41 | # Example:
# scripts/process_gbcIV.sh run all
#
proto="runVC"
#######################################################
# Full models are from data/reconstuctions Matthew Kersting sent on
# March 6, 2020.
# Note we do not have a full reconstruction for cell 18
# in that dataset.
########################################... |
20a1354acbc605ab0e72bde5dfc668dbb3eb552df0843ebd44bde95d6b68f369 | Shell | 1,611 | 37 | #!/bin/bash
#SBATCH -n 1 # number of comands issued in batch script at any times
#SBATCH --cpus-per-task=8 # number of cores to allocate each task
#SBATCH -N 1 # Request 1 node
#SBATCH --time=10:00:00
#SBATCH --gres=gpu:1 ... |
8c420c60a70a34b7fcaf4aaa3a4641a6563fd8a4e011341e08963aed3d7f1335 | Shell | 1,611 | 37 | #!/bin/bash
#SBATCH -n 1 # number of comands issued in batch script at any times
#SBATCH --cpus-per-task=8 # number of cores to allocate each task
#SBATCH -N 1 # Request 1 node
#SBATCH --time=10:00:00
#SBATCH --gres=gpu:1 ... |
534beadbd90be5d187563984e18d9d3ef3df4977bd5476f5cf083167543b618f | Shell | 1,625 | 41 | # Submit training of ENN models on LBA data
CUTOFF=06
MAXNUM=600
for REP in $(seq 1 3); do
SB_FILE=run-id30_cutoff-${CUTOFF}_maxnum-${MAXNUM}_rep${REP}.sb
cp template-run-id30.sb ${SB_FILE}
sed -i "s/MAXNUM/${MAXNUM}/g" ${SB_FILE}
sed -i "s/CUTOFF/${CUTOFF}/g" ${SB_FILE}
sed -i "s/ --load/-rep${RE... |
3a6a611a015d3be1404fbe53e82f276e94fd0f63586b6bd17bc530a19e3cf9f7 | Shell | 1,631 | 16 | #!/bin/bash
#SBATCH --partition=long
#SBATCH --time=72:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=8G
#SBATCH --output=/data/user/mdefende/datasets/MDP-diff/jobs/noddi/sub-MDP001_dir98_1.1e-9.txt
module load rc/matlab/R2019a
module load FreeSurfer/6.0.0-centos6_x86_64
mri_convert /data/us... |
ea852d279e4a325adfe28be112875df6f1618e8fc8f0febf38bd1589f2ac9b76 | Shell | 1,638 | 54 | #!/bin/bash
#BSUB -M 64000
#BSUB -W 12:00
#BSUB -n 8
#BSUB -R "span[hosts=1]"
#BSUB -J STAR_align_batch1
#BSUB -o STAR_align_batch1.out
#BSUB -e STAR_align_batch1.err
module load STAR/2.7.9
genomeDir_='/data/aronow/Kang/induced_neuron/ChangHui_RNAseq_fastq/isoform_RSEM/star_reference/GRCh38_p13_index'
num_threads=8
... |
a3453518c9be1a965eaaf82350701541047931be5bd6656f28446fda2a177f5d | Shell | 1,654 | 29 | #!/usr/bin/env bash
# Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
#
# This file is part of VirtualFlow.
#
# VirtualFlow is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 ... |
c595be2bd50f23d17684ae592bdb1509d306413357a7b67640a533f46d263dda | Shell | 1,654 | 36 | #!/usr/bin/env bash
# Copyright 2017 Google Inc.
# All Rights Reserved.
#
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of... |
b8ff967786ec27e37954a0e06202dc7a23c73941d3978f4f5e7d85da4ed48594 | Shell | 1,658 | 75 | #!/bin/bash
# Copyright 2021 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless require... |
2befc9a555fb3be297b735f34dbd2995bdab47631638841600775f292c54898d | Shell | 1,659 | 34 |
rm -rf ./tmp
mkdir ./tmp
stdbuf -i0 -o0 -e0 Rscript big_matrix.R ./data/Annotations/median.csv.gz ./tmp/hipred_median.csv ./tmp/hipred_median.txt
# how does mean/max perform ...
stdbuf -i0 -o0 -e0 Rscript big_matrix.R ./data/Annotations/mean.csv.gz ./tmp/hipred_mean.csv ./tmp/hipred_mean.txt
stdbuf -i0 -o0 -e0 Rscri... |
cf8b9cddfbe4a5da3a79836feddb6bcbaa10fe7573cc7f58e7e44ff181291cf5 | Shell | 1,661 | 32 | source $HOME/.bashrc
rm \#*\#
#gmx pdb2gmx -f l.pdb -o memb.gro -ff charmm36-nov2016-newvs -water tip3 -vsite hydrogens
#gmx pdb2gmx -f out2.pdb -o prot.gro -ff charmm36-mar2019 -water tip3 -ter -his -ss
vmd -dispdev text 1unp.pdb -e gromacs_scripts/select_proteins.tcl
vmd -dispdev text prot.pdb -e gromacs_scripts/nam... |
3f8140f3e5530f691f82f3dab84d6e09617ddd98fe1ac12c87757f39d0ddec61 | Shell | 1,663 | 48 | #!/bin/bash
# shellcheck disable=SC2164,SC2103,SC2086
# Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
export CORE_NUMBER=$1
export INSTALL_PROTOBUF_PATH=$2
export BUILD_TYPE=$3
if [[ -z "$CORE_NUMBER" ]]; then
export CORE_NUMBER=1
fi
if [[ -z "$INSTALL_PROTOBUF_PATH" ]]; then
... |
dc705558d61c0bef8a5359fa993f1d3fdafd7482e877763f33234742f2a8775c | Shell | 1,663 | 48 | # ensure conda is properly initialised, such as by using the line below
# source /cm/shared/engaging/anaconda/2018.12/etc/profile.d/conda.sh
# ensure you are on a machine with CUDA, on a compute cluser you may need to load the modules as shown below
# module load gcc/8.3.0
# module load cuda/10.1
conda activate gln_op... |
22a383e38488c4790a991f34b4db8d0b431d2e639816fe1004d380905549f73b | Shell | 1,664 | 48 | ## USAGE bash gromacs_scripts/make_vsite_systems.sh <SYSNAME>
#rm memb.gro
#rm topol.top
#rm box.gro
#rm ionized.gro
#rm solv.gro
#rm solvate.gro
#rm ions.tpr
vmddisp () {
tempvmdc=$VMDNOCUDA
tempvmdo=$VMDNOOPTIX
export VMDNOCUDA=1
export VMDNOOPTIX=1
vmd -dispdev text -e "$@"
export VMDNOCUDA=$tempvmdc
... |
0213bcced83f55f4658db5202f8a7c63df1f031df6b729501d9b9018327fc3c4 | Shell | 1,667 | 47 | wget -qc ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG002_NA24385_son/NISTv4.1/GRCh37/HG002_GRCh37_1_22_v4.1_draft_benchmark.vcf.gz
wget -qc ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG002_NA24385_son/NISTv4.1/GRCh37/HG002_GRCh37_1_22_v4.1_draft_benchmark.vcf.gz.tbi
wget -qc... |
dda9d20bf331508db8843bb4296f0e365d48623b31c5bfe149c85a41f2e0a104 | Shell | 1,683 | 46 | #!/usr/bin/env bash
# Copyright (C) 2019 Christoph Gorgulla
# Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
#
# This file is part of VirtualFlow.
#
# VirtualFlow is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Fre... |
d5d9ffb5b30cbae63fe7418657f518d2bdbb2e641d8c4f646c3eb8ec60c73491 | Shell | 1,715 | 30 | #!/usr/bin/env bash
# Copyright 2019 DeepMind Technologies Ltd. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Un... |
40fc3cdc66ee7ce40df1397b509be91a6c906b8f64939f52fa59aa482c5bedbb | Shell | 1,718 | 82 | #!/bin/bash
if [ -z $1 ]; then
echo "use $0 -h for help"
exit 0
elif [ $1 == "-h" ]; then
cat << EOF
Usage: '$0 -l filelist -o outdir -p partition -c cpu [-a 10x]'
-a use 10x to trim barcodes
EOF
exit 0
fi
while getopts "l:o:p:c:a:k:" opt; do
case $opt in
l)
filelist="$OPTARG"
;;
o)
outd... |
671db56c5904fda28a74e3734c1d2380a754925cae687dc2d3f2c052a3c975df | Shell | 1,737 | 75 | #!/usr/bin/env bash
#####
## For use with Docker
help_menu="
Usage regenie_docker.sh OPTIONS
Options:
--build create docker image
--test test a generated docker image
--with-bio compile with Boost Iostreams library
--with-mkl compile with MKL library
--rg-dir path to the REGENIE source directory
"
... |
6da706384b05220ce13f103d07065e7ea316255e71563e2dd2c635e2701ce3b8 | Shell | 1,740 | 56 | #!/bin/env bash
#
#SBATCH -p all # partition (queue)
#SBATCH -n 1 # number of cores
#SBATCH -t 20 # time (minutes)
#SBATCH -o logs/outmain_registration.out # STDOUT
#SBATCH -e logs/outmain_registration.err # STDERR
echo "In the directory: `pwd` "
echo ... |
13145f0c169cd09237b4b0fb6f6ac99af40c9a0ab20e448ab9d6ec7bf967a5e1 | Shell | 1,745 | 48 | #!/usr/bin/env bash
# Evaluate on GIFT-Eval, either zero-shot or with a trained prompt.
#
# Usage:
# # prompt-tuned
# GPU=0 CKPT=/path/to/step_0165000 GIFT=/path/to/gift-eval \
# PROMPT=runs/<run>/checkpoint_best.pt \
# bash benchmarks/forecasting/gift_eval/evaluate.sh
#
# # zero-shot baseline (same predict p... |
d820807b757db7974f3ca4f3818092fe1a66ec1603f05f346dd42a340959f31e | Shell | 1,754 | 62 | # Example:
# scripts/process_gbcIV.sh run all
#
PROTO="runIV"
#######################################################
# Full models are from data/reconstuctions Matthew Kersting sent on
# March 6, 2020.
#
#######################################################
CELLNAMES="02 05 06 09 10 11 13 17 18 30"
CONFIG="--conf... |
706b028ca916ebf458a1687117b1a22dc053c06d691f4c482027b5a32fc9da28 | Shell | 1,755 | 48 | #!/bin/bash
# at peak vox location, generate spherical ROIs
# EEGSTV
# Hengda He, Feb 25 2021
ReD='\033[91m'
YelloW='\033[93m'
EndC='\033[0m'
scriptdir="/home/hengdahe/LAB_2021/ROIs/ROI_v3_EEGSTV/Scripts"
groupout_dir="/home/hengdahe/LAB_2021/ROIs/ROI_v3_EEGSTV/GroupLevel/Regions"
echo "group output directory: "${gr... |
3b2b672902c9d6a116cb00693ab86482900e9b5a7eff9044b0da71702c682c66 | Shell | 1,756 | 38 | # ensure conda is properly initialised, such as by using the line below
# source /cm/shared/engaging/anaconda/2018.12/etc/profile.d/conda.sh
conda activate rxnebm
seed=$1
# cd rxnebm/data/cleaned_data/results_${seed}/
cd rxnebm/proposer/retroxpert/OpenNMT-py/experiments/results_${seed}/
mv predictions_on_USPTO50K-aug... |
7a7817e3189c634a58f75a6fc5a5e68c9dd1aad0962ad6d62373cc41b8e44bcb | Shell | 1,763 | 57 | #!/bin/env bash
#
#SBATCH -p all # partition (queue)
#SBATCH -n 1 # number of cores
#SBATCH -t 20 # time (minutes)
#SBATCH -o logs/outmain_registration.out # STDOUT
#SBATCH -e logs/outmain_registration.err # STDERR
echo "In the directory: `pwd` "
echo ... |
e62dcc31e12c737fa240217bd8b6618b72fc0bd452b84057a8d8c0566131b07b | Shell | 1,775 | 57 | #!/bin/bash
sample=$1
if [[ -z $sample ]]; then
echo "sample=$sample"
exit -1
fi
ref=asm
fasta=refdata-$ref/fasta/genome.fa
module load samtools
#### [+] Loading samtools 1.8 ...
# This is co-installed with bcftools
threads=$SLURM_CPUS_PER_TASK
if [ -z $threads ]; then
threads=4
fi
if [ ! -s $sample.bcf... |
2701d819ac21da5c1ca5fc39f7d98234163adef6e397ac370dc2713fee27dd7d | Shell | 1,797 | 60 | #!/bin/bash
#BSUB -M 500000
#BSUB -W 12:00
#BSUB -n 12
#BSUB -R "rusage[mem=500000] span[hosts=1]"
#BSUB -J STAR_align_leafcutterFormat_batch1
#BSUB -o STAR_align_leafcutterFormat_batch1.out
#BSUB -e STAR_align_leafcutterFormat_batch1.err
module load STAR/2.7.9
genomeDir_='/data/aronow/Kang/induced_neuron/ChangHui_R... |
f9178634360a3cfcd62a3587b284a4ac98c467b28d9bbae9a09d71223daafc4f | Shell | 1,800 | 39 | #!/bin/bash
# Copyright 2023 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless require... |
b6bea1c12b260f993c0f4b658d589f0ae442c17eb45612196f82ce2a87952896 | Shell | 1,807 | 60 | #!/bin/bash
#BSUB -M 500000
#BSUB -W 12:00
#BSUB -n 12
#BSUB -R "rusage[mem=500000] span[hosts=1]"
#BSUB -J STAR_align_QuantTps_batch1
#BSUB -o STAR_align_QuantTps_batch1.out
#BSUB -e STAR_align_QuantTps_batch1.err
module load STAR/2.7.9
genomeDir_='/data/aronow/Kang/induced_neuron/ChangHui_RNAseq_fastq/isoform_RSEM... |
5f7d8a874a97ee28f90fde92b6b818bc2b01363f2ae4ddb098c751e2c4a550e0 | Shell | 1,825 | 43 | #!/bin/bash
# 2.3.3. Denoising
# 2.3.3.2. Thermal noise
# create template FEAT and PNM files using Feat and PNM GUI and save them under ...derivatives/sub-FeatExample
# copy these for each subject and change the name
# see the following preprint: " ", and following dataset: https://openneuro.org/datasets/ds004386
#... |
ff3d177ec79b85b3c0f508f748572e21f80ca54efcd607cdf4866879a1b19823 | Shell | 1,851 | 53 | #!/bin/bash
if [ -z $1 ]; then
echo "Usage: ./genomecov.sh <genome_id> [bam]"
echo "Requires summary.csv and <genome_id>.changes.vcf.gz"
exit -1
fi
module load bedtools
module load samtools
module load bcftools
bam=aligned.bam #aligned, pos-sorted
genome=$1
if [ ! -z $2 ]; then
bam=$2
fi
if [ -s aligned.genom... |
06c2946b7244a8ce46713a1a4cfdd93b80a6aa233e6f0dd7f3ceaf8a9192780a | Shell | 1,858 | 58 | #!/bin/sh
# Discover the job ID to run, from either a grid environment variable and a
# command line offset, or directly from the command line.
#
if [ x$SLURM_ARRAY_TASK_ID = x -o x$SLURM_ARRAY_TASK_ID = xundefined -o x$SLURM_ARRAY_TASK_ID = x0 ]; then
baseid=$1
offset=0
else
baseid=$SLURM_ARRAY_TASK_ID
offs... |
9ef336cf630180314a3143ff8793b134c021f10fe2dfc309715288ef3cabfebb | Shell | 1,866 | 47 | #!/bin/bash
# python vcnmodel/model_run.py VCN_c06 --type Bushy --modeltype II --protocol initIV --hocfile VCN_c06_Full.hocx --model XM13_nacncoop \
# -r 1 \
# --tagstring noDendNa\
# --saveall --noparallel\
# #--soma_autoinflate --dendrite_autoinflate
#
# python vcnmodel/model_run.p... |
d4f9cca716d53b3960ee78ed0fa489eec0e304b3b05f436fd149d15c06d84fef | Shell | 1,871 | 61 | #!/bin/bash
NUMPARAMS=$#
if [ $NUMPARAMS -lt 3 ]
then
echo " USAGE :: "
echo " $0 inWarp WhichTypeOfMagnitude outputmagnitudeimage.nii "
echo " WhichTypeOfMagnitude == Laplacian Grad Euclidean "
echo " the numbers that come out of this depend on some itk filters being dimensionally correct and consistent. "
echo "... |
4df785d5ecc9cdd96a5432bc2fc98b8113088bbaa55fa748025e60b764a08236 | Shell | 1,880 | 82 | #!/bin/sh
# Simulate astrocyte with the specified number of processes (single run).
# $1 - The number of processes.
# $2 - The process distribution scheme:
# 1 - only master works,
# 2 - only slaves work,
# 3 - master and slaves work together.
#
# Other input parameters are specified in the file "init.ho... |
a18648e0825fa7d8ec2dfaca7e4db755467af4bfa3f09da962504c68950ac07a | Shell | 1,889 | 54 | #!/bin/bash
CELLNAMES="02" # " 05 06 09 10 11 13 17 18 30"
#CONFIG="noscale.toml" #"autoscale.toml"
CONFIG="toml/autoscale_multisite_10dB_parallel.toml"
RUNTEXT="running the AN PSTH for Revcorr"
TABLES="data_XM13A_nacncoop_normal data_XM13A_nacncoop_pasdend data_XM13A_nacncoop_actdend"
echo $RUNTEXT
# for t in $TABLE... |
0d949d7ddea81520e5a7e13828d437017c3ac54698bf4e7fdef1b21dc2999fd7 | Shell | 1,894 | 60 | #!/bin/bash
# every normalized by CPMs
# # mC prepare
# SingleCellFusion_prep \
# -i \
# "./datasets/mc/genes_forBICCN2_CEMBA_3C_171206_mCG.h5ad" \
# "./datasets/mc/genes_forBICCN2_CEMBA_3C_171207_mCG.h5ad" \
# -icov \
# "./datasets/mc/genes_forBICCN2_CEMBA_3C_171206_CG.h5ad" \
# "./dat... |
b7925d844682db64f9ba639265208d372630eb9ffd6023c9739e5119eabfb4fe | Shell | 1,896 | 57 | #!/usr/bin/env bash
# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
# From https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=wgEncodeRegDnase
# DNase I Hypersensitivity in 95 cell types from ENCODE
# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
CLUSTS="w... |
6761a7c2ff2929cfb3880f95b1e84d4bab850d3a36ea86e260ea78e69ac6356f | Shell | 1,899 | 40 | #!/bin/bash
#SBATCH -n 1 # number of comands issued in batch script at any times
#SBATCH --cpus-per-task=16 # number of cores to allocate each task
#SBATCH -N 1 # Request 1 node
#SBATCH --time=1:00:00
#SBATCH --gres=gpu:0 ... |
6136af154e9a96427ef9045f0e14b702863ca5c6fcd11e1d1dcc8f8741ca94c7 | Shell | 1,906 | 41 | #!/usr/bin/env bash
# Copyright 2017 Google Inc.
# All Rights Reserved.
#
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of... |
06e40b68f9e097ed44cef46cc29ee15bcb0a788620431076d996eb713cb9acce | Shell | 1,911 | 53 | #!/usr/bin/env bash
# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
# From https://www.biorxiv.org/content/10.1101/822510v2
# Index and biological spectrum of accessible DNA elements in the human genome
# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
# DNas... |
91efbf7e6c88f00f9c54a2f67193d9899d8f7915ad6fb2170f4bf96ed3402e24 | Shell | 1,914 | 48 | #!/bin/bash
if [[ -z $1 ]] || [[ ! -e asm.fasta ]] ; then
echo "Usage: ./_submit_scaff10x_v4.0.sh <genome_id> [dir_path_of_fastq.gz_files] [job_id_to_wait_for]"
echo "Requires asm.fasta and input.fofn - give the dir path to R1 fastq.gz, R2 fastq.gz files to automatically generate input.dat"
echo -e "\t<genome_id>: ... |
90a4236442447536d308d9fe5100dfc60dfa852f28f1155f5774810c6c9d63c1 | Shell | 1,919 | 27 |
python displayresult_model_run.py VCN_c08 --protocol runANPSTH -r 25 -f 16000 --inflation 1.528
python displayresult_model_run.py VCN_c09 --protocol runANPSTH -r 25 -f 16000 --inflation 1.489
python displayresult_model_run.py VCN_c11 --protocol runANPSTH -r 25 -f 16000 --inflation 1.398
python displayresult_model_run... |
2b8233b1e6a557b20538544f37d222d314ddeedd761ac1635b2d6c8e2036cd3b | Shell | 1,921 | 47 | #!/usr/bin/env sh
BASE=~/git/NIF-Ontology
BASESC=$(echo ${BASE} | sed 's/\//\\\//g')
echo $BASESC
CONVFILE=/tmp/owl_to_convert.txt
find "${BASE}"/Backend -name '*.owl' > /tmp/back_files
find "${BASE}"/BiomaterialEntities/ -name '*.owl' > /tmp/be_files
find "${BASE}"/DigitalEntities/ -name '*.owl' > /tmp/de_files
find ... |
d55f0ab5348de09fb76522e181c949e377a3c278fc3d3df6451fde907eff7518 | Shell | 1,926 | 56 | # Example:
# scripts/process_gbcIV.sh run all
#
#######################################################
# Full models are from data/reconstuctions Matthew Kersting sent on
# March 6, 2020.
# Updated 30 July 2021
#######################################################
PROTO="-P runANPSTH"
###########################... |
12871dde41221897eb5e2fe856c63dae5b89d8e3f715462dc888d3ae80d61ebd | Shell | 1,927 | 57 | # Example:
# scripts/process_gbcIV.sh run all
#
#######################################################
# Full models are from data/reconstuctions Matthew Kersting sent on
# March 6, 2020.
# Updated 30 July 2021
#######################################################
PROTO="-P runANPSTH"
###########################... |
9f4f80718de8c7141f650724e5d49a8d5dd36c8fbaf67f52335c9b69b528867f | Shell | 1,927 | 86 | #!/bin/bash
set -e
i=$SLURM_ARRAY_TASK_ID
sample=$1
if [ -z $i ]; then
i=$2
fi
if [[ -z $sample ]]; then
echo "sample=$sample"
exit -1
fi
module load freebayes/1.2.0
#### [+] Loading freebayes 1.2.0
module load samtools/1.9
#### [+] Loading samtools 1.9 ...
# This is co-installed with bcftools
modul... |
3bdcb4afa235c04715f7a7a8c6ed9892d49f36ef74d1cf69216760191ac9b7ef | Shell | 1,950 | 76 | #!/bin/bash -norc
DIR="$( cd "$( dirname "$0" )" && pwd )"
cat <<EOF
Trying to establish local installations of any missing Perl modules
(as logged in $DIR/setup-deps.log).
Please be patient, as this step may take a little while.
EOF
mkdir -p "$DIR/_cpan/CPAN"
echo '1;' >> "$DIR/_cpan/CPAN/MyConfig.pm"
perl -I"$DIR/... |
04fcd5d6e293821f5d9c7418d3312e599f1a6f149f3a031348d6a5e9a432d0bd | Shell | 1,954 | 84 | #!/bin/bash
# meryl 0.0.1
# Generated by dx-app-wizard.
set -x -e -o pipefail
main() {
sudo chmod 777 /usr/bin/meryl
echo "Value of fastq: '${fastq[@]}'"
echo "Value of kmer: '$kmer'"
for i in ${!fastq[@]}
do
one_fastq_jobs+=($(dx-jobutil-new-job -ikmer="$kmer" -ifastq="${fastq[$i]}" m... |
ad2350831c84cf2807c41d7ed7be4d3b6810baa46dcc5e93f7a4ae8b3f67cdcb | Shell | 1,957 | 58 | #!/bin/bash
if [[ -z $1 ]] || [[ ! -e input.fofn ]] ; then
echo "Usage: ./_submit_minimap2.sh <ref.fasta> [jid]"
echo -e "\tAssumes <input.fofn> in the same path"
echo -e "\t[jid]: set --dependency=afterok:[jid]"
exit -1
fi
ref=$1
ref=`echo $ref | sed 's/.fasta$//g' | sed 's/.fa$//g' | sed 's/.fasta.gz$//g' | sed... |
92edf7b6e8b9abb0d9a8aa95d0b235ce5345d9248030633909393184f672e42d | Shell | 1,967 | 47 | #!/bin/bash
#SBATCH -n 1 # number of comands issued in batch script at any times
#SBATCH --cpus-per-task=8 # number of cores to allocate each task
#SBATCH -N 1 # Request 1 node
#SBATCH --time=10:00:00
#SBATCH --gres=gpu:1 ... |
3b58edbffc8a3ea8b6948da16a22f3e297b5a3a0e8c90e716b55574791d16986 | Shell | 1,978 | 35 | source $HOME/.bashrc
rm \#*\#
#gmx pdb2gmx -f l.pdb -o memb.gro -ff charmm36-nov2016-newvs -water tip3 -vsite hydrogens
#gmx pdb2gmx -f out2.pdb -o prot.gro -ff charmm36-mar2019 -water tip3 -ter -his -ss
#echo -e "0\n2\n1\n0\n" | gmx pdb2gmx -f waterless.pdb -o memb.gro -ff charmm36m_newvs-may2020 -water tip3 -ter
#gm... |
735d570036f2c8258103cd1eac206262c2059c72e306d89739b481c32fef39b2 | Shell | 1,986 | 61 | #!/bin/bash
if [ -z $1 ]; then
echo "Usage: ./_submit_freebayes.sh <sample_id> [jobid_to_set_dependency]"
echo "Reference fasta and .fai needs to be here: refdata-asm/fasta/genome.fa and refdata-asm/fasta/genome.fa.fai"
exit -1
fi
sample=$1
if ! [ -e aligned.bam ]; then
ln -s $sample/outs/possorted_bam... |
8d29e8e1796f7d83ef63f302e34893e34f7c10d4d30bdf6f518df8af2fae98d2 | Shell | 1,995 | 76 | #! /bin/bash
echo "Usage: ./_submit_bwa.sh <ref.fasta> <fastq.map> <out>"
ref=$1
fastq_map=$2
out=$3
if [ -z $ref ]; then
echo "No <ref.fasta> given. Exit."
exit -1
fi
mkdir -p logs
if [ ! -s $ref.fai ]; then
cpus=4
mem=10g
name=$out.index
script=$VGP_PIPELINE/bwa/bwa_index.sh
args="$ref"
partition=quick
... |
ae4b016ae41b9621a9b38d8892fae5c1932fe244cc88b312148ead4b5b43e665 | Shell | 1,996 | 61 | #! /bin/bash
if [ -z $1 ]; then
echo "Usage: ./_submit_mashmap.sh <job-name>"
exit -1
fi
genome=$1
if [ -e ../purge_haplotigs/${genome}_curated.fasta ]; then
ln -s ../purge_haplotigs/${genome}_curated.fasta
ln -s ../purge_haplotigs/${genome}_curated.haplotigs.fasta
fi
if [ -e ../../${genome}_v1.p.fasta ]; then
... |
e501796c0e49cc08f26996f5a488f85904f107d3e43439f1c6f3b8ac1d42f8b2 | Shell | 2,013 | 39 | #!/usr/bin/env bash
SCRIPTPATH="$( cd "$(dirname "$0")" ; pwd -P )"
./build.sh
VOLUME_SUFFIX=$(dd if=/dev/urandom bs=32 count=1 | md5sum | cut -c 1-10)
DOCKER_FILE_SHARE=picai_prostate_segmentation_processor-output-$VOLUME_SUFFIX
docker volume create $DOCKER_FILE_SHARE
# you can see your output (to debug what's goi... |
e298e6a34efa4b7e0bde86a3f13e15c135dd2e1f65a342621e82ffe703a41c44 | Shell | 2,029 | 76 | #!/bin/bash
set -e
#set variables species abbreviation
SPECIES=$1
ABBR=$2
SIZE=$3
dw_date=`date "+%Y%m%d-%H%M%S"`; aws s3 --no-sign-request ls s3://genomeark/species/${SPECIES}/${ABBR}/genomic_data/pacbio/ | grep -oP "m.*.subreads.bam" | uniq > ${SPECIES}/file_list_$dw_date.txt
while read p; do
if ! [[ $p == *scra... |
735ee5e1149ae2b3349668042fbd57ac465399596f23f9bbcb0bc63a4c4aa3e9 | Shell | 2,031 | 89 | #!/bin/sh
Usage() {
cat <<EOF
usage: Functional_thirdlevel_v3.sh -i <cope>
e.g. sbatch Functional_thirdlevel_v3.sh -i cope1
EOF
exit 1
}
if [ $# -le 1 ];
then
Usage
exit 1
fi
while [ $# -ge 1 ];
do
case "$1" in
-i)
cope=$2;
shift;;
esac
shift
d... |
587de9fad06e72184b61cd9c65753ef8e81cb7a7d4f745c34f4e9a88c5cdc0a4 | Shell | 2,036 | 48 | #!/usr/bin/env bash
#
# Copyright 2024 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unle... |
38b8fe964a01deadb05d7f11509f91dfe6838d93ad5f7c588b146911b793a4da | Shell | 2,041 | 43 | #!/usr/bin/env bash
# Test a Linux release archive where users will run it.
#
# packaging/linux/test-in-docker.sh dist/baysor-<version>-linux-x86_64.tar.gz
#
# Extracts the archive and runs packaging/smoke_test.sh
# 1. natively on this machine,
# 2. in bare almalinux:8 and debian:10 containers (glibc 2.28, the fl... |
fad5bbbf4a8a38f76f29d7717270aadb8b38f9f58e05ece280bc34f5da782bc9 | Shell | 2,045 | 78 | # Example:
# scripts/process_gbcIV.sh run all
#
proto="testIV"
#######################################################
# Full models are from data/reconstuctions Matthew Kersting sent on
# March 6, 2020.
# Note we do not have a full reconstruction for cell 18
# in that dataset.
#######################################... |
c27f2da6959187404e56db76690244878f431436f66f765b15e851f2dd7a06e7 | Shell | 2,051 | 88 | #!/bin/sh
Usage() {
cat <<EOF
usage: Functional_higherlevel.sh -i <Subject>
e.g. sbatch Functional_higherlevel.sh -i Subject_1
EOF
exit 1
}
if [ $# -le 1 ];
then
Usage
exit 1
fi
while [ $# -ge 1 ];
do
case "$1" in
-i)
subject=$2;
shift;;
esac
s... |
e678f159cb1e6d446ece00a79d7191a5dd757783e8eda957c4af02c0b2c9ec69 | Shell | 2,052 | 46 | #!/bin/bash
#SBATCH -n 1 # number of comands issued in batch script at any times
#SBATCH --cpus-per-task=1 # number of cores to allocate each task
#SBATCH -N 1 # Request 1 node
#SBATCH --time=0:10:00
#SBATCH --gres=gpu:0 ... |
7ae874b0ab3d1222ea1f9a0ecfd3a2262618069ef3aa6f9478d3e29da5026834 | Shell | 2,055 | 49 | #!/bin/bash
#SBATCH -n 1 # number of comands issued in batch script at any times
#SBATCH --cpus-per-task=8 # number of cores to allocate each task
#SBATCH -N 1 # Request 1 node
#SBATCH --time=10:00:00
#SBATCH --gres=gpu:1 ... |
82664717e502ec57ffa24c4f972846f0142cfee1dc236f3def68e490c1f1f676 | Shell | 2,071 | 89 | #!/bin/sh
Usage() {
cat <<EOF
usage: Functional_thirdlevel_v3.sh -i <cope>
e.g. sbatch Functional_thirdlevel_v3.sh -i cope1
EOF
exit 1
}
if [ $# -le 1 ];
then
Usage
exit 1
fi
while [ $# -ge 1 ];
do
case "$1" in
-i)
cope=$2;
shift;;
esac
shift
d... |
a4b52379e52a66c13c86e0533c94f223cba0ff37ee2a7954535f2306b33dc404 | Shell | 2,073 | 41 | # dataset=USPTO50K-aug-untyped
seed=$1
dataset=USPTO50K-aug-untyped_${seed}
dataset_prefix=USPTO50K-aug-untyped
suffix=test-prediction
source /cm/shared/engaging/anaconda/2018.12/etc/profile.d/conda.sh
conda activate retroxpert_
# modified with seed
python3 ../../onmt/bin/translate.py --model ../../experiments/checkp... |
549f8add145d9cb0a6c30d9270b0fab8423cadae14db1227d2f355fb5b38c703 | Shell | 2,093 | 81 | #!/bin/bash
SPECIES=$1
ID=$2
REF=$3
rm -r $ID
mkdir -p $ID
mkdir -p ${ID}/log/
dw_date=`date "+%Y%m%d-%H%M%S"`
printf "Collecting data using: aws s3 --no-sign-request ls s3://genomeark/species/${SPECIES}/${ID}/genomic_data/10x/\n"
aws s3 --no-sign-request ls s3://genomeark/species/${SPECIES}/${ID}/genomic_data/10... |
e65ffa0dc3a9a2dc8478bd23abc0332c6a5cd7bb6ac5bd12acca140518d9f96d | Shell | 2,108 | 66 | #! /bin/bash
if [ ! -e "input.fofn" ] || [ ! -e "asm.fasta" ]; then
echo "Run ngmlr in parallel. Requires <input.fofn> and <asm.fasta>"
echo "No input.fofn or asm.fasta found. Exiting."
exit -1;
fi
if [ -z $1 ]; then
echo "Usage: ./run.sh <jobname>"
exit -1;
fi
cpus=32
mem=52g
name=ngmlr_$1
script=$VGP_PIPELINE... |
27ccab578d0c491e3b25313ffa1aad3e9586ffbdea12aee2c1cb5590dfbd633c | Shell | 2,122 | 42 | #!/bin/bash
# Copyright 2023 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless require... |
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