sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
671bbe9a2397665eb8531b30643baf6bebca888f47049f2afa83ff8c6a69480d | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=jumbo # the requested queue
#SBATCH --nodelist=f03-13
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=64 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=8046 ... |
68b894804b4aefda48079ec5bde7ce69931ddc96c0899212d53af8c8418dbd26 | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f02-10
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=36 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=12893 ... |
6cd096bf11083b8557398791774f7072c242d2907d7714aeb24fd674dbbe6b21 | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f03-24
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=55 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=16120 ... |
6f30305f71eea7c219f85de7ef98f026c9afb9f436bd4225da7289a065e2eabd | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f02-10
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=44 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=12893 ... |
702b258e1430e9ae7978cb37837f6940f105344533f73a4ab9b70684c80e90c4 | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f03-24
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=90 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=16120 ... |
70e0112e7780efb63bf16d806043f07e50a0bb257ea39c5700dfd949319785ff | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f03-24
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=50 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=16120 ... |
734f9d01d53ecd7bf9270523bc23c1f5f8f9e01ae38d2e9b316d252fef124c26 | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f02-10
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=38 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=12893 ... |
74e08a133f57c9d1dc69157d9b2b87ad7035dd630794eeabf3c203f1f01050ca | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f02-10
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=65 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=12893 ... |
76e0fd6df2be92084dd886468ece6abfaa2fd564c3c20e5045944f953d7507fd | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f02-02
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=25 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=4000 ... |
7d69f69a6983a734c3ef7477a141c896a4d9118bdefd04ade63c3188e69a2abf | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f02-10
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=40 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=12893 ... |
7db5c3a5f7bc5f7c1631be076822a2ca5562245b80e8a54d73a1bb88bf517f7c | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f03-24
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=35 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=16120 ... |
828ef41f419febd988aa14ebe4378550417c717062ba667194088038b724e3ed | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f02-10
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=28 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=12893 ... |
894a42930627ee0ca3b9c1bf2097f6bc12221be40fde8c5198059b468e18bc13 | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f03-24
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=38 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=16120 ... |
8b86ecd11b716fd635db208586a78ccab99134a1769c3a19ae6cb86572be3fc5 | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=epyc # the requested queue
#SBATCH --nodelist=f03-09
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=128 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=3985 ... |
8d82f986d7f14b7a13d3aec858a50b6fe6acdadf908cc2b1296061b03cac599f | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=epyc # the requested queue
#SBATCH --nodelist=f02-13
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=192 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=2682 ... |
8de66f43fc435645778cf3053d2dc09434cef0a0e4abe95cfeab220d1ddde627 | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f02-10
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=68 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=12893 ... |
8ed111eb97a1584a45f2d4b3d4fb6f501ecebf9cdd5fa7f442ac8c3847d915d9 | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f03-24
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=25 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=16120 ... |
98a272715760001dabb30e4d0fa25abadd6d0b9231fb2cb7ddb54d95673ce2bb | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f02-10
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=52 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=24000 ... |
9f30589f9b4e416c7ac3bba379bdfaf0c78adb1f328ff2b766f4f64b3d6a8d6e | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f02-10
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=70 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=12893 ... |
aa4e24642ddfc34c3bc5a31aef7f3fb3df71d8c5034e41948463234ad72de2dd | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f02-10
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=55 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=12893 ... |
af893d291302fb90bd1def995ce86383da8dcb4f685922dc8330b3cbf509805e | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f03-24
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=75 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=16120 ... |
b3ad0e1beb4545475081e27c7f9f9ce9ec9be363ddb662a1b06f0cf90290dfcc | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f03-24
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=80 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=16120 ... |
b89bafecf12677efb81ffae2a070f257b7c77f189a213dde4f2559eb7e15cc06 | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=jumbo # the requested queue
#SBATCH --nodelist=f03-15
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=64 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=8046 ... |
c11e9b932381b5d5d8a7e718faa5d28f71a0245cef3c35896afca36435c8f14e | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f03-24
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=60 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=16120 ... |
ceee4468779438716bacb427d5e1aa48c560645f4919679911144eb1a4090e7d | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f02-02
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=40 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=4000 ... |
d60e8d9f29dfc4b30030f6b6128d4722f1314f1883da92f34d8ea4a99f571cc0 | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f02-10
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=80 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=12000 ... |
dddbe17613a183a0ab508b77df305d5e47aec0e7ed33bf28dda3c572020dd3af | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f03-24
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=94 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=16120 ... |
dfbd5a9051b9c95bce851c475a6add113651374353acfb3b668a97433e0e2d6c | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f02-10
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=50 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=12893 ... |
e043784f96563c54e92cf0edfa9741cf5cb2876182a579ebbed56c70712ee639 | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f02-02
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=20 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=4000 ... |
e1ae40fb98b3fc222b2fd866f361039c75474df1f0c44e0c14d6e0be52b48bb9 | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f02-10
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=45 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=12893 ... |
e45a1a1118955cbf61bb33c01f74c4bc66e58fa259197de2eda3e1ec7f585233 | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f02-02
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=38 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=4000 ... |
e72cf59d49cb44c3411cef4d2b17abfd7f7bd09e3c168f80c922efc34268fcb6 | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f03-24
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=72 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=16120 ... |
ebbb11f4e11674aee6ce5d0f8ce986a22fd3741951be5e182ea1e5f9bd15ef11 | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f02-10
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=78 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=12893 ... |
f2924595f077289c1511863232037d1188e01aa2d293272aad7aeff235198803 | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f02-10
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=20 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=12893 ... |
f46743c3ed12cc8163cc2cbd8101c5aec4c4cff9240f2c561cc7f119d41f0c49 | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f02-10
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=60 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=12893 ... |
f65abf3b29a7d7e7e63cb25ca0bc6d40f0d712aaa34edaf35b26cf17f4662739 | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=jumbo # the requested queue
#SBATCH --nodelist=f02-05
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=64 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=8046 ... |
f7ba0c958d3d6a7b3d4918ffd7b563d4da150ed6159a19510226f8d6742b5bd7 | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f03-24
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=32 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=16120 ... |
fb7a098454afd4ddfdc6183d46dc72a87ad9d92b44c75e3d7fad3fd6f807fac4 | Shell | 1,470 | 33 | #!/bin/bash
#SBATCH --partition=mammoth # the requested queue
#SBATCH --nodelist=f02-10
#SBATCH --job-name=THALAMOCORTICAL # name the job
#SBATCH --nodes=1 # number of nodes to use
#SBATCH --ntasks=25 # total number of tasks (preocesses)
#SBATCH --mem-per-cpu=12893 ... |
a07aed256f6f8733bbb6605ac324b62f78005be600089ab543d6919ea392533c | Shell | 1,476 | 39 | #!/bin/bash
#This script autogenerates the conda install commands for TRACES_install.sh
# based on the dependencies in the dependencies.yml file
#It attempts to modify the target in place, with a backup which is either
# deleted or restored depending on the success of the modification
#This script requires yq (a CLI... |
cee3fb884b36b8f03ec6f082d3cfbeb904c15fd025c204e319d5f3442265b74f | Shell | 1,482 | 45 | #!/bin/sh
# """
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software
# and associated documentation files (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, cop... |
de9a5225cfd57c3cf36510d95d74cf2fbeff9c83c3d8431e9eb187fe9ac8f706 | Shell | 1,501 | 45 | #!/bin/bash
# """
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software
# and associated documentation files (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, c... |
375b6ce572422718cd0f2c65d6e01f0fe07d2c73d23d2cb7816c7609d0ff31b0 | Shell | 1,509 | 45 | #!/bin/bash
# """
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software
# and associated documentation files (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, c... |
fcbb9f7393fab6fac318f832c76bf957caa3c9180f1a5396f672025aa4f964e1 | Shell | 1,514 | 45 | #!/bin/bash
# """
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software
# and associated documentation files (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, c... |
bea257a656996814d51c753f85804604cc366401e22cdde16cfca4a6012704a1 | Shell | 1,515 | 55 | #!/bin/bash
# -----------------------------------------------------------------------------
# cli_glm_power_analysis.sh - CLI wrapper for run_glm.py in power analysis mode
# This script is called by qsub_power_analysis.sh
# -----------------------------------------------------------------------------
echo "===========... |
27bcca8453b784e842a67e9e6fa06f6c98ce916c354a22511f5713eb28b8f7d0 | Shell | 1,521 | 43 | #!/bin/bash
#This script autogenerates the display version commands for TRACES_get_program_versions.sh
# based on the dependencies in the dependencies.yml file
#It attempts to modify the target in place, with a backup which is either
# deleted or restored depending on the success of the modification
#This script req... |
5032e7ee66f94914693870e84bf48167bbb1efa8395f1f67849c515a3e1e1a2a | Shell | 1,524 | 47 | #!/bin/bash
# -----------------------------------------------------------------------------
# Generate run combinations for power analysis
# This script generates run_combinations files for num_of_runs from 1 to 10
# -----------------------------------------------------------------------------
# Configuration
code_dir... |
dc60f12df65cebfb9f7373eedfdd0adf0817f699359a423ee5c616cce61d30ec | Shell | 1,535 | 25 | #!/bin/sh
### Job name
#PBS -N indexPlants
### Number of nodes
##PBS -l nodes=1:ppn=8
#PBS -l nodes=1:ppn=64
#PBS -q bigmem
#PBS -j oe
cd /gpfs/scratch/fas/gerstein/rrk24/ANNOTATIONS/Genomes_BacteriaFungiMammalPlantProtistVirus
mkdir STAR_GENOME_PLANTS1
/gpfs/scratch/fas/gerstein/rrk24/bin/STAR_2.4.0i/bin/Linux_x86_... |
d7b7811e6f6bf979c334f908f114fade37b7bed7e04670dcf8d1c4600bc4d39f | Shell | 1,539 | 25 | #!/bin/bash -e
MMSEQS="$1"
QUERY="$2"
BASE="$4"
DB1="$5"
SEARCH_PARAM="--num-iterations 3 --db-load-mode 2 -a --k-score 'seq:96,prof:80' -e 0.1 --max-seqs 10000"
EXPAND_PARAM="--expansion-mode 0 -e inf --expand-filter-clusters 0 --max-seq-id 0.95"
export MMSEQS_CALL_DEPTH=1
"${MMSEQS}" createdb "${QUERY}" "${BASE}/qdb"... |
15629b2c30f29e8ccd759ce41a5181a19dc31361c0f743ccf829d40899113c89 | Shell | 1,541 | 71 | #!/bin/bash
set -e
usage() {
cat << EOF
usage: bash $0 OPTIONS
examples:
Build doc with PyTorch-backend: bash $0 -p
Build doc with MXNet-backend: bash $0 -m
Build doc with TensorFlow-backend: bash $0 -t
Build incrementally with PyTorch-backend: bash $0
Remove all outputs and restart a PyTorch build: bash $0... |
7d13ac4ca6f179b63c2e53fb562076118d12e1980f7624dbdb2aa475f456f1e0 | Shell | 1,550 | 48 | #!/bin/bash
# Helper script to build graphbolt libraries for PyTorch
set -e
mkdir -p build
mkdir -p $BINDIR/graphbolt
cd build
if [ $(uname) = 'Darwin' ]; then
CPSOURCE=*.dylib
else
CPSOURCE=*.so
fi
# We build for the same architectures as DGL, thus we hardcode
# TORCH_CUDA_ARCH_LIST and we need to at least comp... |
1f659a9f33afdc144a106f701eaeff24219394ac860c1c80ef185a26f5802033 | Shell | 1,571 | 50 | #!/bin/bash
#
# EXTREME SENSITIVE ALIGNMENT OF VIRAL READS
#
# IT ASSUMES THAT THE FOLLOWING FASTQ FILES EXIST (FOR INPUT):
# o_fw_pr.fq o_rv_pr.fq o_fw_unpr.fq o_rv_unpr.fq
#
# $1 -> REFERENCE FASTA FILE
# $2 -> ORGAN
# $3 -> VIRAL INITIALS
# $4 -> NUMBER OF THREADS
# $5 -> REMOVE DUPLICATIONS
#
rm -f index-$2-$3-fil... |
5f8d7fc10c657ccbf59b27e0f9970acc8cea85f42bab84852f263148d109aca5 | Shell | 1,572 | 44 | #!/bin/bash
#
THREADS="$1";
OUTPUT="../output_data/TRACES_mtdna_authentication";
#
# ==============================================================================
#
CHECK_FILE () {
if [ ! -f $1 ];
then
echo -e "\e[31mERROR: file $1 not found!\e[0m"
echo "For addition information, see the instructions at ... |
5177ec233607a7f926c88630174f45999324a834c3dc04e88bae8a66c110ef59 | Shell | 1,585 | 60 | #!/bin/bash
#
#declare -a VIRUSES=('B19' 'HV1' 'HV2' 'HV3' 'HV4' 'HV5' 'HV6' 'HV6A' 'HV6B' 'HV7' 'HV8' 'POLY1' 'POLY2' 'POLY3' 'POLY4' 'POLY5' 'POLY6' 'POLY7' 'POLY8' 'POLY9' 'POLY10' 'POLY11' 'POLY12' 'POLY13' 'POLY14' 'TTV' 'HBOV1' 'HBOVNOT1' 'HBV' 'HPV' 'VARV' 'SV40' 'CUTA' 'HERV');
declare -a ORGANS=( $(cat ../meta... |
e07c0afdc6afc17fb37a16b55e43dabb9d9e5284fd99315a3990051fe058f448 | Shell | 1,607 | 96 | #!/bin/bash
# input arguments
DATA="${1-DD}" # ENZYMES, DD, PROTEINS, COLLAB, IMDB-BINARY, IMDB-MULTI
device=${2-0}
num_trials=${3-10}
print_every=${4-10}
# general settings
hidden_gxn=96
k1=0.8
k2=0.7
sortpooling_k=30
hidden_final=128
batch_size=64
dropout=0.5
cross_weight=1.0
fuse_weight=0.9
weight_decay=1e-3
# ... |
2298b5215595f5bd9fd4c5ac147d848eed8063c8ef7570c9ebd66c26a2245ef9 | Shell | 1,639 | 36 |
mkdir Fastq
## SW211 (X4689NOSN,X5130NOSN,X4870NOSN)
# 20210618_MGIseq
mkdir Fastq/SW211
ln -s /home/CBFG/20210618_MGIseq/Sample_SW211/SW211_1.fq.gz Fastq/SW211/SW211_S1_L001_R1_001.fastq.gz
ln -s /home/CBFG/20210618_MGIseq/Sample_SW211/SW211_2.fq.gz Fastq/SW211/SW211_S1_L001_R2_001.fastq.gz
## SW212 (X5742PDSN,X57... |
f9add9b200fdcd12c6be44ec2ff7feaf7849f936296a299b7fe67b1e715b93f7 | Shell | 1,641 | 50 | # """
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software
# and associated documentation files (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify,... |
baac47e9fe6835b8e70be478f6213d6940c3d4ddf4138691dee0e245cb6cdc13 | Shell | 1,645 | 53 | # """
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software
# and associated documentation files (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify,... |
73d48cb53f268fc2db91b7181b4b444bd49386af5158a06d96285b7b0e1ac9ca | Shell | 1,661 | 51 | #!/bin/bash
# Job name:
#SBATCH --job-name=make_atlas
#
# Account:
#SBATCH --account=fc_cerebellum
#
# Partition:
#SBATCH --partition=savio2
# Quality of Service:
#SBATCH --qos=savio_normal
#
# Wall clock limit:
#SBATCH --time=10:00:00
#
## Command(s) to run:
module load python/3.7
source ~/.bash_profile
source $(pipe... |
86d1b9f3940f8e8dbced386da25ecbce241b72bb0879a42ec7a60c370caf4cbe | Shell | 1,675 | 44 | #!/bin/bash
#SBATCH --mem-per-cpu 5G -n 2 -c 1 -N 1
#SBATCH --time 10:00:00
#SBATCH --partition=psych_day
#SBATCH --job-name randomise
#SBATCH --output=logs/%j-randomise.out
# Initialise FSL properly
source "$FSLDIR/etc/fslconf/fsl.sh"
module load FSL
export FSLOUTPUTTYPE=NIFTI_GZ
# Move to the right directory
cd "./... |
4a45955bcc5b290c42f3d399a082375ead5885247a999a73d34ca9a655b970f4 | Shell | 1,686 | 45 | #!/bin/bash
#This script autogenerates the conda update commands for TRACES_update.sh
# based on the dependencies in the dependencies.yml file
#It attempts to modify the target in place, with a backup which is either
# deleted or restored depending on the success of the modification
#This script requires yq (a CLI ... |
33f1169a8a2a643cd2f83c670bd99f14f3dad901c3ff913c90a558ca63590198 | Shell | 1,709 | 49 | #!/bin/sh
# """
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software
# and associated documentation files (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, cop... |
a6786440f48fbd191fd4c10247753d4f6927c39dd803a1fc33008ab99513b0be | Shell | 1,710 | 47 | # Bash shell script to run all simulations and analysis
# Individual Neuronal models
python ./Neuron_models/RS_pyramidal_model.py
python ./Neuron_models/RS_pyramidal_Kv_model.py
python ./Neuron_models/RS_inhib_model.py
python ./Neuron_models/RS_inhib_Kv_model.py
python ./Neuron_models/FS_model.py
python ./Neuron_model... |
575e9e91348080c59868ebda7eb8e65a7e648c96ed9876079acd1bbc8d13c6ae | Shell | 1,712 | 54 | #!/bin/bash
#
# Collects the pull-requests since the latest release and
# aranges them in the CHANGES.rst.txt file.
#
# This is a script to be run before releasing a new version.
#
# Usage /bin/bash update_changes.sh 1.0.1
#
# Setting # $ help set
set -u # Treat unset variables as an error when substituti... |
1a2e82a70a5ab56692cafa82cd39f1505f32a07f0f9e3280f235a880f2c8e3fb | Shell | 1,717 | 49 | #!/bin/sh
# """
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software
# and associated documentation files (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, cop... |
404f323f4f1249c258bc1177a175d47d9f65aa2ebd2e90412bfb8f21f786bc7a | Shell | 1,724 | 53 | #!/bin/sh
# """
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software
# and associated documentation files (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, cop... |
a5a06272cd4d915f3837ef36a70e6713baad98e32e3a798a3118e5c585d9121f | Shell | 1,733 | 45 | #!/bin/bash
#This script autogenerates the conda install commands for TRACES_install.sh
# based on the dependencies in the dependencies.yml file
#It attempts to modify the target in place, with a backup which is either
# deleted or restored depending on the success of the modification
#This script requires yq (a CLI... |
53566127e85649332dd158d93b301a77ba0644d7347105d2c62ae159e4ea9592 | Shell | 1,747 | 56 | #!/bin/bash
# Test the CI pipeline locally using Docker.
#
# This simulates the GitHub Actions Ubuntu environment to catch issues
# (missing dependencies, import errors, build failures) before pushing.
#
# Usage:
# bash scripts/test_ci_local.sh # test with Python 3.12 (default)
# bash scripts/test_ci_local... |
8b40d92456e5c12839c922f055c6aa1e27330390260df73a6303d941eef85c36 | Shell | 1,759 | 44 | #!/bin/bash
set -e
bash base_pretrain_finetune.sh simple_vit_bicubic simple_vit dense-gait
bash base_pretrain_finetune.sh simple_vit_bicubic simple_vit grew
bash base_pretrain_finetune.sh cait_bicubic cait grew
bash base_pretrain_finetune.sh cait_bicubic cait dense-gait
bash base_pretrain_finetune.sh t2t_bicubic t2t... |
33e591f1f9ba1bbaf7fc35e1d708aa79557c3a7b63b9b5b25f88adbeedf548fd | Shell | 1,762 | 62 | #!/bin/bash
#
declare -a VIRUSES=("B19V" "BuV" "CuV" "HBoV" "AAV" "BKPyV" "JCPyV" "KIPyV"
"WUPyV" "MCPyV" "HPyV6" "HPyV7" "TSPyV" "HPyV9" "MWPyV"
"STLPyV" "HPyV12" "NJPyV" "LIPyV" "SV40" "TTV" "TTVmid"
"TTVmin" "HAV" "HBV" "HCV" "HDV" "HEV" "SENV" "HPV2"
... |
da24781dd3b7b8edf37098fd39a4786eca42058880eacbd99bd387c80956b22c | Shell | 1,766 | 45 | # -----------------------------------------------------------------------------
# Copyright (c) Yongning Lei 2024
# All rights reserved.
#
# This script is distributed under the Apache-2.0 license.
# You may use, distribute, and modify this code under the terms of the Apache-2.0 license.
# See the LICENSE file for deta... |
58d8d3913de36cb0f9d26a21cc90f945b16d73da4dba68b6d64fac7bbc40d3ec | Shell | 1,768 | 51 | #!/bin/bash
PROGRAM_EXISTS () {
tool=$1; shift
call=$1; shift
printf "Checking %s ... " "$tool";
if ! [ -x "$(command -v "$call")" ]; then
echo -e "\e[41mERROR\e[49m: $tool (called as $call) is not installed." >&2;
echo -e "\e[42mTIP\e[49m: Try: ./TRACESPipe.sh --install" >&2;
else
... |
bb62521f8c303bbf0ca45300b608b86a0b0da2d88830a4e888254b432376a0f1 | Shell | 1,833 | 56 | #!/bin/bash
#
# ALIGNMENT OF MITOCHONDRIAL READS
#
# IT ASSUMES THAT THE FOLLOWING FASTQ FILES EXIST (FOR INPUT):
# o_fw_pr.fq o_rv_pr.fq o_fw_unpr.fq o_rv_unpr.fq
#
# $1 -> REFERENCE FASTA FILE
# $2 -> ORGAN
# $3 -> NUMBER OF THREADS
# $4 -> REMOVE DUPLICATIONS
# $5 -> HIGH_SENSITIVITY = 1 ?
#
# INDEX
rm -f index_fil... |
50c2029b78fb0c1ed67f1fcbe24cebf1e8d51c65b589488e521864246341e1bd | Shell | 1,845 | 40 | #!/bin/bash
#
# ==============================================================================
# ============================ UPDATE PIPELINE TOOLS ===========================
#
#BEGIN AUTO-GENERATED SECTION - UpdateCmds : DO NOT MODIFY
#==================================================
#This code snippet generated on... |
960f38c23e1a68e64b2be6dfebe4e3209eb5d2c2c48f91842e6da0db1ab395f6 | Shell | 1,853 | 62 | #!/bin/bash
set -e
. /opt/conda/etc/profile.d/conda.sh
if [ $# -ne 1 ]; then
echo "Device argument required, can be cpu, gpu or cugraph"
exit -1
fi
if [[ $1 != "cpu" ]]; then
# CI is now running on g4dn instance. Specify target arch to avoid below
# error: Unknown CUDA Architecture Name 9.0a in CUDA_S... |
c353f5a2b6fdd7d03e8b5e57c8a95d12ebacd3809f699127ba0dce4476c120c0 | Shell | 1,854 | 63 | #!/bin/bash
#SBATCH -n 1
#SBATCH -p general
#SBATCH --mem=4g
#SBATCH -t 6:00:00
#-------eQTL
# Progenitor
module add plink;
link="/proj/steinlab/projects/R00/eQTLanalysis/path_QTL/genotype/eQTL/"
i=$1
file="/proj/steinlab/projects/R00/eQTLanalysis/path_QTL/genotype/eQTL/truncated/progenestrun${i}.txt"
while read -r c... |
255c57585de4cb502eb2049c0eed2dc5a8a2e83ce6271ae75abbb7899f2cc8c6 | Shell | 1,863 | 70 | #!/bin/bash
output_dir=$1
# files with links to the data to be downloaded
SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
data_links="${SCRIPT_DIR}/links_verm_data.txt"
references_links="${SCRIPT_DIR}/links_verm_references.txt"
mkdir -p $output_dir
# make a tmp dir for all the downloads ... |
c7e5bf5206589960aca4f947399a5abcdb1bd349fd006fd432f09291b910abd0 | Shell | 1,894 | 58 | #!/bin/bash
#
# ALIGNMENT OF VIRAL READS
#
# IT ASSUMES THAT THE FOLLOWING FASTQ FILES EXIST (FOR INPUT):
# o_fw_pr.fq o_rv_pr.fq o_fw_unpr.fq o_rv_unpr.fq
#
# $1 -> REFERENCE FASTA FILE
# $2 -> ORGAN
# $3 -> VIRAL INITIALS
# $4 -> NUMBER OF THREADS
# $5 -> DUPLICATIONS
# $6 -> HIGH_SENSITIVITY
#
# BUILD THE INDEX
rm ... |
0eeb7ef89f6d3a9171e7bd7c3a30126f6251cb5550f764b8dbe0eedc3653f78b | Shell | 1,909 | 49 | #!/bin/bash
#
# moreFilters: http://samtools.github.io/bcftools/howtos/variant-calling.html
#
Reference=$1; # EXAMPLE: cy.fa
Alignments=$2; # EXAMPLE: cy_aligned_sorted-heart.bam
Organ=$3; # Example: heart
#
echo "Using Reference : $Reference";
echo "Using Alignments : $Alignments";
echo "Using Organ ... |
0e82bdf1bda547306f77c261219eaafe53bba68bd44470d345cdab0e6c009133 | Shell | 1,918 | 71 | #!/bin/bash
output_dir=$1
# files with links to the data to be downloaded
SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
data_links="${SCRIPT_DIR}/links_jain_data.txt"
references_links="${SCRIPT_DIR}/links_jain_references.txt"
mkdir -p $output_dir
# make a tmp dir for all the downloads ... |
61b85a5962d67f39a34e60af228b2232d4cf095cf6775b44ccded017cfef5721 | Shell | 1,923 | 44 | #!/usr/bin/env bash
# Build and test CarafeSharp on Linux (including WSL2). Arguments pass through to build.ps1:
# ./build.sh CPU build and tests
# ./build.sh -Torch cuda CUDA build and the Cuda test category
# ./build.sh -NoTests build only
#
# Installs what is missing with... |
d339a6c3a8b21b262586bf527e695c8bc35e4c987926b3eaf8bbfda7ddf8d6ae | Shell | 2,011 | 42 | #!/bin/bash
#
VIRUS="$3";
ORGAN="$4";
THREADS="$5";
#
if [ ! -f "$1" ] || [ ! -f "$2" ];
then
echo -e "\e[38;5;208mWARNING: $1 or $2 file not found!\e[0m"
echo -e "\e[38;5;198mDon't panic! This warning may be cause by absence of previous results\e[0m."
echo "For addition information, see the instructions at the... |
99353a276fab0e20a3afbe47fd37e3ac47b45e1d7a6d3724be04607fe1cbe824 | Shell | 2,032 | 45 | mkdir SRA
## Public1NOSN (GSM4157068, Sample_6_N3)
# SRR10433204
wget https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-run-19/SRR10433204/SRR10433204.1 -O SRA/SRR10433204.1
# SRR10433205
wget https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-run-15/SRR1043320/SRR10433205.1 -O SRA/SRR10433205.1
# SRR... |
4e8818c38cf296b6a554d6579fe5a249ec3ca6eee7c3443e4384062c47a51c43 | Shell | 2,037 | 62 | #!/bin/bash
#
# IT ASSUMES THAT THE FOLLOWING OUTPUT TRIMMED FILES EXIST:
# NP-o_fw_pr.fq NP-o_fw_unpr.fq NP-o_rv_pr.fq NP-o_rv_unpr.fq
#
ORGAN="$1";
DB="$2";
TOP_SIZE="$3";
THREADS="$4";
TSIZE="$5";
CACHE="$6";
#
RNAMES="NP-o_fw_pr.fq:NP-o_fw_unpr.fq:NP-o_rv_pr.fq:NP-o_rv_unpr.fq";
#
# ===============================... |
065cc733e238cb8ffce6cafa879f796b732981e10301b7929d11dad762d75419 | Shell | 2,042 | 50 | #!/bin/bash
# Set up FSL (if not already done so in the running environment)
# Uncomment the following 2 lines (remove the leading #) and correct the FSLDIR setting for your setup
export FSLDIR=/opt/fsl
. ${FSLDIR}/etc/fslconf/fsl.sh > /dev/null 2>&1
# Let FreeSurfer know what version of FSL to use
# FreeSurfer uses... |
783624fe4474343a33ac6a20cb6bfcd896a306cd3d992d005318c20954c4e41b | Shell | 2,042 | 64 | #!/bin/bash
#
THREADS=8;
OUTPUT="../output_data/TRACES_mtdna_authentication";
#
DOWNLOAD=1;
RUN=1;
#
# ==============================================================================
#
CHECK_FILE () {
if [ ! -f $1 ];
then
echo -e "\e[31mERROR: file $1 not found!\e[0m"
echo "For addition information, see th... |
e248474f5e19741be98a1d34c020173d1bc2a59ccf66c2a7c41281b8f51038d7 | Shell | 2,046 | 57 | mkdir Fastq
##=======================================================================================================================================================================================
#### X4870NOSN
ln -s /home/ajl1213/Projects/PD/SciAdv_Data/snATACseq/0c_SingleLibs/Fastq/X4870NOSN Fastq/
#### X4996N... |
0f5ab88d0babe343a0aafe223e4583c5fb774b6564913e4e448eacb5d66f129c | Shell | 2,057 | 92 | #!/bin/bash
set -e
usage() {
cat << EOF
usage: bash $0 OPTIONS
examples:
Start a CPU only build: bash $0 -c
Start a CUDA build: bash $0 -g
Build incrementally: bash $0
Remove all intermediate output and restart a CPU only build: bash $0 -c -r
Build with extra cmake arguments: bash $0 -c -e '-DBUILD_TORCH=ON... |
ceb66b0b82268920c0442c38d0bfadc73734f27b3695d2ea4b7adce67cb2b970 | Shell | 2,099 | 79 | #!/bin/bash
ap_loc=$(which afni_proc.py)
if [[ $? != 0 ]]
then
echo "Cannot find afni_proc.py; is it installed?"
exit 1
fi
if [[ ! $QC_FS_ROOT ]]
then
echo "QC_FS_ROOT is not set."
echo "Please set this manually or source a setup file."
exit 1
fi
sid=$1
if [[ ! $sid ]]
then
echo "You must p... |
63dec9b9eed62dfc8fd3fb85eb0cfebb12133e40083080a31f21a0788ed9aba7 | Shell | 2,104 | 69 | #!/bin/bash
#
#
THREADS=8;
OUTPUT="../output_data/TRACES_mtdna_authentication";
#
DOWNLOAD=1;
RUN=1;
#
# ==============================================================================
#
CHECK_FILE () {
if [ ! -f $1 ];
then
echo -e "\e[31mERROR: file $1 not found!\e[0m"
echo "For addition information, see ... |
e683ac2502fd84d1bd2ab59489ab076c09484dde6ca72be858c918394126ade4 | Shell | 2,167 | 75 | #!/bin/bash
output_dir=$1
# files with links to the data to be downloaded
SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
data_links="${SCRIPT_DIR}/links_jain_data.txt"
references_links="${SCRIPT_DIR}/links_jain_references.txt"
mkdir -p $output_dir
# make a tmp dir for all the downloads ... |
614a29e9ceccb94e28f5e63b0fc54381ffe013010311024e07f13e87b70c3d14 | Shell | 2,172 | 64 | # """
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software
# and associated documentation files (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify,... |
fe1e54fa4c5cef713850bf1823e3543fb5d25ee39a069970d622fc80ee35851a | Shell | 2,182 | 60 | #!/bin/bash
#
readarray -t VIRUSES < viral_names.txt
#declare -a VIRUSES=('B19' 'HV1' 'HV2' 'HV3' 'HV4' 'HV5' 'HV6' 'HV6A' 'HV6B' 'HV7' 'HV8' 'POLY1' 'POLY2' 'POLY3' 'POLY4' 'POLY5' 'POLY6' 'POLY7' 'POLY8' 'POLY9' 'POLY10' 'POLY11' 'POLY12' 'POLY13' 'POLY14' 'TTV' 'HBOV1' 'HBOVNOT1' 'HBV' 'HPV' 'VARV' 'SV40' 'CUTA' 'HE... |
51c9796435f02b8fd128f2e3e4b8d4c8bbf3dc7efa39deec3fb7169621e38ae7 | Shell | 2,209 | 63 | #!/bin/bash
# executable modules
check_uTR=check_uTR/acc
checkRM=check_RepeatMasker/checkRM
checkTRF=checkTRF/checkTRF
tmp=tmp
#tmp=tmp_backup
num_TRs=1000
listError=(0.0 0.01 0.03 0.05 0.1 0.15)
listAllowance=(0 0.01 0.02 0.03)
listPattern=("AC_AG" "ACC_GTT" "AAG_AG" "AAG_AGG" "AAAG_AG" "AAAG_AG_AAAG" "AAAG_AG_AGGG... |
384b0e8e7a4c2090d4dad273dd3de59fd02322d51487803c0530cdd0e5a6769d | Shell | 2,212 | 53 | #!/bin/bash
#
# moreFilters: http://samtools.github.io/bcftools/howtos/variant-calling.html
#
Reference=$1; # EXAMPLE: TTV.fa
Alignments=$2; # EXAMPLE: ttv_aligned_sorted-heart.bam
Organ=$3; # Example: heart
Label=$4; # Example: TTV
#
echo "Using Reference : $Reference";
echo "Using Alignments ... |
b7cf537465af2e75a12cf796b141f4c075d5a8a3ce193c8f857bf4bf3713dd92 | Shell | 2,243 | 76 | # -----------------------------------------------------------------------------
# Copyright (c) Yongning Lei 2024
# All rights reserved.
#
# This script is distributed under the Apache-2.0 license.
# You may use, distribute, and modify this code under the terms of the Apache-2.0 license.
# See the LICENSE file for deta... |
1343fbf8a9c175ccad30062e4996ebf55905252d1ad76c990d3847c2503babf0 | Shell | 2,247 | 67 | #!/bin/bash
#
# IT ASSUMES THAT THE FOLLOWING OUTPUT TRIMMED FILES EXIST:
# NP-o_fw_pr.fq NP-o_fw_unpr.fq NP-o_rv_pr.fq NP-o_rv_unpr.fq
#
ORGAN="$1";
DB="$2";
TOP_SIZE="$3";
THREADS="$4";
TSIZE="$5";
CACHE="$6";
#
RNAMES="NP-o_fw_pr.fq:NP-o_fw_unpr.fq:NP-o_rv_pr.fq:NP-o_rv_unpr.fq";
#
# ===============================... |
17cac24056ae768ab6b3dbcbd18a1973cef531de5bc4fa0af3be7ff148083413 | Shell | 2,286 | 41 | #!/bin/bash
#
# ./TRACES_gid_damage_patterns.sh AB550331.1 FR 8
#
GID="$1"
ORGAN="$2";
THREADS=$3;
#
CHECK_ADAPTERS_AR () {
if [ ! -f adapters_ar.fa ];
then
echo -e "\e[31mERROR: adapter sequences (adapters_ar.fa) not found!\e[0m"
echo "TIP: before this, include valid adapters for AdapterRemoval"
ech... |
1af48d08c9d1a100d273f3c8e7cde78f81b6c42ba3fe252db5b45c57c1a7b367 | Shell | 2,288 | 54 | #!/bin/bash
#SBATCH --time=15:00:00 # walltime
#SBATCH --ntasks=1 # number of processor cores (i.e. tasks)
#SBATCH --nodes=1 # number of nodes
#SBATCH --mem-per-cpu=12540M # memory per CPU core
# Compatibility variables for PBS. Delete if not needed.
export PBS_NODEFILE=`/fslapps/fslutils/generate_pbs_nodefil... |
750f6cff1c873841f426f6679da82c7510180f5fc7e98dae972168add9049bef | Shell | 2,294 | 86 | #!/bin/bash
function usage {
printf "\nUsage: run_ica.sh [options] FILE\n"
printf "\n"
printf "OPTIONS\n"
printf " -i|--iter <n_iter> Number of random restarts (default: 100)\n"
printf " -t|--tolerance <tol> Tolerance (default: 1e-6)\n"
printf " -n|--n-cores Number of cores... |
53c0e886e5a170de7ff2644e0992ea013a2038bd1b0ef5d348c2b3d560c6c7ab | Shell | 2,321 | 76 | # """
# MIT License
# Copyright (c) 2024-2025 Yongning Lei
# Permission is hereby granted, free of charge, to any person obtaining a copy of this software
# and associated documentation files (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify,... |
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