sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
f660b8e8fb94ad7cb7179d4d3e558831851e7144e2373690a9d37a88f0494b03 | Shell | 306 | 10 | #!/bin/bash
docker run \
-v /var/run/docker.sock:/var/run/docker.sock \
-v "${HOME}":/output \
--privileged -t --rm \
singularityware/docker2singularity boutiques/example1:test
IMGNAME=$(ls "${HOME}"/boutiques_example1_test*.simg)
mv --verbose "${IMGNAME}" ./boutiques-example1-test.simg
|
5342e92f31892bd54ecfb274583e7086ec615d6dc756fe107bc2a77e0b80a351 | Shell | 307 | 7 | python launcher_scripts/run_from_config.py configs/iceberg/msg_simulation/dag_inten_train_msg_simulation.yaml
inten_status=$?
if [ "$inten_status" -ne 0 ]; then
exit "$inten_status"
fi
python launcher_scripts/run_from_config.py configs/iceberg/msg_simulation/dag_inten_contr_finetune_msg_simulation.yaml
|
8c57709db0ec404d9384ba029c6200c83d88bc0db8aaf391a6d6ed59612b16c6 | Shell | 308 | 6 | #!/bin/bash -l
export SIM_FOLDER=$(pwd); \
export LOG_LOC=${SIM_FOLDER}/synth_cells_$(date "+%Y%m%d_%Hh%Mm%Ss").out; \
module load unstable circuit-build && \
nohup circuit-build run synthesize_morphologies --bioname ${SIM_FOLDER}/bioname --cluster-config ${SIM_FOLDER}/bioname/cluster.yaml &> ${LOG_LOC} &
|
0e42cf006e66378e55be30b73c6e184c403e2cf1ddc476ff2e1765b4c9019ca7 | Shell | 309 | 7 | #!/bin/sh
in_dir="RNA-STAR-Output-Folder" \
mysample=$in_dir"Sample-Folder/"
rsem_dir=$in_dir"Sample-Folder/rsem/rsem"
rsem-calculate-expression --bam --no-bam-output -p 28 --paired-end --forward-prob 0 $mysample"Aligned.toTranscriptome.out.bam" "RSEM-Index-Folder" $rsem_dir >& $rsem_dir"/rsem.log"
|
2fca6fff617b5a6be47c5ad0141deafb021dadbb1be87e47a2bbfc34e3a83a72 | Shell | 309 | 3 | convert xc:white xc:red xc:orange xc:yellow xc:green1 xc:cyan xc:blue xc:blueviolet xc:black +append -filter Cubic -resize 600x30! -flop rainbow_lut.png
find . -name '*.png' -exec convert {} -colorspace gray rainbow_lut.png -clut -filter Point -resize 363x363! $(dirname {})/$(basename {} .png).color.png \;
|
277c55ebf1caa02d35b0d007f53d6acd598366aced1eea6a9d07eee6a753f1c5 | Shell | 310 | 13 | #!/usr/bin/env bash
echo "QC script called"
while getopts ':i:o:r:' flag; do
case "${flag}" in
i) Fastqs_Joined="${OPTARG}" ;;
o) FastQC_Destination="${OPTARG}" ;;
*) echo "Unexpected option ${flag}" ;;
esac
done
eval "fastqc ${Fastqs_Joined} --outdir ${FastQC_Destination}"
|
e1b3906907de898750cbf0097c2b189ae9169409c375a46a89d72b5260185a5b | Shell | 311 | 20 | #!/bin/bash
check_output() {
if [ $? == 0 ]; then
echo "pass"
exit 0
else
echo "fail"
exit 1
fi
}
verificarlo-c++ --std=c++11 test.cpp -o test --verbose
check_output
export VFC_BACKENDS="libinterflop_ieee.so --debug"
./test 2> output
diff ref output
check_output
|
1525e5d7b218f094ab09386e7b5f5b52664e41fa469575d61590fe8c7eb6c22b | Shell | 313 | 18 | #!/bin/bash
dropbox=../../dropbox
data=schneider50k
tpl=default
num_cores=8
num_parts=1
save_dir=$dropbox/cooked_$data/tpl-$tpl
python find_centers.py \
-dropbox $dropbox \
-data_name $data \
-tpl_name $tpl \
-save_dir $save_dir \
-num_cores $num_cores \
-num_parts $num_parts \
$@
|
7c9bd2f4dbb11e6d0ac1cc5f89acd910fa54f4ee6e35ef44358274449a6257db | Shell | 313 | 11 | #building docker image on a Mac
version=$(awk -F'"' '/version=/ {print $2}' setup.py)
docker pull --platform linux/amd64 brunoasm/varkoder:latest
docker buildx build --push \
--platform linux/amd64 \
--cache-from brunoasm/varkoder:latest \
-t brunoasm/varkoder:$version \
-t brunoasm/varkoder:latest .
|
fe9cffeaec01113b4d206e58a38544478aab7b8d8c22cfa7b65554356c637181 | Shell | 313 | 6 |
# python3 convert_result.py;
# Run 3D drift correction from picked fiduciary beads in Picasso Render GUI
set -e
python3 ../remap_nup_groups.py /home/miguel/Projects/smlm_z/publication/models/zeiss_red_beads/out_24_nvidia6_bak/out_nup_alt_2_pic_updated/nup_renders3/nup.hdf5 emitter_remapped_undrift_picked.hdf5; |
3c408696cc954b3cf17b7c4182116a092474a0c0d259cb59041927dd8abaf988 | Shell | 315 | 5 | makeblastdb -in $1.$2.1.fas -dbtype nucl -out $1.$2
blastn -task dc-megablast -db $1.$2 -query $1.$2.1.fas -outfmt 6 -evalue 1e-40 -out $1.$2.1.aba.blast
mafft-linsi --adjustdirection $1.$2.1.fas | sed 's/_R_//g'> $1.$2.1.aln.fas
iqtree2 -redo -s $1.$2.1.aln.fas -m GTR+G -B 1000 -bnni --prefix $1.$2.1
rm $1.$2.n*
|
22ac13c475b0c71fa491d7394587a4130da7d502abe6706ea50645095f4c8fbc | Shell | 316 | 14 | #!/bin/bash
set -eu
GROUP=$1
neg=$2
pos=$3
# atlas
atlas=`dirname $2`/atlas_rot.nrrd
# outfile: Overlay of Atlas and Pos and Neg
out=`dirname ${neg}`"/pv_cells_group${GROUP}_Merge_corrected.tif"
/home/athena-admin/Desktop/Fiji.app/ImageJ-linux64 --headless -macro Macro.ijm "${atlas}","${pos}","${neg}","${out}"
|
4d0b42f6a372e486f97ba6a6fe1c6b07cd3cfe36381f8e891245c8a25a8459cb | Shell | 316 | 13 | #!/bin/sh
# Add dependencies
apt update -y
apt install libxext-dev -y
apt install libxrender1 -y
apt install libmagic-dev -y
# Run migrations
flask --app Webapp/app.py db upgrade --directory Webapp/migrations
# Run server
gunicorn "Webapp.sources:create_app('prod')" --bind=0.0.0.0 --timeout 600 --chdir ./Webapp
|
8caecc523d4f1f679e14a8cb1d2f761400ca9506356f773fd9f63053067ce492 | Shell | 318 | 5 | export MODULEPATH=/opt/software/easybuild-AMD/modules/all:/etc/modulefiles:/usr/share/modulefiles:/opt/software/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core
module purge
module load UCX-CUDA/1.14.1-GCCcore-12.3.0-CUDA-12.1.1 Python/3.11.3-GCCcore-12.3.0
|
f4031a3e138b5b73dcc85dd7d9dc9e40a20af42c78f0fd14d8c4354e5d4ee741 | Shell | 318 | 8 | #building docker image on a Mac
version=$(awk -F'"' '/version = / {print $2}' pyproject.toml)
docker pull --platform linux/amd64 brunoasm/varkoder:latest
docker buildx build --push \
--platform linux/amd64 \
--cache-from brunoasm/varkoder:latest \
-t brunoasm/varkoder:$version \
-t brunoasm/varkoder:latest .
|
0d6a1f6693b9b6d3d20c8559ff6e16bd5d46e527b4d115cebe1e95a24d6d4c2f | Shell | 320 | 14 | #!/bin/bash
if [ "$(uname)" == "Darwin" ]
then
export LDFLAGS="${LDFLAGS} -headerpad_max_install_names"
fi
$PYTHON setup.py install
# Add more build steps here, if they are necessary.
# See
# http://docs.continuum.io/conda/build.html
# for a list of environment variables that are set during the build process.
|
74db1db393e6b930c243bcbc498075438c7af9db42eb75d98c9a0b2ec8f5888e | Shell | 321 | 12 | #!/bin/bash
OUTDIR=$1
#workaround to deactivate instrumented libm option when VERROU_COUNT_DENORM is active
#if [[ -z "${VERROU_COUNT_DENORM}" ]]; then
LIBMOPTION=instrumented
#else
# LIBMOPTION=manual_exclude
#fi
valgrind --tool=verrou --rounding-mode=random --libm=$LIBMOPTION\
./unitTest >${OUTDIR}/res.dat... |
74a1aef11618d9a9a0d7380a3019072f931dc39f2c57a4c3ef40d16ac775de1e | Shell | 323 | 19 | #!/bin/sh
#SBATCH -p gpu
#SBATCH -t 7-00:00
#SBATCH --mem 20G
#SBATCH -n 4
#SBATCH --constraint=a100|v100
#SBATCH --gres=gpu:2
#SBATCH -o training_params.out
sleep 30
scontrol show jobid=$SLURM_JOBID
module load Anaconda3
source activate barcoding
python training_params.py
scontrol show jobid=$SLURM_JOBID
ex... |
7040ecd67d4e8d3a4aa7c7ecccbd07e4000aa02781522512aea70b51cd7f9b07 | Shell | 325 | 11 | DATA=muv
TDATA=muv
NS=10
NQ=16
pretrain=1
gpu_id=1
seed=0
nohup python -u main.py --epochs 5000 --eval_steps 10 --pretrained $pretrain \
--n-shot-train $NS --n-shot-test $NS --n-query $NQ --dataset $DATA --test-dataset $TDATA --seed $seed --gpu_id $gpu_id\
> nohup_${DATA}${TDATA}-${setting}_s${NS}q${NQ}seed${seed} 2>... |
0cdee03ba9e0ab4011bbc1188845f15fc3868430ddf189ab6562d241943e18d4 | Shell | 327 | 6 | #!/bin/bash
i="098"
wget https://egg2.wustl.edu/roadmap/data/byFileType/chromhmmSegmentations/ChmmModels/coreMarks/jointModel/final/E${i}_15_coreMarks_hg38lift_mnemonics.bed.gz
wget https://egg2.wustl.edu/roadmap/data/byFileType/chromhmmSegmentations/ChmmModels/coreMarks/jointModel/final/E${i}_15_coreMarks_mnemonics.... |
4f9fd1a1aeee5850b01fd5f99958f1df1c07df8561a549ae4b91d0d1eb286944 | Shell | 327 | 20 | #!/usr/bin/env bash
set -e
INFO=$1
DST=$2
tmpdir=`mktemp -d`
rsync -rptz --copy-links --port=33444 ftp.rcsb.org::ftp_data/biounit/coordinates/all/*.pdb1.gz ${tmpdir}/
for it in `zcat ${INFO} | cut -f 1 | sort |uniq`
do
file=${tmpdir}/${it}.pdb1.gz
if [[ -f ${file} ]]
then
mv ${file} ${DST}
fi
done
#rm -r ${t... |
c2e218877c8a8841c5f82697c08a5ec6d710416b7b771b52b24e6553d106f302 | Shell | 327 | 16 | #!/bin/bash
set -e
set -o pipefail
# prepare survival data
Rscript -e "rmarkdown::render('01-run_survival_pcs.Rmd')"
# Run survival models
Rscript --vanilla 02-survival-summary.R
# Plot survival models
Rscript --vanilla 03-plot-survival.R
# Generate survival summary table
Rscript --vanilla 04-pc-ancestry-correlati... |
3bbed12bb79ef67517cf808f1e1e87215776bd0f870c56021bba8e025c1c7710 | Shell | 328 | 12 | #!/bin/bash
OUTDIR=$1
#workaround to deactivate instrumented libm option when VERROU_COUNT_DENORM is active
#if [[ -z "${VERROU_COUNT_DENORM}" ]]; then
LIBMOPTION=instrumented
#else
# LIBMOPTION=manual_exclude
#fi
valgrind --tool=verrou --rounding-mode=random --libm=$LIBMOPTION\
./unitTestInteger >${OUTDIR}/... |
9e912d31fa1a7504f5ea401ce317bf6a7872a0b2dceebb953b8e6f50f4d11429 | Shell | 328 | 13 | #!/bin/bash
if [ $# != 2 ]; then
echo "gpus and task_name should be specified!! "
echo "usage: sh fleet_run.sh "0,1,2,3" train.task.0420"
fi
if [ "$1" = "all" ]; then
dev="0,1,2,3,4,5,6,7"
else
dev=$1
fi
CUDA_VISIBLE_DEVICES=$dev fleetrun --log_dir ../fleet_logs/$2 main.py --config config.yaml --task_... |
21d56d15187cd216077cf4b8afaf3d7093050657cfdb51e5729c565ff9aeb590 | Shell | 329 | 13 | # Empirical data
#snakemake --unlock
#snakemake -j 10 -k --rerun-incomplete
# Simulated data
for FILE in config/simulated_mammals_*.yaml;
do
echo "Running ${FILE}"
cp -f "${FILE}" config/config.yaml
snakemake --unlock
snakemake -s workflow/Simulations.smk -j 6 -k --rerun-incomplete
done
# Copy figures
./copy_ar... |
756e8914085a519f148f98077be21bdd1c63cd6466209a5d63abf074a44281d3 | Shell | 329 | 19 | #!/bin/sh
#SBATCH -p gpu_requeue
#SBATCH -t 1-00:00
#SBATCH --mem 20G
#SBATCH -n 2
#SBATCH --constraint=a100|v100
#SBATCH --gres=gpu:2
#SBATCH -o sample_quality.out
sleep 30
scontrol show jobid=$SLURM_JOBID
module load Anaconda3
source activate barcoding
python sample_quality.py
scontrol show jobid=$SLURM_JOB... |
c028106786329cd2c2e13c2fbabb4fb3914cfd260f65a67f48d129edf289661f | Shell | 331 | 5 | #!/bin/bash -l
source inputs.sh && \
export LOG_LOC=${SIM_FOLDER}/post_proc_$(date "+%Y%m%d_%Hh%Mm%Ss").out; \
nohup /gpfs/bbp.cscs.ch/project/proj135/home/petkantc/axon/axonal-projection/axon_projection/validation/circuit-build/post_proc_axon_synth.sh ${SIM_FOLDER} ${AXONS_REGION} ${MTYPE} ${A_S_CFG} ${A_P_OUT} &> ${... |
2604381547f8276a25fe0a823c38f1deeb368dd383d7ee67f5baa1f117d141c7 | Shell | 333 | 16 | #!/bin/bash
set -e
set -o pipefail
# prepare survival data
Rscript -e "rmarkdown::render('01-prepare-survival.Rmd')"
# Run survival models
Rscript -e "rmarkdown::render('02-run-survival.Rmd')"
# Plot survival models
Rscript --vanilla 03-plot-survival.R
# Generate survival summary table
Rscript --vanilla 04-surviva... |
5d73be6c4d656725c06927f15a42f250f098c0c894a737842a485d533420d09a | Shell | 334 | 13 | #!/bin/bash
GENOME=$1
OUTPUT=$2
bgdata_out=`bgdata get datasets/genomereference/${GENOME}`
genome_path=`echo ${bgdata_out} | awk '{print $NF}'`
for file in $(ls ${genome_path}/chr*.txt); do
basename ${file} | sed 's/chr/>/g' | sed 's/.txt//g' >> ${OUTPUT}
fold -w61 ${file} | awk '{printf "%61s\n", $0}' >> ${... |
341bd3522cdec42c1ad2bc953973c0920d1724307bcf8fb319bdb2ea2f971758 | Shell | 336 | 23 | #!/bin/bash
set -e
FILE=$1
BASE=`basename ${FILE%.fastq.gz}`
OUTDIR=seqqs
mkdir -p $OUTDIR
if [ ! -s $FILE ]
then
echo "File is missing or empty: $FILE"
exit 65
fi
if [ -s $OUTDIR/${BASE}_len.txt ]
then
echo "Output file already exists: $OUTDIR/${BASE}_len.txt"
exit 64
fi
# Run seqqs
zcat $FILE | seqqs -p ... |
5be9d5d9c550680b6a6078d6fbca2036f5c0e3490788f6694e1be4484d4b8454 | Shell | 336 | 11 | #! /bin/sh
# Display the SHA1 of the commit in which configure.ac was last modified.
# If it's not checked in yet, use the SHA1 of HEAD plus -dirty.
if [ ! -d .git ] ; then
# if no .git directory, assume they're not using Git
printf 'unknown'
else # show the commited git version
printf '%s' `git show -s --pretty... |
6e16512da0c50a794f61bb8c010e184f8a9f8d1abef647bac6e290c1b79ba33e | Shell | 336 | 18 | #!/bin/bash
cd $(dirname $0)
cd ..
source ~/.bashrc
root_path="$(pwd)/../../.."
export PYTHONPATH="$root_path/":$PYTHONPATH
python sample.py \
--nsample 1000 \
--vocab data/zinc/vocab.txt \
--model vae_models/model.iter-441000 \
--config configs/config.json \
--output samplin... |
e72591caeac778041dd871fc7ecb78a712d7fb7addcd934068109f54283e7a8b | Shell | 337 | 12 | #create project's directory using dcm2bids_scaffold
#then use xnat-get to download data from XNAT with subjects' ids (-d)
xnat-get -p AM23b -t ./neurogrieg/sourcedata --scans \
'anat_t1w' \
'SpinEchoFieldMap_mid_AP' \
'SpinEchoFieldMap_mid_PA' \
'task-stories r1' \
'task-stories r2' \
'task-stories r3' \
'task-cet' \
... |
2327177fcbfd270b83dc124c79becee8331e02301f5b94412de63b72b77b7c9a | Shell | 338 | 21 | #!/bin/bash
function run() {
cd $1
#/usr/bin/time -f"Elapsed time: %C %x %es"
./test.sh &>${1}.log
if [[ $? != 0 ]]; then
echo "Test failed: ${1}"
cat ${1}.log
exit 1
else
echo "Test passed: ${1}"
fi
cd ..
}
run test_pow2
run test_string_equal
echo "All tes... |
617ff7fe55f1ecf06742b0832a38660d3e13616bb94373a080a61b8d2d3a0ef3 | Shell | 338 | 12 | #!/bin/bash
# You need to have compiled Oat with Point Grey support and have two gige
# cameras installed on your computer to use this...
# Two cameras streaming with default parameters
oat frameserve gige raw0 -i 0 -c config.toml cam0 &
oat frameserve gige raw1 -i 1 -c config.toml cam1 &
# Look at both
oat view raw... |
387e8db677d385251f39cda48d03351bb9a7d5cf6a795791bc09ccd869829ed1 | Shell | 339 | 19 | #!/bin/sh
FILE=$1
NUM=$2
index=$(cat $FILE | cut -f $NUM |head -n 1)
echo $index
values=$(cat $FILE | cut -f $NUM | sort -u |grep -v $index)
allvalues=$(cat $FILE | cut -f $NUM | grep -v $index)
for value in $values ;
do
count=$(cat $FILE | cut -f $NUM | grep -v $index |grep $value |wc -l)
echo $value , $c... |
b46a1759285f4e85f6a5063c6736de0ceede3fb90a7694d15ce14677766e6825 | Shell | 340 | 15 | #!/bin/sh
tail -n +2 Bembidion.csv | while read line
do
echo working on $line
accession=$(echo $line | cut -d , -f 1)
taxid=$(echo $line | cut -d , -f 2)
fastq-dump -N 10000 -X 110000 --skip-technical --gzip --read-filter pass --readids --split-spot --split-files --outdir ./Bembidion/$taxid/$accession $accession
do... |
018ffc6db4b84c0f2833656174ec6c63f4977d927a2e4ef31a2d0600be1f70f6 | Shell | 341 | 4 | #!/bin/sh
cd reconstruction
python generation_audiotransformer_VGGsound_decoded_features.py config/recon_vggsound_fmriprep_rep4_500voxel_vggishish_allunits_fastl2lir_alpha100.yaml
python generation_audiotransformer_VGGsound_decoded_features.py config/recon_vggsound_attention_fmriprep_rep4_500voxel_vggishish_allunits_fa... |
ff9334955bc0abacc91ee00bbeb145c1f2467ab6f2f3989c0101dfeb90e982be | Shell | 341 | 20 | #!/bin/bash
dropbox=../../dropbox
data_name=$1
tpl_name=default
save_dir=$2
export CUDA_VISIBLE_DEVICES=0
python main_test.py \
-dropbox $dropbox \
-data_name $data_name \
-save_dir $save_dir \
-tpl_name $tpl_name \
-f_atoms $dropbox/cooked_$data_name/atom_list.txt \
-topk 50 \
-beam_siz... |
5f008b851e5673188517fba4aea0f4bb9ca57d132033d7d11431069a5a0d2331 | Shell | 342 | 11 | #!/bin/bash
#Run in Docker on Calcus:
#docker run -it -u 1023:1023 -v /home/grieg:/data --entrypoint bash dcm2bids
# Assuming the directories are named AM23b1012i, AM23b1013a, etc.
for dir in sourcedata/AM*; do
subj_id=$(basename "$dir" | sed 's/AM23b//')
dcm2bids -d "$dir" -p "$subj_id" -c code/am23b.json --auto_e... |
7efc14245192a9fd81cd91692015e861847080c7ab82da8b5e22978f0049ca75 | Shell | 342 | 11 | # the proper usage is documented in the README, you need to specify data_dir, output_dir and model_name_or_path
# run ./finetune.sh --help to see all the possible options
python finetune.py \
--learning_rate=3e-5 \
--fp16 \
--gpus 1 \
--do_train \
--do_predict \
--n_val 1000 \
--val_check_in... |
dd7f484d804e34fbdeaa7daf24024b285d0b6bcefc52558ef35ee28faf800426 | Shell | 342 | 18 | #!/usr/bin/env bash
BACKEND=$1
EXP=$2
PREC=$3
BIN=$4
TMPDIR=$(mktemp -d -p .)
cd $TMPDIR
export VFC_BACKENDS="$BACKEND ${PREC} --mode rr"
for i in $(seq 100); do
export VFC_BACKENDS_LOGFILE="tmp"
${BIN} >>output_${BACKEND}_${EXP}
done
echo Testing $EXP with $BACKEND
diff output_${BACKEND}_${EXP} ../ref_${EXP... |
2ba11801810cecf4637cf80f5d5003816de3a51cb10d00dd2bf13293fb2dfddf | Shell | 345 | 12 | #!/bin/sh
# cp ORI/PlasmoDB-26_Pfalciparum3D7.gff genes.gff
# cp ORI/PlasmoDB-26_Pfalciparum3D7_Genome.fasta sequences.fa
cat ORI/PlasmoDB-26_Pfalciparum3D7_AnnotatedCDSs.fasta \
| perl -pe 's|>(.*?) .*|>rna_\1-1|' \
> cds.fa
cat ORI/PlasmoDB-26_Pfalciparum3D7_AnnotatedProteins.fasta \
| perl -pe 's|>(.*?) .*|>rn... |
27ab443daa215b5294c49041974f6998050294356218d3143e01585d20f7d247 | Shell | 346 | 23 | #!/bin/bash
set -e
FILE=$1
GENOME=genome/combined
BASE=`basename ${FILE%.fastq.gz}`
OUTDIR=bam
mkdir -p $OUTDIR
if [ ! -s $FILE ]
then
echo "File is missing or empty: $FILE"
exit 65
fi
if [ -s $OUTDIR/$BASE.bam ]
then
echo "Output file already exists: $OUTDIR/$BASE.bam"
exit 64
fi
subjunc -i $GENOME -r $FI... |
47e9a0e0a1800209ea31182200c6756bc1e5f6eef5aef244e434462d4dba9826 | Shell | 347 | 11 | #!/bin/bash
#SBATCH -p shared # partition (queue)
#SBATCH -n 1 # number of cores
#SBATCH --mem 10000 # memory pool for each cores
#SBATCH -t 1-0:00 # time (D-HH:MM)
#SBATCH -o lmcai.out # STDOUT
#SBATCH -e lmcai.err
module load Anaconda2
source activate g... |
aaf350d0ce6ad7dbecf02737dcf2a0e8fa371fdef0ee17b60440322f3ff3c119 | Shell | 347 | 14 | _oat() {
COMPREPLY=()
local word="${COMP_WORDS[COMP_CWORD]}"
if [ "$COMP_CWORD" -eq 1 ]; then
COMPREPLY=( $(compgen -W "$(oat commands)" -- "$word") )
else
local command="${COMP_WORDS[1]}"
local completions="$(oat completions "$command")"
COMPREPLY=( $(compgen -W "$completions" -- "$word") )
... |
ae6107320e6a8ea735a159463fac00d423ee4b86ed6768d8c285a1192b0474a0 | Shell | 350 | 19 | #!/bin/bash
export VFC_BACKENDS_LOGGER=False
make clean
make dd
if grep "archimedes.c:16" dd.line/rddmin-cmp/dd.line.exclude; then
echo "line 16 should not be flagged (round-off)"
exit 1
fi
if grep "archimedes.c:17" dd.line/rddmin-cmp/dd.line.exclude; then
echo "success !"
exit 0
else
echo "missing line 1... |
718ed169844319f11eeb89228038392497b914ffd6dc0088bc026ed4b25b2255 | Shell | 351 | 15 | #!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -N dominance
#$ -j y
#$ -l mem_free=2G
#$ -l h_rt=24:00:00
#$ -t 1-11
#$ -pe smp 8
#$ -o $HOME/logs
module load CBI miniconda3/23.5.2-0-py311
conda activate brainspace
export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH
python3 diffusion_neuromaps/src/dominance.py
[[ -n "$JO... |
fc78273ae5e31defd8c7fb41f8ba897f0620088e18980d2ade6b37c2198e0b7f | Shell | 351 | 1 | TOKENIZERS_PARALLELISM=true python run_mlm_performer.py --output_dir experiments --dataset_name wikipedia --dataset_config_name 20200501.en --model_name_or_path bert-large-cased --tokenizer_name bert-large-cased --do_train --overwrite_output_dir --per_device_train_batch_size 4 --learning_rate 5e-4 --warmup_steps 100 -... |
5024d43da1cfbc12e926694357fe7e2dec74043d2a7eb9b8317e2506b1758d1e | Shell | 352 | 22 | #!/bin/bash
set -e
COMMON_VERSIONS=(3.5 3.6 3.7)
build(){
docker build . -t cpdb:${1} --build-arg PYTHON_VERSION=${1}
}
run(){
docker run --rm cpdb:${1}
}
for version in ${@-${COMMON_VERSIONS[@]}}
do
echo "building image for version $version"
build ${version}
echo "running tests for version $ve... |
8b83546aff4caa56b8e967bbc66b7df8ff8a101ae244af38103cd293cae17fe6 | Shell | 352 | 11 | #!/bin/bash
echo 'DEPRECATION PENDING: this script will be removed soon.'
# Now that the CLI interface has been improved, it is preferable to
# directly invoke these commands where needed, rather than obscuring
# them in an additional script layer.
source $HOME/callicog/.env && \
source $CALLICOG_VENV/bin/acti... |
ecd5686867e308ec2a06c1de92d680a04bf413b38d9220f7e3f0a0871176b043 | Shell | 353 | 1 | TOKENIZERS_PARALLELISM=true python run_mlm_performer.py --output_dir experiments --dataset_name wikipedia --dataset_config_name 20200501.simple --model_name_or_path bert-base-cased --tokenizer_name bert-base-cased --do_train --overwrite_output_dir --per_device_train_batch_size 4 --learning_rate 5e-4 --warmup_steps 100... |
285e6dddf2454e65fa0d74d83f651c284e43cb6b169e4d75b3f7e26a5a400b4a | Shell | 354 | 19 | #!/bin/bash
export VFC_BACKENDS_LOGGER=False
make clean
make dd
if grep "archimedes.c:16" dd.line/rddmin-cmp/dd.line.exclude; then
if grep "archimedes.c:17" dd.line/rddmin-cmp/dd.line.exclude; then
echo "success !"
exit 0
else
echo "missing line 17 (cancellation)"
exit 1
fi
else
echo "missing... |
5cd9d7f5d3e16a94356f3bac55d797d1935a22b051167704c3aab1a15ec90f83 | Shell | 354 | 11 | #!/bin/sh
for i in dotConditionNumber dotConditionNumberWithoutAssert dotConditionNumberRewrite dotConditionNumberWithoutAssertRewrite
do
export BIN_NAME=./$i
cmd="verrou_plot_stat --samples=10 --rep=stat.$i --rounding=random,random_det,random_comdet,nearness,nearness_det,nearness_comdet runVerrou.sh extrac... |
f6061532c57b76684d4ccdad03a6add15b5b526a0db8c3ff976a0e707c05369e | Shell | 354 | 8 | #! /bin/bash
# example script showing how dummy test data were created sith setup_data.py file
# change module load for runs on different systems
module load conda/23.11-py311
conda activate daxos
python3 setup_data.py --seed 1 --n 10000 --output_file example_data_train.hdf5
python3 setup_data.py --seed 2 --n 5000 --... |
218e73555d31041d86d9c8b2c255173ce8730c6d9e57c5d33feafc5c8b113b14 | Shell | 355 | 9 | #!/bin/bash
# Print the chessboard included with this example and paste onto a piece of cardboard
# Move the chessboard around under the camera in many orientations during detection
# Press the 'h' key while the calibration window is highlighted for more help.
oat calibrate camera raw -n maze -f ~/Desktop -h 9 -w 6 -... |
9b870d1ecc305f310dae01bcc17face064448c384b7c1e50d85b54aedc67cefd | Shell | 356 | 6 | apt update
apt install -y lsb-release wget software-properties-common gnupg
bash -c "$(wget -O - https://apt.llvm.org/llvm.sh)"
update-alternatives --install /usr/bin/clang clang /usr/bin/clang-20 100
update-alternatives --install /usr/bin/clang++ clang++ /usr/bin/clang++-20 100
update-alternatives --install /usr/bin/c... |
8584d18c0a513ed287dc45628dcfcb4ff6926d4c61182d7d7e40efe1863231e1 | Shell | 357 | 23 | #!/bin/bash
set -e
FILE=$1
GENOME=genome/combined
BASE=`basename ${FILE%.fastq.gz}`
OUTDIR=bam
mkdir -p $OUTDIR
if [ ! -s $FILE ]
then
echo "File is missing or empty: $FILE"
exit 65
fi
if [ -s $OUTDIR/$BASE.bam ]
then
echo "Output file already exists: $OUTDIR/$BASE.bam"
exit 64
fi
subread-align -i $GENOME ... |
ff2aaef7620e0e6f32a9ff01be5daa073a63b4ffe3584f34b21c2a7a98f06eef | Shell | 357 | 19 | #!/usr/bin/bash
set -xe
if [ -z "${INTOGEN_DATASETS}" ]
then
echo "ERROR: Define the INTOGEN_RELEASE variable"
exit -1
fi
ANNOTMUTS=$1
SCOPE=$2
OUTPUT=$3
python3 /mutrate/compute_mutrate.py mutrate \
--annotmuts ${ANNOTMUTS} \
--scope ${SCOPE} \
... |
38133d4fd344d86a1b654f8f6b3b98012aec94bace64892887d0a5e3f7440c54 | Shell | 359 | 18 | #!/bin/bash
set -e
source ../paths.sh
if [ -z "${FLANG_PATH}" ]; then
echo "this test is not run when not using --with-flang"
# Exit with 77 to mark the test skipped
# https://www.gnu.org/software/automake/manual/html_node/Scripts_002dbased-Testsuites.html
exit 77
fi
cd NPB3.0-SER
mkdir -p bin
./run-... |
f7915abb2783372c2b4b1d8f6fdcce0bfe2aff1246400a1c454d89b39d02512a | Shell | 364 | 19 | #!/usr/bin/env bash
# Copyright Beman Dawes, 2010
# Distributed under the Boost Software License, Version 1.0.
# See www.boost.org/LICENSE_1_0.txt
cp ../tut1.cpp .
cp ../tut2.cpp .
cp ../tut3.cpp .
cp ../tut4.cpp .
cp ../tut5.cpp .
cp ../path_info.cpp .
rm tut1 2>~/junk
rm tut2 2>~/junk
rm tut3 2>~/junk
rm tut4 2>~/j... |
41b45e514056fbf173c0f0de5a6c1e67b9b3bb3b59a6ee4e68f2427dac7d2f8f | Shell | 365 | 15 | #!/bin/sh -e
zcat c_briggsae.WS230.annotations.gff3.gz \
| grep -v SNP \
| grep -v translated_nucleotide_match \
| grep -v repeat_region \
| grep -v inverted_repeat \
| grep -v tandem_repeat \
| grep -v nucleotide_match \
> genes.gff
# Add fasta sequence
echo "###" >> genes.gff
echo "##FASTA" >> genes.gff
zcat... |
a0a3fe49359f9b71e1676c7cb3511acb928514d7774f897c4184a7ff810d5f9f | Shell | 369 | 12 | #!/usr/bin/env bash
# simple script to pack up source
echo "packing up $1.tar.gz"
mkdir $1
make clean
cp -r --preserve=all *.m4 src config.h.in configure.ac Makefile.am Makefile.in configure install-sh config.sub config.guess depcomp ChangeLog NEWS README COPYING AUTHORS INSTALL THANKS $1
(cd $1; find -name .svn -ex... |
bf0b6cfd4a3a9cae95fc9f1ee001d2d9984c9d34013e824a6cad519e115eb0a1 | Shell | 369 | 7 | . run_scripts/scarf_model/01_run_scarf_gen_train.sh
python run_scripts/scarf_model/02_sweep_scarf_gen_thresh.py
. run_scripts/scarf_model/03_scarf_gen_predict.sh
. run_scripts/scarf_model/04_train_scarf_inten.sh
python run_scripts/scarf_model/05_predict_form_inten.py
python run_scripts/scarf_model/06_run_retrieval.py
p... |
0f58dd96c1309bac8f2b15b0e3d86c11674bb4fcda7ab6106eed6f90aaadbbbf | Shell | 370 | 12 | #!/bin/bash
#SBATCH --job-name=ome
#SBATCH --out=omeconvert_%j.log
#SBATCH --time=1-
#SBATCH --ntasks=1 --cpus-per-task=10
#SBATCH --mem=100G
#SBATCH --partition=pi_gerstein
module load miniconda
conda activate spatial
python /home/ah2428/project/xenpred/scripts/omeconvert.py /home/ah2428/girgenti/ah2428/xenium/data/5... |
d52c2f4d2cd2817125eba261600b804fcb233385d475cb4a438a96375b2d263e | Shell | 371 | 14 | # Add parent directory to python path to access lightning_base.py
export PYTHONPATH="../":"${PYTHONPATH}"
python finetune.py \
--data_dir=$CNN_DIR \
--learning_rate=3e-5 \
--train_batch_size=$BS \
--eval_batch_size=$BS \
--output_dir=$OUTPUT_DIR \
--max_source_length=512 \
--max_target_length=56 \
--val_check_interval... |
747790958c22d75ff4d001d9dbe50002e5e6b2095b0de15ef37a2c786e99be69 | Shell | 374 | 17 | module load BEDTools/2.30.0-GCCcore-10.2.0
peaksdir=/gpfs/gibbs/pi/gerstein/jz435/ShareZhangLab/PTSD/ATAC/peaks
cd $peaksdir
celltypes=('EXC' 'OLI' 'INH' 'OPC' 'MIC' 'END' 'AST')
for i in ${celltypes[*]}
do
for j in ${celltypes[*]}
do
echo $i $j
bedtools jaccard -a $i.peaks.bed -b $j.peaks.... |
f7f3243c6e070618f9531aed4f330f8da62e00de2291ec63d5d8658fe9034393 | Shell | 374 | 5 | python train.py -fold 0 -model_name trfeplus -dataset TATN -gpu 0 -lr 1e-3
python train.py -fold 1 -model_name trfeplus -dataset TATN -gpu 0 -lr 1e-3
python train.py -fold 2 -model_name trfeplus -dataset TATN -gpu 0 -lr 1e-3
python train.py -fold 3 -model_name trfeplus -dataset TATN -gpu 0 -lr 1e-3
python train.py -fol... |
7fd235f440639c179d8315b778ff9f8200cf6bbda20320665dc77bdd72333f66 | Shell | 375 | 14 | set -eu
device=-1
methods=(nfp ggnn schnet weavenet rsgcn relgcn relgat megnet)
prefix=eval_
for method in ${methods[@]}
do
result_dir=${prefix}${method}
python train_tox21.py --method ${method} --device ${device} --out ${result_dir}
python predict_tox21_with_classifier.py --in-dir ${result_dir}
done
pyt... |
e091c309858bc4c021ac148ef8c515c69dc5f306af09c086805d77934c545bd0 | Shell | 375 | 18 | #!/bin/bash
#$ -N cellstate
#$ -l h_rt=168:00:00
#$ -V
#$ -cwd
#$ -l h_vmem=500G
echo -e "\n"
echo -e "==================================="
echo -e Date and Time: `date +"%Y-%m-%d %T"`
echo -e $1
echo -e "==================================="
echo -e "\n"
mkdir -p ./${2}
Rscript $1 > ./${2}/ctrl_job.logs 2> ./${2}/ctrl... |
14c9a0bbe61ab977e34fa14a46366e38d9d84748947afb27b7d1ee651d3df178 | Shell | 376 | 16 | python paper/figure2.py
python paper/figure3.py
python paper/figure4.py
python paper/figure5.py
python paper/figure6.py
python paper/figure7.py
python paper/figure8.py
#python paper/figureS1.py
#python paper/figureS2.py
#python paper/figureS3.py
#python paper/figureS4.py
#python paper/figureS5.py
#python paper/figureS... |
312aee68551564ca403b00720d431da97975736faa33768b406547b4047e428f | Shell | 379 | 13 | #!/bin/sh
zcat db/miRNA/human_predictions*.txt.gz \
| ./scripts_build/mirna2bed.pl \
| sort -k1,1 -k2,2g \
> db/miRNA/human_predictions.bed
# This is for IGV
bgzip db/miRNA/human_predictions.bed
tabix -p bed db/miRNA/human_predictions.bed.gz
# Uncompress for java programs (they choke on bgzip input)
zcat db/miRNA... |
eb6237bbec54e9fe4cc71aeed7d5dcfa75543950bd33f4da2a9a1ea2b5e69f2e | Shell | 379 | 25 | #/bin/bash
if [ "$#" -eq 0 ]; then
echo "A directory argument is required"
fi
cd $1
diffList=$(find . -name "*stdout.diff")
for diff in $diffList
do
stdout=${diff/stdout.diff/stdout.out}
stderr=${diff/stdout.diff/stderr.out}
echo $diff
cat $diff
echo ""
echo $stdout
cat $stdout
e... |
a854fd635461503a6aba609e5fe50a6df320b43fa4968557cb3c378ba1801791 | Shell | 381 | 10 | SUBJECT_ID="sub-0${1}"
HEMI="$2h"
PRF_MODEL=prf_Iso_fit_hrf_False
FS_DIR=../relational_neural_control/in_vivo_validation/in_vivo_fmri_dataset/data_FS/$SUBJECT_ID
PRFPY_DIR=../relational_neural_control/in_vivo_validation/in_vivo_fmri_dataset/prf_output/${PRF_MODEL}
freeview -f $FS_DIR/surf/$HEMI.sphere:overlay=$PRFPY... |
ad0cad1a8892e78aa8e74ce7eebfaaf9c2315efd4f72f8b9baf9bf2e04f4463e | Shell | 381 | 6 | #!/bin/bash -l
export SIM_FOLDER=$(pwd); \
export AXONS_REGION="['Isocortex']"; \
export A_S_CFG=/gpfs/bbp.cscs.ch/data/project/proj135/home/petkantc/axon/axonal-projection/axon_projection/validation/config_synth_favored_new_atlas.cfg; \
export A_P_OUT=/gpfs/bbp.cscs.ch/data/project/proj135/home/petkantc/axon/axonal-pr... |
da81ad2de50091b2387a8024648c41ad1f47755619bea2467d6b171cfe944daf | Shell | 382 | 13 | #!/bin/bash
set -e
set -o pipefail
# perform exon annotation of BRAF fusion breakpoints
Rscript -e "rmarkdown::render('01-get-breakpoint-exons.Rmd')"
# Breakpoint distribution analysis by predicted ancestry
Rscript -e "rmarkdown::render('02-fusion-breakpoints-by-ancestry.Rmd')"
# Survival by breakpoint type
Rscript... |
14b6889eeb34c1445c10fd1e53b48616ce201d89e445b43fa357489921f671ab | Shell | 384 | 10 |
PREFIX=" " ./run.sh 2>/dev/null > resNative
PREFIX="valgrind --tool=verrou " ./run.sh 2>/dev/null >resNearest
PREFIX="valgrind --tool=verrou --rounding-mode=random " ./run.sh 2>/dev/null >resRandom
PREFIX="valgrind --tool=verrou --rounding-mode=nearness " ./run.sh 2>/dev/null >resNearness
PREFIX="valgrind --tool=v... |
796d812672c373a9dd68775e62ad60bf474a58069e07eb1ea39b87d92edb20e0 | Shell | 384 | 21 | #!/bin/bash
set -xe
if [ -z "${INTOGEN_DATASETS}" ]
then
echo "ERROR: Define the INTOGEN_DATASETS variable"
exit -1
fi
# define the paths
DEST=$1
SOURCE=$2
path_output=${DEST}/info_functional_sites.json
unzip -o ${SOURCE}/phosphosite.zip -d ${DEST}
# parse the data
python ${SOURCE}/parse_ptms.py --pa... |
89eeeae924ed64cb47146146c52d294ddc89e289bc95ad80b725e2f63c2355ad | Shell | 384 | 24 | #!/bin/bash
set -e
# Run md5sum on the input file and save in subdirectory "md5sum".
FILE=$1
BASE=`basename ${FILE%.fastq.gz}`
OUTDIR=md5sum
mkdir -p $OUTDIR
if [ ! -s $FILE ]
then
echo "File is missing or empty: $FILE"
exit
fi
if [ -s $OUTDIR/$BASE.md5.txt ]
then
echo "Output file already exists: $OUTDIR/$B... |
eb938c7dfbbfd3be7bca1b32f8b7cc7bdba2ba00f97fef0dd94ffd9eb55cdacb | Shell | 384 | 16 | #!/bin/sh
conda activate sra
cat runs_notincluded_to_download.txt | while read line
do
echo working on $line
accession=$(echo $line | cut -d , -f 1)
famid=$(echo $line | cut -d , -f 2)
fastq-dump -N 10000 -X 510000 --skip-technical --gzip --read-filter pass --readids --split-spot --split-files --outdir varkoder_SRA... |
893a0128f37beaa74f2eb4bfb94876f75e802c001d262257c8c475c808837395 | Shell | 386 | 13 | #!/bin/sh
cp $HOME/Downloads/Sitalica_164_v2.1.cds cds.fa
cp $HOME/Downloads/Sitalica_164_v2.1.protein protein.fa
cp $HOME/Downloads/Sitalica_164_v2 ../genomes/Sitalica_164_v2.1.fa
# Fix CDS names in GFF file (there are some errors in the GFF)
cat $HOME/Downloads/Sitalica_164_v2.1.gene \
| sed "s/\.version2.1.CDS... |
35137af5dd4799d2878762db40c6d9af802a88b4c7d6c83a4c3f2d6fd58ad4e8 | Shell | 387 | 19 | #!/bin/bash
# stop on error
set -e
# find location
# =============
script="$(readlink -f "$0")"
dir="$(dirname "$script")"
# compile scywalker-report
echo "Building scywalker-report"
cd $dir/../rust/scywalker-report
./install.sh
echo "Finished building genomecomb other tools"
cp $dir/../rust/scywalker-report/targ... |
e053c3a23b539a7e35a085d2ba267d76a81c446f1bd21ff7394a8deffc785fe0 | Shell | 390 | 22 | #!/usr/bin/env bash
TYPE=$1
BIN=$2
BACKEND=$3
TMPDIR=$(mktemp -d -p .)
cd $TMPDIR
REF=../ref_${TYPE^^}
IFS=" "
for OPTION in " " "--daz" "--ftz" "--daz --ftz"; do
export VFC_BACKENDS="${BACKEND} --mode=ieee ${OPTION}"
while read x y op; do
$BIN "$x" "$y" "${op}" >>log_${TYPE^^}
done <../value.${... |
17145bb0cd721513e1da4d68c8fd0cc8691f4673d43607a7865f22cc35c8b3f4 | Shell | 392 | 19 | #!/bin/bash
# consolidates diffusion estimates in preparation for statistical analysis
# Input:
# 1 - full path of py(Baby)AFQ directory
dir_in = ${1}
e=(`echo ${dir_in}/*`);
mkdir -p ${dir_in}/nodes
for i in ${e[@]}; do
echo $i
cp ${i}/derivatives/afq/sub-01/ses-01/sub-01_ses-01_dwi_space-RASMM_model-pro... |
a7d0fb73d38f082352969f71b15a475dfc27c8272d66ed121962d54b53850f62 | Shell | 392 | 9 | #!/bin/bash
awk '{print $1}' ../analysis/results_dropout/dropoutDIV_sig > ../analysis/results_dropout/adapt
while read j; do
p=$(cat ../6_keys/bos_key | grep $j| awk '{print $1'})
cat ../6_keys/final_sor_key | grep $p >> ../analysis/results_dropout/shrew_sigShrewDO
cat ../6_keys/hom_key | grep $p >> ../analysis/r... |
6f2349090bac691937c04a903bb3be48449b7d8828fce26d80656d40abd85263 | Shell | 395 | 16 | #!/bin/bash
#
#SBATCH --job-name=extract_sid
#SBATCH --time=01:00:00
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=2
#SBATCH --output=EGA_RNA_DAN_SID.%j.txt
samtools=/data/anderslab/MelBrM/Programs/samtools-1.10/samtools
# Start samtools
for d in $(find /data/anderslab/MelBrM/RawData/MDACC/EGA/ -name "*.bam") :
do
... |
40b613329862c0921e2de84aa39aa59eaa8261085af21e652e3d1aec420ea003 | Shell | 396 | 12 | #!/bin/bash
#need to download orthofinder from github
#change path below and run this in folder with fa files
cd ../data/0_refs/
for f in *pep.all.fa ; do python /orthofinder_tutorial/OrthoFinder/tools/primary_transcript.py $f ; done
#then run orthofinder on the primary transcript folder output
source activate /path... |
e132a8c794f61a63bad94c6d6cd6d9fdf8d4b07d3ae2e88ec1846326d7967045 | Shell | 398 | 12 | #!/usr/bin/env bash
# Install cats on the slurm custer
# This relies on a cluster already setup and running, if not run
# ./cluster/start.sh
set -eou pipefail
docker exec slurmctld mkdir /tmp/cats
for file in pyproject.toml ./cats; do
docker cp "$file" slurmctld:/tmp/cats
done
docker exec slurmctld uv tool install... |
5cd39e021b7218a098e5fcfba92f619d91bf180416e475493c81d6414f1299b0 | Shell | 400 | 11 | #!/bin/sh
# Create GFF file with sequence
(cat ORI/Sbicolor_255_v2.1.gene_exons.gff3.gz ; echo "#" ; echo "##FASTA"; gunzip -c ORI/Sbicolor_v2.1_255.fa.gz ) > genes.gff
# Create protein file
gunzip -c ORI/Sbicolor_255_v2.1.protein.gz | sed "s/^>.*ID=\(.*v2.1\) annot.*/>\1/" > protein.fa
# Create CDS file
gunzip -c ... |
9346dfa0795d4052ecef6d18f2b755df05a8813098b8f96aef4a737fc209502b | Shell | 400 | 17 | #!/usr/bin/env bash
echo "MultiQC Script Called"
while getopts ':e:f:' flag; do
case ${flag} in
e) Experiment=${OPTARG} ;;
f) MultiQC_Flags="${OPTARG}" ;;
*) echo "Unexpected option ${flag}" ;;
esac
done
#Build the string
Base_String="multiqc ${Experiment} -f -o ${Experiment}... |
892b03676807fc98e8ea6063540b0cf411a929bb77ebbbdc6bb4af8d170cbc69 | Shell | 403 | 11 | #!/bin/bash
echo "downloading pretrained model checkpoints..."
mkdir pretrained_checkpoints
cd pretrained_checkpoints
wget https://s3.amazonaws.com/models.huggingface.co/bert/gpt2-pytorch_model.bin
wget https://s3.amazonaws.com/models.huggingface.co/bert/gpt2-medium-pytorch_model.bin
wget https://s3.amazonaws.com/mode... |
84c2f97b35c1830fde86ca0fd47fcc663c5ef4a5234408832d66bb04b90de7d5 | Shell | 404 | 12 | #!/bin/sh
echo
echo "WARNING: This database contains too many errors (88% of proteins do not match!)"
echo
cat ORI/AphidBase_OGS2.1b_withCDS.gff3 > genes.gff3
echo "##FASTA" >> genes.gff3
cat ORI/assembly2_scaffolds.fasta | sed "s/^>gi|[0-9]*|gb|\(.*\)\..*|.*/>\1/" | grep -v "^$" >> genes.gff3
cp ORI/aphidbase_2.1b_... |
8d4a5ba6ccca253dbd4b15f95135bd8b736b05b8bebf8220e518eaed4d9a01f1 | Shell | 404 | 16 | #/bin/bash
set -e
# Verificarlo should not fail
verificarlo-c -O2 -c rotg.c 2> error
if [[ $(arch) == "x86_64" ]]; then
# But is should report the unsupported FP80 type on x86
if grep "Unsupported operand type: x86_fp80" error; then
echo "verificarlo-c correctly reported unsupported x86_fp80 type"
... |
3040b072a96c0838f78bd8f1a418ab750fc3a1d01430ac07c4b2e02f6e95b65c | Shell | 406 | 14 | #!/bin/bash
#SBATCH --job-name=gatk-stage3
#SBATCH --account=dcibioinformatics
#SBATCH --mail-user=lwr11@duke.edu
#SBATCH --mail-type=END,FAIL
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=12
#SBATCH --mem-per-cpu=16G
#SBATCH --output=./logs/log-%j
module load python/3.7.4-gcb01
# run stage2
python3 ../../dcibioinformat... |
e0cf963eb71a27fc1f01074bb8b04ce9f648f8704e5bad1628f81e3f4666eb7e | Shell | 406 | 14 | #!/bin/bash
#SBATCH --job-name=gatk-stage2
#SBATCH --account=dcibioinformatics
#SBATCH --mail-user=lwr11@duke.edu
#SBATCH --mail-type=END,FAIL
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=12
#SBATCH --mem-per-cpu=16G
#SBATCH --output=./logs/log-%j
module load python/3.7.4-gcb01
# run stage2
python3 ../../dcibioinformat... |
0cb5184988c65a8929fec558d80518f906376f6f3c1f3483e9c00bdb6ed75e9e | Shell | 412 | 19 | #!/bin/bash
tests="$tests $(find . -maxdepth 1 -type d -name 'test_*' | sort)"
count=$(echo $tests | wc -w)
# Print number of tests detected
echo "1..$count tests"
for t in $tests ; do
if [ -e $t/clean.sh ] ; then
echo $t OK
bash -c -l "cd $t && ./clean.sh"
else
echo $t does not have... |
6cce4c8cf0f0bfdf82745d731f777243c9b7c7bf596e313c37373bae4c7f0d38 | Shell | 413 | 14 | #!/bin/bash
#SBATCH -o ./slurm_output/R-%x.%j.out
#SBATCH -t 8:00:00 # walltime = 1 hours and 30 minutes
#SBATCH -n 1 # one CPU (hyperthreaded) cores
#SBATCH -p normal
#SBATCH --mem=32G
#SBATCH --array=1-6%30
SBATCH --mail-type=NONE
# Execute commands to run your program here, taking Python for ... |
3d506013b8e32fcb829642724a4049443587db0d02598268df2fcf16b974a0e7 | Shell | 414 | 22 | #!/bin/bash
set -e
export VFC_BACKENDS="libinterflop_mca.so --precision-binary64 40"
verificarlo-c test.c -o test --function=f
./test >outputf1 2>outputg1
./test >outputf2 2>outputg2
if diff outputf1 outputf2 >/dev/null; then
echo "f output should differ"
exit 1
fi
if diff outputg1 outputg2 >/dev/null; the... |
ceb7425fb7f972293ac171807091c8551b62da1056fa2d728204d7ebd4237927 | Shell | 415 | 14 | #!/bin/bash
# change path parameters for iFS (and not FS)
module load ncf fsl/6.0.4-ncf
export FREESURFER_HOME=/n/gaab_mri_l3/Lab/DMC-Gaab2/tools/tkt_tools/infant_freesurfer/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export FS_LICENSE=/n/gaab_mri_l3/Lab/DMC-Gaab2/tools/tkt_tools/infant_freesurfer/freesurf... |
ee88a14746583474709b029673d4dc27c23ef7fcd38a9b0a77243287509f2fdf | Shell | 415 | 14 | #!/bin/bash
#SBATCH --job-name=Duke-stage4_3
#SBATCH --account=dcibioinformatics
#SBATCH --mail-user=lwr11@duke.edu
#SBATCH --mail-type=END,FAIL
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
#SBATCH --mem-per-cpu=16G
#SBATCH --output=./logs/log-%j
module load python/3.7.4-gcb01
# run:
python3 ../../../dcibioinformatic... |
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