sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
c9779f125e8f20770bfdaacc62a4b712bb059178a030cd4da9888a1b447cf3d6 | Shell | 243 | 10 | #!/bin/bash
# Original works: https://github.com/hemberg-lab/scRNA.seq.datasets/
mkdir -p ./RAW;
cd ./RAW;
# download data
wget -O data.tar \
'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE84133&format=file'
tar -xvf data.tar
gunzip *.gz
|
26b42dade0f293d337b9622fd17c7cb6424ed6ddaad45018ac154a2dfc900474 | Shell | 244 | 6 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/main_analyses/computeWNC.R "PNC"
|
417131e12cbacf14d02d1f15bcaebdeb2263762ecde51024621bd733b1d8f38f | Shell | 244 | 5 | timestamp=$(date +"%Y%m%d%H%M%S")
jobname="sbrnet_synthetic_data_gen_${timestamp}"
qsub -N "${jobname}" -o "/projectnb/tianlabdl/jalido/sbrnet_proj/.log/qsubs/${jobname}.qlog" /projectnb/tianlabdl/jalido/sbrnet_proj/scripts/gen_syn_data.qsub
|
6405573f65133294c2bc89f45f7e1d62098e9542a46f42b9c5a137a968e23985 | Shell | 244 | 6 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/main_analyses/computeWNC.R "NKI"
|
66890405e292f70ee399f524c05d5e3b2b829f6859c950e19f878098d28ac1f1 | Shell | 244 | 6 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/main_analyses/computeWNC.R "HBN"
|
76934709ec4efeb3770c54b1be1e16a48ffbaa1036dfbd6669ed65fbc4993d3e | Shell | 244 | 6 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/main_analyses/computeBNC.R "NKI"
|
9e1415c8d6fbff4ab8a96cc180a54b4b46344f489be5241e55110cb703e64e39 | Shell | 244 | 6 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/main_analyses/computeGBC.R "PNC"
|
a8fed41bd32514b5c193cf4e17e020502a236e595c753d8bc5e6bf7d2504db69 | Shell | 244 | 5 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/main_analyses/computeWNC.R "HCPD"
|
b45cf38983a154d03acab619f6a81ea5de09b9b9c4dc4dbdf7bc5347151a2f76 | Shell | 244 | 6 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/main_analyses/computeGBC.R "HBN"
|
51f0bbd639b3e267b5707c0cbd0f1165c65e52cbb36482aab295d3f5b14afbff | Shell | 245 | 5 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/main_analyses/fitGAMs_FCmetrics.R $1
|
5459bd35a2ce5c530e03fa3018e71e7836f0daa50be4408215590b6dbd61236b | Shell | 245 | 6 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/main_analyses/computeEdge.R "HBN"
|
5758f723cdbab39d3bac0dabe6fef0bab18604e577b800d91aa101cd74ac73c8 | Shell | 245 | 6 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/main_analyses/computeEdge.R "NKI"
|
65ab6ffe24f650108f329e199188fbe7cf6b6972d8a4c1070ddf9e83b7f86e51 | Shell | 245 | 7 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/main_analyses/computeBNC.R "HBN"
|
7b2e78e3335af0a5097af780c2f0c4489b3789802b69ef027d1d265652f6309e | Shell | 245 | 7 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/main_analyses/computeGBC.R "NKI"
|
e97faee6c6c6bdde0aa06edefc9710ea6dc4df6abe48753c05fd83becb9c109d | Shell | 245 | 6 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/main_analyses/computeGBC.R "HCPD"
|
6abc99a19bd3a47e3461ea38da157a5e8d6b4de7f9b6ed31a3f3ad1cf1dbcd7e | Shell | 246 | 7 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/main_analyses/computeEdge.R "PNC"
|
72cde6c56f6b70646e0bd64cfc9b7f0278584c0db9d8f1246c178fef94d77369 | Shell | 246 | 6 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/main_analyses/computeEdge.R "HCPD"
|
4bfbe5ebdb08ee027bc2c08ad4163ec7c8b36a5a28651a2b832d1c3d3f773d35 | Shell | 247 | 7 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/main_analyses/fitGAMs_edges.R $1
|
a12a22fa93b19b790145a1f488d61ce12dc18bfa9689d2519c4c7735e9dcff7f | Shell | 247 | 9 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/main_analyses/computeBNC.R "PNC"
|
d6ff425401565aa1950c26c5f4e579727b13f8b1b63f1b4283eb74a4b9d055be | Shell | 247 | 8 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/main_analyses/computeBNC.R "HCPD"
|
198625ea82a2d2efc1df0c11fc0dbad138638fe6e3162e1ded0c29870e56f7c0 | Shell | 248 | 1 | $ROSETTA/main/source/bin/rosetta_scripts.tensorflow.linuxgccrelease -parser:protocol ./XML/deamidation_prediction.xml -l ./data/mut_N21.list -parser:script_vars position=21 ptm=Deamidation -out:file:score_only n21_deamidation_new_score.score -beta
|
3ba90096c40b9a8af7cf8dc587a29203b538bbc60c29ffde26eb235fe3321912 | Shell | 250 | 5 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/sensitivity_analyses/computeGBC_nonGSR.R |
6379c9c8926382793851987194731643a9b8236467ed36bace8a1aa18fdab481 | Shell | 251 | 16 | #!/bin
for i in $(seq 0 $(( $3 - 1)))
do
{
for j in $(seq $1 $3 $2)
do
if [ $(($j+$i)) -lt $(($2+1)) ]
then
echo "train model $(($j+$i))"
python model.py $(($j+$i)) $i 2>/dev/null
fi
done
}&
done
wait
echo "all the models are finished"
|
28acd070f6ba8f763b99bc4268efa224b5fc0cb94058455b3042d1c03900dd5a | Shell | 253 | 6 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/connectivity_matrices/HBN/HBN_makeConnMatrices.R
|
e02b2108c27bca96744c70510a4a4798f82dd47f87b5f9b6b276d0a908022592 | Shell | 253 | 11 | #!/bin/bash
#SBATCH -N 1
#SBATCH -n 10
#SBATCH --mail-user=avlant@mit.edu
#SBATCH --array=0-14
#############################################
# Load module
module load python3/3.6.4
python3 synthNetDataScreen.py --selectedCondition $SLURM_ARRAY_TASK_ID |
e3c80e8de9a380f1bb40d9c46efcca0593e5c4adac9d5816e056f86184e533d1 | Shell | 253 | 5 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/sensitivity_analyses/fitGAMs_GBC_nonGSR.R $1
|
43cdfb4e2056ee9b9af7fdd936a4e0e3e7f2a0957fa10616a8b5710d24057b2e | Shell | 254 | 5 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/sensitivity_analyses/fitGAMs_networkpair.R $1
|
6e87c2ca922b7e229e7d31ced5729ef3593be9ab5f87d7fc695632b3dff29a70 | Shell | 254 | 7 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/connectivity_matrices/PNC/PNC_makeConnMatrices.R
|
9de4e0ab4fd1281da5fbaaadb952c8b6cff3a039616a02da1830afe1cdf39d3a | Shell | 254 | 6 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/connectivity_matrices/NKI/NKI_makeConnMatrices.R
|
1a2475788496c8db21ae49758f15d9647e080fa40cf480e11d3c6908ad25938d | Shell | 255 | 6 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/connectivity_matrices/HCPD/HCPD_makeConnMatrices.R
|
3141be2d355fbd45c66d6e7f59de0daeecc87be9964279be5dec160b2df976e1 | Shell | 255 | 1 | /home/s215v/.aspera/connect/bin/ascp -i /home/s215v/.aspera/aspera.openssh -QT -l100m -k1 -d /home/s215v/Workspace/DSB_Paper/reports/00-upload_ncbi/SRA subasp@upload.ncbi.nlm.nih.gov:/uploads/p.wei_dkfz-heidelberg.de_HG4axnHT/20221220-dripseq_groseq_htgts |
ffa40365cf0eae3724ba696152d7219436030c2c9b66a24c8e9802f3845ff5aa | Shell | 255 | 5 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/sensitivity_analyses/fitGAMs_GBC_restOnly.R $1
|
2c30bd6aa489b7e3f4b2de9a6762745bdc46f65f637ccf579fe74e6e05cd98d5 | Shell | 258 | 10 | #!/bin/bash
#make sure subject name is cleaned on both json and bids filepath
subject=$(jq -r .subject bids/sub-sub11061/anat/sub-sub11061_T1w.json)
if [ $subject != "sub11061" ]; then
echo "bad subject $subject"
exit 1
fi
echo "check.sh all good"
|
2e86bb4f9b92190a315b3818b6f706ad98514b47556781d54c1c34fcbe4e1270 | Shell | 259 | 5 | for ((i=0;i<42;i+=1))
do
echo "processing $i"
python funatlas_plot_intensity_map.py --nan-th:0.3 --req-auto-response --exclude-ds-tags:mutant --ds-exclude-i:$i --no-plot --no-merge-bilateral --matchless-nan-th-from-file --enforce-stim-crosscheck
done
|
1f13f50cad57488606277698bcc2474f92d1b287d08afec870cf1df9d68c1d94 | Shell | 260 | 6 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/sensitivity_analyses/computeGBC_restOnly.R "HBN"
|
3611d53562888ff2967c80951fa6dcfe6f50bf0f91accc756bbd5faa37e3fa44 | Shell | 260 | 5 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/sensitivity_analyses/computeGBC_restOnly.R "HCPD"
|
42acdf319bff1a86a329dd3f2baf08d677cda77a367ad986b4b32463503d4542 | Shell | 260 | 6 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/sensitivity_analyses/computeGBC_restOnly.R "PNC"
|
0050b7ad5b69d047ae568d7a7361e1ac48ecd438b40dbfc18359484a3848a9b7 | Shell | 261 | 10 | #!/bin/bash
#SBATCH --partition=gpuq
#SBATCH --qos=gpu
#SBATCH --gres=gpu:1g.5gb:1
#SBATCH --ntasks-per-node=1
#SBATCH --job-name="gc_can_1"
#SBATCH --time=0-24:00:00
#SBATCH --output /scratch/nsutton2/gc_sim/gc_can_1_results.txt
#SBATCH --mem=20G
./rebuild.sh
|
1fedb7732d50fce22436b316054b7b72ec6eb98963667cbce4b0d5ad10ad173b | Shell | 261 | 6 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/connectivity_matrices/HBN/HBN_makeConnMatrices_restOnly.R
|
60bf3b76ff363dc21daca57531a732a176cfba6d0e0d0a5599f8eefc05b8598b | Shell | 263 | 8 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/connectivity_matrices/PNC/PNC_makeConnMatrices_nonGSR.R
|
43507b1db922d0917e51ddca942813f6c88f6d1752b2d42f23bf2b22810ebbbf | Shell | 264 | 11 | #!/bin/bash
# run the extract_fitness program
export make_clean="rm extract_fitness"
export make="g++ -Wall -g -std=c++11 extract_fitness.cpp -o extract_fitness"
export run=" && ./extract_fitness"
command=$make_clean
eval $command
command=$make$run
eval $command |
7bb10608490f53440ec1abb555603cebe36cdbb2440e40836ca6634e9de54335 | Shell | 264 | 6 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/connectivity_matrices/HCPD/HCPD_makeConnMatrices_restOnly.R
|
d62b2b9f684643e0096df324ab5ff93b97b7f4fecd93f849019dcd35447b96bd | Shell | 264 | 9 | # Note that bartender does not run on all systems -- particularly redhat linux
reformat_csv=$1
output=$2
### 1. clustering lineage barcodes based on umi and NT position information, using Bartender v1.1
bartender_single_com -f reformat_csv -o output -d 5 -z 5
|
50ab40449f8720bb661312e7c1db8e49c1086e1d436f7a2e61f0349b2bfa0421 | Shell | 265 | 11 | #!/bin/bash
for of_case in $@; do
casename=$( basename "$of_case" )
casedir=$( dirname "$of_case" )
tar -czvf "${casedir}/${casename}.tar.gz" "$of_case"
if [ "$?" == 0 ]; then
echo "Removing ${of_case}"
rm -r "$of_case"
fi
done
|
b8c0bbe9464eba50496daaafb89db0d27e85112f62e9ac6cf4f2ef633560b72d | Shell | 265 | 8 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/connectivity_matrices/PNC/PNC_makeConnMatrices_restOnly.R
|
a11f65994b80b663f36a01e7534f1d6491889164353cee02c0521a04222e7b6d | Shell | 266 | 5 | for n in $(cat pubmed_list_as_xls2.txt);do
str=$(grep $n ../tmp/pubmeddata/*|sed 's/..\/results\/pubmeddata\///g'|cut -d\: -f1|sed 's/-/ /g'|sed 's/.txt//g'|tr ' ' '\n'|sort|uniq|tr '\n' ' ');
echo $n","$str
done > ../results/pubmed_keywords_as_xls2.csv;
|
ee6dfbf95ee518ed7dfab8fb1ab495e0e228e2ce094222fe5d80c0a0ee2f9214 | Shell | 267 | 7 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/sensitivity_analyses/computeNetworkPair_conn.R "HCPD"
|
fa8d5909d1b2fa2f3df7def654823a55517ba0a4d8737954ea1663590e7605d1 | Shell | 267 | 8 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/sensitivity_analyses/computeNetworkPair_conn.R "NKI"
|
fe0a005846d3c909da0abac718a4b457c0e7186afb4c87db8306a5799cd566e5 | Shell | 267 | 5 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/sensitivity_analyses/fitGAMs_GBC_absvalue_thresholded.R $1
|
5b2fbac3d378d9b6c5879a35b290a293b068b1c5f4f152d095fa37f5fb701c3e | Shell | 268 | 8 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/sensitivity_analyses/computeNetworkPair_conn.R "HBN"
|
61388c14263ceb16cb36bae65a9ff587e59961ee63931c7979e4f73baf484e02 | Shell | 268 | 8 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/sensitivity_analyses/computeNetworkPair_conn.R "PNC"
|
d90dfd676f2f2bf5c41d58b1b99ed42909626a651c75cad28e42ca261c0b603f | Shell | 270 | 12 | #!/bin/bash
# download data
wget -O zeisel.txt \
'https://s3.amazonaws.com/scrnaseq-public-datasets/manual-data/zeisel/expression_mRNA_17-Aug-2014.txt'
# remove some headers
sed -i '1d' zeisel.txt
sed -i '2,10d' zeisel.txt
# assign labels
sed -i '1s/ #//' zeisel.txt
|
346f87718d63042563e06106798d21730333057205dbb0800dea954b6473a6bb | Shell | 272 | 6 | #! /bin/bash
# About the flags:
# -X is needed for github cancel to work.
# Otherwise srun needs two successive ctrl-C / SIGINT to cancel
# -u was found to enable colors. --pty would also work.
srun -X -u -t 1:00:00 -c4 --mem=32g --gres=gpu:2 buildbot/build.sh $@
|
342ae368752dfbbe4c78561fc8de3f5300dda0cde9b74c09a2a4d05555f45ab4 | Shell | 273 | 8 | #!/bin/bash -l
# -l option is interactive login shell
#$ -pe omp 4
# Load the newest version of matlab on SCC
module load matlab
# Additional qsub options here . . .
matlab -nodisplay -r "runBatchfNIRSJob($NSLOTS); exit"
# matlab -nodisplay -r "runBatchfNIRSJob($1); exit"
|
a4678cb5e326ab5e016fa2bbd9700c68d9dac5363f2b91e24667d7f1bd554320 | Shell | 277 | 10 | #!/bin/bash
#SBATCH --partition=gpuq
#SBATCH --qos=gpu
#SBATCH --gres=gpu:A100.40gb:1
#SBATCH --ntasks-per-node=1
#SBATCH --job-name="auto_mod_8"
#SBATCH --time=0-05:00:00
#SBATCH --output /scratch/nsutton2/gc_sim/auto_mod_8_results.txt
#SBATCH --mem=20G
srun sh ./auto_mod.sh
|
9bcba812960b2dd9be3a9759370f4f9d9932adb0fcca2c6a77461ba89f6f7695 | Shell | 283 | 7 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/sensitivity_analyses/computeGBC_absvalue_thresholded.R "PNC" "absvalue" |
19988ec35ba935369a4d10bc96783ba172156246278076afa39679f745ec3bd7 | Shell | 286 | 7 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/sensitivity_analyses/computeGBC_absvalue_thresholded.R "PNC" "thresholded" |
7b18700ce00bc8bc22c2d5531aeefabc29204ff552a544077f820c10a497e8a6 | Shell | 286 | 4 | # We used to have a script here to set up all the include and library search
# paths for the vg build. But now the Makefile knows how to do it all for the
# build, and the vg binary knows where to look for its dynamic libraries.
echo 1>&2 "Sourcing source_me.sh is no longer necessary"
|
0a274edda371ee697327d8c73488760fc4c8a9b9b3f9af2feb42c7332e368897 | Shell | 289 | 5 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/sensitivity_analyses/makeConnMatrices_thresholded_absvalue.R "PNC" "absvalue"
|
1b9ed8c63953d82f39c5bdead9a27133b917e8c247664ea42a51fdf8014bc57b | Shell | 290 | 13 | #!/usr/bin/env bash
set -e
# Fix ownership of output files
finish() {
# Fix ownership of output files
user_id=$(stat -c '%u:%g' /data)
chown -R ${user_id} /data
}
trap finish EXIT
# Call tool with parameters
./../opt/fastq-dump/sratoolkit.2.8.2-1-ubuntu64/bin/fastq-dump "$@"
|
05dbdb32a743e3528a8f404fe4cc121de35ef5c8e020f5fbc72a14373173ad46 | Shell | 291 | 9 | #!/bin/bash
# download data
wget -O data.txt.gz \
'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE57249&format=file&file=GSE57249%5Ffpkm%2Etxt%2Egz'
gunzip data.txt.gz
# download extra data
wget 'https://s3.amazonaws.com/scrnaseq-public-datasets/manual-data/biase/biase_cell_types.txt'
|
5d0cad6498c114b3780609d0fa3f811d4c012cf7ff8a121fc3730931ccba0681 | Shell | 292 | 5 | #!/bin/bash
singularity run --cleanenv \
/cbica/projects/network_replication/software/docker/r-packages-for-cubic_0.0.4.sif \
Rscript --save /cbica/projects/network_replication/manuscript/code/scripts/sensitivity_analyses/makeConnMatrices_thresholded_absvalue.R "PNC" "thresholded"
|
83aefb350af99f7891227fcb758d136467f568b0d0680a7dae77cf8bf52c594a | Shell | 298 | 7 | #!/bin/bash
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93374/suppl/GSE93374_Merged_all_020816_DGE.txt.gz
gunzip GSE93374_Merged_all_020816_DGE.txt.gz
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93374/suppl/GSE93374_cell_metadata.txt.gz
gunzip GSE93374_cell_metadata.txt.gz
|
b3a07accdbf4005baf150ba114c37ca229022a3df6f63fb8c5accd74fbaefb47 | Shell | 298 | 10 | #!usr/bash
ltrfa=$1
wd=$2
name="`echo $3 | sed 's/_/ /g'`"
Cpu=$4
mkdir -p ${wd}/RM_result/
RepeatMasker-4.1.2/RepeatMasker -e rmblast -pa ${Cpu} -s -species "${name}" -no_is -dir ${wd}/RM_result -a -source -html -gff -u -lcambig ${ltrfa} 1>${wd}/RM_result/log.o.txt 2>${wd}/RM_result/log.e.txt
|
2605931ac440479aca61d449cd7594bf8c0c6022cbe96d1cd8611fcf03ab89b8 | Shell | 299 | 14 | #!/bin/bash
JOBID=$1
USERID=$2
GROUPID=$3
JOBNAME=$4
SESSION=$5
#$6 = resource list
#$7 = resource used
#$8 = queue name
#$9 = account string
echo "epilogue/cleantmp.sh: removing /tmp/$JOBID"
sleep 10 #give singularity/cleanupd to do some work (before getting killed by wall)
rm -rf /tmp/$JOBID
|
45b5ddbf8591e4594d3d3a28f847b14e7c655048655f89523f087b4c76179290 | Shell | 300 | 7 | #!/bin/bash
DIR=$(cd "$(dirname "$0")"; pwd)
BASEDIR=$(realpath $DIR/..)
bsub -P scicompsoft -o std%J.out -e std%J.out -n 20 -R "span[ptile=4]" bash -i $BASEDIR/../ray-integration/ray_cluster.sh -c "python $BASEDIR/neuronbridge/validate_ray.py --nomatches" -n "neuronbridge-python" -m 20000000000
|
5cd62575c23e3525cc2861d177687ae942e2b09d24ece85096967d24aad7f17e | Shell | 300 | 10 | mkdir run
while read domid; do
echo $domid
mkdir $domid
cd $domid
perl ~/soft/DaliLite.v5/bin/dali.pl --pdbfile1 ../../pdbstyle-2.08/$domid.ent --db ../pdbids_imported.txt --dat1 ./ --dat2 ../imported --clean
mv mol1?.txt ../run/$domid.txt
cd ..
rm -r $domid
done < domids_imported.txt
|
f667604a2cdb2f2ee35492f2dec01510b0c5c39b9d38d5bad5be8a1e58772de4 | Shell | 300 | 1 | "${SCHRODINGER}/utilities/multisim" -JOBNAME SH2_wt_MD_10 -HOST localhost -WAIT -maxjob 1 -cpu 1 -m SH2_wt_MD_10.msj -c SH2_wt_MD_10.cfg -description "Molecular Dynamics" SH2_wt_MD_10.cms -mode umbrella -set stage[1].set_family.md.jlaunch_opt=["-gpu"] -o SH2_wt_MD_10-out.cms -lic "DESMOND_GPGPU:16"
|
be711a5e7ab247b763986e176c384c36743bc9fdd448d371d55e738324865475 | Shell | 301 | 2 | python eval_rcmvsnet_tanks.py --split "intermediate" --loadckpt "./pretrain/model_000014_cas.ckpt" --plydir "./tanks_submission" --outdir './tanks_exp'
python eval_rcmvsnet_tanks.py --split "advanced" --loadckpt "./pretrain/model_000014_cas.ckpt" --plydir "./tanks_submission" --outdir './tanks_exp' |
f724677f734b9bb534252ffcb2a92483da58013be8ca96eaed7a53c5db4fbc5e | Shell | 301 | 6 | #!/bin/bash
wget -O data.csv.gz \
'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE85241&format=file&file=GSE85241%5Fcellsystems%5Fdataset%5F4donors%5Fupdated%2Ecsv%2Egz'
gunzip data.csv.gz
wget https://s3.amazonaws.com/scrnaseq-public-datasets/manual-data/muraro/cell_type_annotation_Cels2016.csv
|
7ee65ae1a3c377cdac0a2aaec336b39be74b21a9c7aba8af7a14f1ba21cbbb1e | Shell | 302 | 16 | #!/bin/bash
#$ -V
#$ -cwd
#$ -M xavier.graubove@crg.eu
#$ -m a
#$ -q long-sl7,mem_512_12h,short-sl7
#$ -l virtual_free=20G,h_rt=12:00:00
#$ -o tmp/
#$ -e tmp/
ref=$1 # blast db
que=$2 # query fasta
out=$3 # output
bin=$4 # binary
${bin} -db ${ref} -query ${que} -outfmt 6 -out ${out} -num_threads 16
|
9d32ec720e6f5f3005a0e26c55f22ebb4b37e7c279f6dca1a9bf0797daf8e887 | Shell | 302 | 13 | #!/bin/bash
#SBATCH -N 1
#SBATCH -n 10
#SBATCH --mail-user=avlant@mit.edu
#SBATCH --array=0-19
#SBATCH --nice=100000
#SBATCH --exclude=c[5-22]
#############################################
# Load module
module load python3/3.6.4
python3 macrophageNetCrossValidation.py --leaveOut $SLURM_ARRAY_TASK_ID |
483e1ac345d5d604013d8aff94f4e7c3bc538f13b1de04797c5bde355457265d | Shell | 309 | 9 | #!/bin/sh
# This script is for the author to protect docs and analysis outputs private before acceptance
# We will move docs in a privae repository tentatively during revision
for v in $(find docs/jupyternb -name "*privatedoc.ipynb")
do
mv $v $(dirname $v)/$(basename $v "_privatedoc.ipynb").ipynb
done
|
5e8c06278f6858973185d674931925492151ccf23fead83ce5b4efb969db1ecf | Shell | 309 | 7 | #!/bin/bash
DIR=$(cd "$(dirname "$0")"; pwd)
BASEDIR=$(realpath $DIR/..)
bsub -P scicompsoft -o std%J.out -e std%J.out -n 20 -R "span[ptile=4]" bash -i $BASEDIR/../ray-integration/ray_cluster.sh -c "pixi run python $BASEDIR/neuronbridge/validate_ray.py --nomatches" -n "neuronbridge-python" -m 20000000000
|
5bce6aebc036965809ce28367b70564b1a039a14697e931ee45d6a816a7ec296 | Shell | 310 | 11 | REV1=`(cd $us2/develop;svn info|grep Revision)`
REV2=`cut -f2 -d\" include/us_revision.h`
if [ "$REV1" != "$REV2" ]
then
echo $REV1
echo $REV2
# Remove return character from string when running under cygwin
REV1=`echo $REV1 | sed s/\r//`
echo "#define REVISION \"$REV1\"" > include/us_revision.h
fi
|
89af5c5d1cd0cfcf2388f724f95524fdea6daeba3c0bd22b380d56d544b79fc0 | Shell | 310 | 13 | #!/bin/bash
#SBATCH -N 1
#SBATCH -n 10
#SBATCH --mail-user=avlant@mit.edu
#SBATCH --array=0-19
#SBATCH --nice=100000
#SBATCH --exclude=c[5-22]
#############################################
# Load module
module load python3/3.6.4
python3 macrophageNetCrossValidationScramble.py --leaveOut $SLURM_ARRAY_TASK_ID |
07927e3c4ddd721f16796f4e1cf20b4e4ca445622035179095686eee912fb46d | Shell | 319 | 8 | mkdir imported
while read domid_pdbid; do
domid=$(echo $domid_pdbid | cut -f1 -d " ")
pdbid=$(echo $domid_pdbid | cut -f2 -d " ")
echo $domid
perl ~/soft/DaliLite.v5/bin/import.pl --pdbfile ../pdbstyle-2.08/$domid.ent --pdbid mol1 --dat ./ --clean
mv mol1?.dat imported/${pdbid}A.dat
done < domids_pdbids.txt
|
2020fc7148b3d3bf834598b7bb02bfd70d82a20d7979e2b051a90ebd021b01dd | Shell | 319 | 10 | #!/bin/bash
python3 rename_input.py
echo '==============================='
echo 'Run nnUnet Prediction'
echo '==============================='
cd nnUNet/nnunet
# Change the call according to your parameters.
python3 inference/predict_simple.py -i $INPUTDIR -o $OUTPUTDIR -t $TASK_NAME -tr nnUNetTrainer -m 3d_fullres
|
0f5bc843fb703c0f7e2fbc0f56f0615f6ee2f5700419cd7609acb640ff18e809 | Shell | 320 | 6 | # Use fasatq-dump in atropos-tools to fetch some RNA-seq.
ACCN=SRR521458
docker run -v $(pwd):/dump --rm jdidion/atropos_paper_analysis bash -c \
"/opt/fastq-dump/fastq-dump-wrapper.sh --split-files --gzip -O /dump ${ACCN}" && \
docker build -f Dockerfile -t jdidion/atropos_rnaseq:latest . && \
rm ${ACCN}_*.fastq.gz
|
d7fb8d9a72473532d90dc33e05659fac4ad8ec0afc374924d0e7eac0001fa4cb | Shell | 321 | 5 | for n in $(cat scopus_list_as_xls2.txt);do
str=$(grep $n ../tmp/scopus/*|sed 's/..\/results\/scopus\///g'|cut -d\: -f1|sed 's/%22_%22/ /g'|sed 's/%20/-/g'|sed 's/%22_[0-9]/ /g'|sed 's/[0-9]//g'|sed 's/scopus%//g'|tr ' ' '\n'|sort|uniq|tr '\n' ' ');
echo $n","$str
done > ../results/scopus_keywords_as_xls.csv;
... |
b84fabbdbb89ac2375c94bc30d322b886abaee8d9eb6afa8b6894a220ce39225 | Shell | 322 | 13 | #!/bin/bash
DATASETS=("ds000030" "ds000228")
DATASET_PATH="/lustre04/scratch/${USER}/openneuro"
mkdir -p ${DATASET_PATH}
for dataset in ${DATASETS[*]}; do
echo "Get ${dataset}"
cd ${DATASET_PATH}
datalad install https://github.com/OpenNeuroDatasets/${dataset}.git
cd ${dataset}
datalad get . -r
don... |
ff5d637b8fc7364f5113054a4b0ad5117a2333e036223343e1ebc76fac246221 | Shell | 322 | 9 | MAIN_ROOT=$PWD/../../..
# check extra kenlm module installation
if [ ! -d $MAIN_ROOT/tools/kenlm/build/bin ] > /dev/null; then
echo "Error: it seems that kenlm is not installed." >&2
echo "Error: please install kenlm as follows." >&2
echo "Error: cd ${MAIN_ROOT}/tools && make kenlm.done" >&2
return 1
f... |
10308cb19b969dd07f87f5acc49c5ffd1b2c2e1fee7c241e597bd850bbdba745 | Shell | 325 | 5 | export PATH=/usr/bin:$PATH
fa=$1
mkdir -p known/repeatmasker;
cd known/repeatmasker;
nohup perl /GACP_2016a/01.repeat_finding/find_repeat/bin/find_repeat.pl --queue st.q -repeatmasker -cpu 70 -cutf 40 -run qsub -resource vf=3G -lib /database/repbase/repeatmaskerlibraries-20170127/Libraries/RepeatMaskerLib.embl.lib ${f... |
4e976753823a71df7bdaecfdb7fd21a777cbfbc2eb34b188a90d2b4742430484 | Shell | 325 | 8 | #! /bin/bash
v=$1
sed -i -e "s/version:.*$/version: $v/g" treeshrink/meta.yaml
conda-build treeshrink/
conda convert --platform all /Users/uym2/anaconda3/conda-bld/osx-64/treeshrink-$v*.tar.bz2 -o /Users/uym2/anaconda3/conda-bld/
anaconda upload -u smirarab --force /Users/uym2/anaconda3/conda-bld/*/treeshrink-$v*.tar... |
240026e147975099bd4070cd2d8ae6dc702e5d15400a017cf768a6d75b4bcf09 | Shell | 326 | 8 | #!/bin/sh
get_id=$(id)
nb_id=${get_id[@]:4:3}
docker_name=$((basename $PWD) | tr '[A-Z]' '[a-z]')-jupyterlab-1
sed -i '' -e s/CONTAINER_NAME/${docker_name}/ $(dirname $0)/docker-compose.yml
sed -i '' -e s/YOUR_ID/${nb_id}/ $(dirname $0)/docker-compose.yml
git update-index --assume-unchanged $(dirname $0)/docker-compos... |
ee3f794a2241e1959181cbed4b74ae4a45da01eba05a1b456aa184f074943e19 | Shell | 328 | 9 | #!/bin/bash
mkdir -p ./RAW;
cd ./RAW;
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93374/suppl/GSE93374_Merged_all_020816_DGE.txt.gz
gunzip GSE93374_Merged_all_020816_DGE.txt.gz
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE93nnn/GSE93374/suppl/GSE93374_cell_metadata.txt.gz
gunzip GSE93374_cell_metadata... |
6e1005467bc824cde845d4c43003de4b9e25d8804ce75e8cca38ea2e87910847 | Shell | 333 | 12 | # This script load the required modules on the cluster
# and sets the necessary environment variables
#modules
module load gcc/8.2.0
module load eigen
module load hdf5/1.10.1
module load python_gpu/3.10.4
# set the stacksize, if not set the benchmark planner will run out of memory and generate a Segfault
export OMP_... |
b8757b3ae0cfc67f27a65a76e9f73ad3c6266866538196e970ab3077d5ba4c31 | Shell | 335 | 20 | #!/bin/bash
source ../settings.sh
PLINK2=${SOFTWARE}/plink2
THREADS=8
MEMORY=$((8192 * ${THREADS}))
BFILE=${OUT}/UKB34886_T1_QCed_230222
for i in {1..22}; do
${PLINK2} --bfile ${BFILE} \
--chr ${i} \
--keep ${OUT}/LD_ref.txt \
--threads ${THREADS} \
--memory ${MEMORY} \
--make-bed \
--out ${OUT}/LD_re... |
efa070f9151361407cf171abf32562586759b01c62308fb0e2d4ad9f7e441b6f | Shell | 335 | 15 | #!/bin/sh
# Exit after any error
set -o errexit
RELEASE_VER=$1
if [ "$RELEASE_VER" == "" ]; then
echo "Usage: setVersion.sh <version>"
exit 1
fi
echo "Changing version numbers to ${RELEASE_VER}"
./mvnw versions:set -DnewVersion=${RELEASE_VER} -DgenerateBackupPoms=false
git commit -a -m "Updated version to $... |
cbafea312f7fee67444979076fa013873acb812b60bed11d23dd4f945f2f8de4 | Shell | 336 | 10 | #!/bin/bash
# get data
wget https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-5061/E-MTAB-5061.processed.1.zip
unzip E-MTAB-5061.processed.1.zip
head -n 1 pancreas_refseq_rpkms_counts_3514sc.txt > labels.txt
sed -i '1s/#samples//' labels.txt
# get metadata
wget https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-5061/E-MTA... |
29e231e4950362c8fcff24d46e58024dd3158a38a63668c2e69fba1812813f7f | Shell | 337 | 17 | #!/bin/bash
# converts a bic .obj file to an stl
#
# Expects that vtk-polydata-to-stl.py is in the path
inputfile=$1
outputfile=$2
if [ -z "$inputfile" -o -z "$outputfile" ]; then
echo "Usage: $0 <input.obj> <output.stl>"
exit 1;
fi
tmpfile=$(mktemp)
bicobj2vtk $inputfile > $tmpfile
vtk-polydata-to-stl.py $tmp... |
178b380e402a0047d042ee5ee88955f77828b075caecb6fb563bab8d32da42b5 | Shell | 344 | 11 | # initialize and activate new conda environment, assumes working installation of miniconda3
conda create -n gpt2_env python=3.6
CONDA_BASE=$(conda info --base)
pip=$CONDA_BASE/envs/gpt2_env/bin/pip
$pip install tensorflow==1.13.1
$pip install fire
$pip install regex
$pip install requests==2.21.0
$pip install tqdm==4.31... |
7b26c38441ca3019cdc4662dea653299b9463dc94e53455043ede9c4564c357c | Shell | 345 | 6 | rm run_unsorted.out run.out
for file in out/*.out; do
echo $file
grep -a -n "^Name of Chain_1:\|^Name of Chain_2:\|TM-score=" $file | sed 's|=|:|g' | awk -F ": " '{print $2}' | awk '{print $1}' | sed 's|../pdbstyle-2.08/||g' | xargs -n 4 | awk '{print $1, $2, $3, $4}' >> run_unsorted.out
done
sort -k1b,1 -nrk3,3 ru... |
8814a42734d69041a72b5bd2ce117b52a9c4fc2af446dc1bf6f485ff976550db | Shell | 345 | 20 | #!/bin/sh
sed -i 's/release/debug/g' libus.pro
sed -i 's/release/debug/g' generic.pri
for each in us*; do
if [ -d $each ]; then
cd $each
echo $each
# This should not be necessary when the .pro files all use generic.pri
for f in *.pro; do
sed -i 's/release/debug/g' $f
done
qmake us*... |
29f515c3d58429f87ec2cd49446cc413ab25de1c80079fa6202e4321a8218811 | Shell | 346 | 53 | my_array=(
ADL
AIN
AQR
AS1
ASE
ASG
ASH
ASI
ASK
AVA
AVD
AVE
AVJ
AWA
AWB
BAG
CEPD
CEPV
DB2
FLP
I1
I2
I6
IL1
IL1V
IL2V
M2
M3
MI
OLQD
RMDD
RMDV
RMD
RIA
RID
RIG
RIV
RMED
RMEV
RME
SMBD
SMDD
URX
URYD
URYV
)
for neuron in "${my_array[@]}"
do
echo "processing $neuron"
python wt_vs_mutants.py --i:$neuron --inclall-occ -... |
61f6a5b273a513a173f57f9d37864f54da1f7c190d2715b2a02b00fdf4fdbfb9 | Shell | 347 | 10 | export param1_vals=(-65.0000 -41.8750 -18.7500 0.000 27.5000 50.6250 73.7500 96.8750 120.0000)
export param2_vals=(-20.0000 -14.7292 -9.4583 -4.1875 1.0833 6.3542 11.690 16.8959 22.1667)
filename=gridness_score.txt
for i in {0..8}
do
sed -i s/a_$i.000000/${param1_vals[$i]}/g $filename
sed -i s/b_$i.000000/${param2... |
f1f5e4de4099a32d028a4bae830cfd4f5aa4be6a5be6e605678dce439f6ee3a8 | Shell | 350 | 11 | #!/bin/bash
mkdir -p AAL
for n in $(cat AAL3v1.nii.txt |cut -d\ -f1); do
outname=$(grep "^$n " AAL3v1.nii.txt |cut -d\ -f2);
echo fslmaths AAL3v1.nii.gz -thr $n -uthr $n AAL/$outname".nii.gz"
fslmaths AAL3v1.nii.gz -thr $n -uthr $n AAL/$outname".nii.gz"
done
# let's make also an empty nii file
fslmaths AAL3v1... |
149a1bd474b76e93242e3745b54e9c619efe6e01e16f21fc5c07f9c0828965c6 | Shell | 356 | 11 | for f in *.EPIC2.bed
do
base=`basename "$f" .EPIC2.bed`
sort -r -g -k 5,5 < $base".EPIC2.bed" > $base"_temp.out"
lncnt=$(wc -l < $base"_temp.out")
percent_linecount_infloat=$(echo "$lncnt*.3" | bc)
float2Int=$(printf %.0f "$percent_linecount_infloat")
head -"$float2Int" $base"_temp.out" > $base"_top03.EPIC2.be... |
83270dd56cb22a3c42491053713da6d3c37b804adadbe7dfc035231c25caad60 | Shell | 364 | 8 | #!/bin/bash
BIM=/cluster/projects/p33/users/elizabept/multimodal/discovery/genos/results/UKB34886_T1_QCed_230222.bim
N_SNP_IN_CHUNK=10000
OUT_PREFIX=/cluster/projects/p33/users/alexeas/elleke/data/snp_chunks/UKB34886_T1_QCed_230222.chunk
split -l ${N_SNP_IN_CHUNK} --numeric-suffixes --suffix-length 3 --additional-suf... |
4e9811560b86d6fbf6129a75e826db9d5a67b3deaa1aea0be82acf1cc3b85a2a | Shell | 365 | 15 | anatomical_area=$1
# Precompute tools location
SCRIPT_DIR=$(dirname ${BASH_SOURCE[0]})
source "${SCRIPT_DIR}/../global-params.sh" ${anatomical_area}
source "${SCRIPT_DIR}/ga-params.sh"
source "${SCRIPT_DIR}/../run-functions.sh" "${SCRIPT_DIR}/run-ga-job.sh" gradscore
echo "Total jobs: $TOTAL_JOBS"
mkdir -p $JOB_LOG... |
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