sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
1b69506b362dce73155851001d700a5e3139661360208bf3b51c3bd8c124c212 | Shell | 77 | 1 | mpirun -np 64 lmp_mpi -partition 8x8 -in in.scp -log log.lammps -screen none
|
47918e7e55194b83d0810f97154706aaecc8ea35802d483db2cdc0c5b8caeb2a | Shell | 77 | 3 | #!/bin/sh
autoreconf --install
automake --add-missing --copy >/dev/null 2>&1
|
a1bad4d0b27b550fedb7cf6aef3b6dfa6adb1a436cb6b7d451a62ae25ae62276 | Shell | 77 | 1 | python pretrain.py --exp_name 'pre-train' --exp_id 1 --step pretrain --gpu 5
|
a3067dc3cf0de2178c0c1006d0fe0c2c8531a7f13d09991937a730ae1cd2a961 | Shell | 78 | 5 | for eachfile in *.bam
do
echo $eachfile
samtools index -@ 20 $eachfile
done
|
f97568563dcb1ebac63157712d38e865074af055fbc3c94c87be5d66f34319af | Shell | 79 | 7 | #!/usr/bin/env bash
pushd statsmodels.github.io
echo "Pushing"
git push
popd
|
f3dc644ac6038f8c5a5d527150924285e906c4c8339e68d582b341921642e4de | Shell | 80 | 3 | #!/bin/sh
tensorboard --logdir=$LOG_DIR --bind_all --path_prefix=$INGRESS_PATH
|
79da2b3325136c43d546ec11fc957b275baac48a3393c336d4a9d75bca7f8783 | Shell | 81 | 6 | #!/usr/bin/env bash
snakemake -p \
--configfile $1 \
--use-conda \
--cores 2
|
ac2f27077a94ceeef15a6807088fad3de33268aabfd5108f88bca485dbe0b2a1 | Shell | 84 | 2 | #!/bin/bash
microk8s.ctr images ls | awk {'print $1'} | xargs microk8s.ctr images rm |
2d3b40248bbd3b35f97e7945d1266c50cf1424539838086f4fd73dee1fb6bff8 | Shell | 85 | 8 | #!/bin/sh
cd 3rdparty/libvncserver && \
rm -rf \
*examples \
utils \
webclients
|
1fef210b5d13f3a8ca83947105345b117373c2fd2c2b42dfda12be43c03147ad | Shell | 86 | 1 | "${SCHRODINGER}/ligprep" -inp ligprep_p38.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR |
74a5a91a7b61cdd142d5505bd3cdf39dcd093e9a350270dd96a5523e1db9577a | Shell | 86 | 1 | "${SCHRODINGER}/ligprep" -inp ligprep_syk.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR |
897ef287785f0e4dc99fc1ed445b5fe63c3d49be98734362340e90f8d2e1480c | Shell | 86 | 5 | #!/bin/bash
make clean
sphinx-apidoc --force --separate -o apidoc ../xopto
make html
|
90bd41bbe799d09e21292af102b47e9c24cbcc221973d5d43ed9b6d8538493f3 | Shell | 86 | 1 | "${SCHRODINGER}/glide" glide-grid_P38-3FLY.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR |
e20747d28012b96f15a19a2ecf425fcb57cd09d1dd08da506cd502da3b308b3e | Shell | 86 | 1 | "${SCHRODINGER}/ligprep" -inp ligprep_eg5.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR |
e20bb5c3026fddb68e4e7b4c21fcf6d8fdb22256472cd15ed4d0e0c148e37cce | Shell | 86 | 1 | "${SCHRODINGER}/glide" glide-grid_EG5-3L9H.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR |
e75cbb566f23731dd2501df6592024f6fc7539d5aaff28635f6936ff8081341b | Shell | 86 | 1 | "${SCHRODINGER}/glide" glide-grid_SYK-4PV0.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR |
209b5d06ce8880f4c99e73d5c4fe71cadd1fb3bda480bec63b3699da6ce19b36 | Shell | 87 | 1 | "${SCHRODINGER}/ligprep" -inp ligprep_cmet.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR |
3e2b8168d6fa980243b865a1d284301dc3de2bf478421248213ff23427a02e38 | Shell | 87 | 1 | "${SCHRODINGER}/ligprep" -inp ligprep_cdk2.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR |
625d7f46507e344fe31731343e96df0e5072627c0446fdc24f28ddfd61870953 | Shell | 87 | 1 | "${SCHRODINGER}/ligprep" -inp ligprep_tyk2.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR |
6412a6c8b904909c6a8d2428485fbaa084ecf9ee7b6e73a2d7357b4fdc549df7 | Shell | 87 | 1 | "${SCHRODINGER}/glide" glide-grid_MCL1-4HW3.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR |
6492a34c251090204f12c623bbfc214c34202a3425c58d9e693a543a1ace2b57 | Shell | 87 | 1 | "${SCHRODINGER}/glide" glide-grid_CDK2-1H1Q.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR |
67d637d1c697e3372f1c31a6ce2d88a0d799853d8f0a41182c4436b9a18a5126 | Shell | 87 | 1 | "${SCHRODINGER}/ligprep" -inp ligprep_pde2.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR |
7a1b6c3e4486146ae63145caeae211db26f8018bb2d73c8999df2aded1d2e452 | Shell | 87 | 1 | "${SCHRODINGER}/glide" glide-grid_TYK2-4GIH.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR |
8b3476cce4c75086549cb2a6aaabc792288899f53c704061ecd5adf81eb61972 | Shell | 87 | 1 | "${SCHRODINGER}/glide" glide-grid_SHP2-5EHR.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR |
945c6329f8c1bdb4397f62afeef0e87e80e2b2cff788bc219533941dce56c044 | Shell | 87 | 1 | "${SCHRODINGER}/ligprep" -inp ligprep_shp2.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR |
a070a6459b2db2c90b7082110d0a757cb85693a29c011dea66c6161fdcdea7a0 | Shell | 87 | 1 | "${SCHRODINGER}/ligprep" -inp ligprep_mcl1.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR |
bbf885193d7630d2e4883d4669ff879de76c9e2c3655a20141d2a2c805e65431 | Shell | 87 | 1 | "${SCHRODINGER}/glide" glide-grid_cMET-4R1Y.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR |
dbf3ed2a1b6e8aabcea1ffc621e17bfb8d6af0c3cf489858bb0533f22b8d0700 | Shell | 87 | 1 | "${SCHRODINGER}/glide" glide-grid_CDK8-5HNB.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR |
dcc7844652db851eacb4b8e19059f440c7ceae25dfe2996fe5919193b75d603f | Shell | 87 | 1 | "${SCHRODINGER}/ligprep" -inp ligprep_jnk1.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR |
ee39452040b7badbc7c607aded7b782e68c9d9d1dbd3c6654ddaa5fd61a94f23 | Shell | 87 | 1 | "${SCHRODINGER}/ligprep" -inp ligprep_cdk8.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR |
f3122cbfa503a9cf5d8751d5e483d9370116dcf13bbaa4e0c594b900291f04a2 | Shell | 87 | 1 | "${SCHRODINGER}/glide" glide-grid_PDE2-4D08.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR |
158e5d2959722e531e3bad34853500771a5b61950c89b0a0542f193fa16690dc | Shell | 88 | 1 | "${SCHRODINGER}/ligprep" -inp ligprep_ptp1b.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR |
326feda3268f513648c31f61373f213ca111d82c8d0e781af040e3595206f8ad | Shell | 88 | 1 | "${SCHRODINGER}/ligprep" -inp ligprep_tnks2.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR |
538422e3e8747228f10934a93a5b3d2155dc9b2cd7b166fd1111cbe23782377f | Shell | 88 | 1 | "${SCHRODINGER}/ligprep" -inp ligprep_hif2a.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR |
5dd5f9945d245521e4a23fbf4669e6470ebbc40cb5dbab122183d697d08b58bd | Shell | 88 | 1 | "${SCHRODINGER}/glide" glide-grid_TNKS2-4UI5.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR |
63c40fe09165838624a5f14faa3f74714f07b9685aa6ef50d896c7d555e2732b | Shell | 88 | 1 | "${SCHRODINGER}/glide" glide-grid_PTP1B-2QBS.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR |
743316c406c870414a23019df53f55e0e4942b339ad394fcec6b8b15ee47809a | Shell | 88 | 1 | "${SCHRODINGER}/glide" glide-grid_HIF2a-5TBM.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR |
1be515a94be95da748e7482a2931950f07fd6c448d3a9379e52d1b63586b14fe | Shell | 89 | 1 | "${SCHRODINGER}/ligprep" -inp ligprep_pfkfb3.inp -HOST localhost:1 -NJOBS 1 -TMPLAUNCHDIR |
aa3cd06c36ba641020636c65127fa660e9a00e221537d559beba3fc7b0707114 | Shell | 89 | 1 | "${SCHRODINGER}/glide" glide-grid_PFKFB3-6HVI.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR |
9ce841db7a545485fdd67324a7f74797a435caf887a1f33e76cf0888ae9dc271 | Shell | 90 | 5 | #!/bin/bash -ef
which mne
mne sys_info -pd
python -c "import numpy; numpy.show_config()"
|
95719b087dde1787f6ca58c4dfdb24f9bd8a5925d96ba284e26d87dfdb5c2b29 | Shell | 91 | 1 | "${SCHRODINGER}/glide" glide-grid_galectin-5E89.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR |
b25cdc5248110770079d6c9dfbd62fc692d8b1322fedcf8de3c4dbe14bb6c968 | Shell | 91 | 1 | "${SCHRODINGER}/glide" glide-grid_thrombin-2ZFF.in -OVERWRITE -HOST localhost -TMPLAUNCHDIR |
6d1c1097d5418a7edba1257536d0641b7ee8d80662b0dc3aac5e134144fe5c39 | Shell | 94 | 1 | "${SCHRODINGER}/glide" glide-dock_SP_P38.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR |
9c3b3533d9e82402209c46824c07026d89678258b3f63ea0df96624af531e7ba | Shell | 94 | 1 | "${SCHRODINGER}/glide" glide-dock_SP_SYK.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR |
a987aea57611324d5124e9dcf475950669163bef8867c33c1a2097ed496d4a56 | Shell | 94 | 1 | "${SCHRODINGER}/glide" glide-dock_SP_EG5.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR |
3e2d28293daa20b2e10b6a04e0d453ce1ae6dc5dfd7d30e9fcdf92b7c965cf90 | Shell | 95 | 1 | "${SCHRODINGER}/glide" glide-dock_SP_CDK8.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR |
4318be180a4a04b0e3d1e3bbdf0cf9c41d8299f3a35f3983a86e7df389109597 | Shell | 95 | 8 | #!/bin/bash
for eachfile in *.bam
do
echo $eachfile
samtools index -@ 20 \
$eachfile
done
|
590cc4e959fd9d4080270cce9c260a597a66f2ad3ee18487b30ab6b96a2381fd | Shell | 95 | 1 | "${SCHRODINGER}/glide" glide-dock_SP_TYK2.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR |
9e77e9390682ee9bd18e525c5da82fbfdb7f122dce5c21d0208467c20af7e9e9 | Shell | 95 | 1 | "${SCHRODINGER}/glide" glide-dock_SP_PDE2.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR |
ce65c24b9c9f37f92e297a9ad4e151cf6887f609ba4463e01d1cd5888085a5c0 | Shell | 95 | 1 | "${SCHRODINGER}/glide" glide-dock_SP_CDK2.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR |
ddb271b8989f690d021dcf082cb530a2bd19c54fa018ecbd2677975f94611ff7 | Shell | 95 | 1 | "${SCHRODINGER}/glide" glide-dock_SP_MCL1.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR |
dfa7ade7ac7298d5456e411f026b19df3351a0735f99a568f522f54c4105bc8a | Shell | 95 | 1 | "${SCHRODINGER}/glide" glide-dock_SP_SHP2.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR |
ece8e33908d82dce6f42220412614e7f3d58a810e15466fddbe849e9d1355dc9 | Shell | 95 | 1 | "${SCHRODINGER}/glide" glide-dock_SP_cMET.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR |
05d2158be7402f26c6677560f046a631561df519b8ca0a1ea65b9931343e5f71 | Shell | 96 | 1 | "${SCHRODINGER}/glide" glide-dock_SP_PTP1B.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR |
bdba80a3f4e88502bf6c33a33a3f20119d64756ff205535fb2b9ba96e954cfca | Shell | 96 | 1 | "${SCHRODINGER}/glide" glide-dock_SP_HIF2a.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR |
d96497b0aecb166fa74368d23305fd62d9ccf417e8bc013df86e39fd1ba97a78 | Shell | 96 | 1 | "${SCHRODINGER}/glide" glide-dock_SP_TNKS2.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR |
c0a30668b83038ebaecad87ccb1c60f679e885373a3113045171bc89d340e185 | Shell | 97 | 1 | "${SCHRODINGER}/glide" glide-dock_SP_PFKFB3.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR |
f4e2ce2e1703ccce275a35223e746c78fc4938482d9976d26b751ef814ddcc4e | Shell | 97 | 1 | git clone https://github.com/GiantElephant123/solid_simulation_data.git deepsolid_simulation_data |
b5e5ddd359ea9197a14c29cb75d33713a2c5af68df923e2804eb73e0928cd696 | Shell | 98 | 5 | #!/bin/bash
mkdir build && cd build
cmake .. -DCMAKE_INSTALL_PREFIX:PATH=..
make && make install
|
0d9a63a2df1c8abed764d6a71853fd1bd16bcdb55f0a63e29a39464edd29af5d | Shell | 99 | 2 | #### Follow this instruction to install our MLNI package on github
https://anbai106.github.io/mlni/ |
73f6d42653285a9f90b7c00a5a7e26c23304eaffd9175fad7c92eee4fb334a9d | Shell | 99 | 1 | "${SCHRODINGER}/glide" glide-dock_SP_thrombin.in -OVERWRITE -adjust -HOST localhost:4 -TMPLAUNCHDIR |
9cebacf80d19e343e6d7d944336c95e065578a50107a8408b63157590c1ad8c4 | Shell | 100 | 5 | #!/bin/bash
set -eu -o pipefail
./init-security.sh &
./opensearch-docker-entrypoint.sh opensearch
|
f43f19fffe07413eeb942714b3b4ea6bb9939ca1768d65b428a6eeaf2b0a895f | Shell | 100 | 2 | set -ex
python test.py --dataroot ./datasets/colorization --name color_pix2pix --model colorization
|
17dadd0cc6cc3082ad5358becbdf4e5e71c8964e7bd46ae3ad97a829df1f48d5 | Shell | 101 | 4 | #!/bin/bash
set -euo pipefail
kind delete cluster --name claude-agent
rm -rf "$(dirname "$0")/certs"
|
37bd34df499ebee211f1b38f93a31029f7671358be369750e961a28cf2b26fdb | Shell | 101 | 4 | #!/bin/bash
sudo veyon-cli authkeys delete tpp/public
sudo veyon-cli config clear
sudo dpkg -r veyon
|
58f2a4f4ca1d93d5dbe33b1f2cf4a3ac2b93e6e965aae49a107716f290e6deeb | Shell | 102 | 1 | "${SCHRODINGER}/ligprep" -inp ligprep_thrombin_recurated.inp -HOST localhost:10 -NJOBS 1 -TMPLAUNCHDIR |
60e95d582757ff55a2ec398247c9d735fb8441ffb5c869dc44a91bee550d17f6 | Shell | 102 | 6 | #!/bin/bash
source scripts/vars.sh
source lib/conda/etc/profile.d/conda.sh
conda activate $ENV_NAME
|
d5220af2d7908fba7bc8bce86e706e93cc036a1f28882f111ebe46b5ac7b5808 | Shell | 104 | 6 | #/bin/bash
for i in {1..4}; do
echo "running run $i"
python test_petric.py --outdir output_$i
done
|
3e95d920ffe21713caefd4c6745e4d3381dbd30f1a6b936090c10f05989b7407 | Shell | 106 | 4 | #!/bin/bash
# Build script for conda package
$PYTHON -m pip install . -vv --no-deps --no-build-isolation
|
86bac9de8cc2064ae20185fd28ecfe7eec6c12581f472874362f4ca3b5bb7646 | Shell | 106 | 3 | #!/bin/zsh
python -W ignore '/home/lthpc/zhongzh/RFD4Hist/Stain_Normalization/process_all.py' --worker 20 |
584fd6b90bc7fe04bdfa12cf6232af552ea7a942ac2469f81f229ee28b81125d | Shell | 107 | 3 | #!/bin/bash
awk -F", " '{if ($2 == "False") print $1}' "../data/remodel_checks.csv" > straggers_list.txt
|
874a50528288edce1a57b69ecc52085de2a15bc76eb71e809b1577dd815f0b90 | Shell | 107 | 2 | #!/bin/bash
exec uvicorn app.main:app --host 0.0.0.0 --port 5000 --workers 1 --root-path $APPLICATION_ROOT
|
c8b43f711431c7398391437e921a9b20465f397cd2ab260aec549ce8ab7d331a | Shell | 108 | 3 | #!/bin/sh
SCRIPT_NAME=$APPLICATION_ROOT exec gunicorn -b :5000 --access-logfile - --error-logfile - run:app |
2347d441d47781974be234f2a426bc8ecf092bb6feeefd34f5f1bdd562b2b462 | Shell | 112 | 8 | #!/bin/bash
# Siwei 26 Mar 2019
for eachfile in *.bed
do
echo $eachfile
md5sum $eachfile >> BED_md5.txt
done
|
65baaa75004c7b1e631b5088c88fbcf93ec0282616c3f1973b74600963264ccc | Shell | 113 | 1 | perl split_domain.v1.pl ../1.Loop_by_HiCCUPS/virus.onlyPart.resolution25.format.matrix 2000 > out1.domains.bedpe
|
46088e9b56c6a01ad99422aa45d51732f0e339f2f9049fd788d4d1bf223b696b | Shell | 115 | 1 | python -u run_regnn.py --dataset DBLP --model regcn --save_postfix DBLP-regcn --dropout 0.5 --repeat 10 --device $1 |
d8186d2d1f3b6baf3307a7905c4006568f40035074bec9ba18033bdd086164c7 | Shell | 115 | 2 | set -ex
python test.py --dataroot ./datasets/maps --name maps_cyclegan --model cycle_gan --phase test --no_dropout
|
45f493cbadf6c0b01aa8dda81ee8cea65e97cac32d388ccfc23cf337d6b82ba7 | Shell | 116 | 12 | #!/bin/bash
for eachfile in R21*.bam
do
echo $eachfile
samtools view \
-H \
$eachfile \
| grep "RG"
done
|
68addbb4434e30cd9321afad42fa5b6e83610d51fface279eca5c8c0b94cdc2b | Shell | 116 | 8 | #!/bin/bash
if [[ $# -eq 0 ]]; then
exec /bin/bash --login
else
cmd="$@"
/bin/bash --login -i -c "${cmd}"
fi
|
ce949ea491b67ad23bf9223f9bfe8aa241809da73818cea5bdfc0fab83d6fffb | Shell | 116 | 1 | python -u run_regnn.py --dataset IMDB --model regcn --save_postfix IMDB-regcn --feats_type 1 --repeat 10 --device $1 |
886e72cd6a0cead618f98687eb02f03bffe703e23c96ce26af1b70eb792d11dc | Shell | 117 | 6 | #!/usr/bin/env bash
set -e
/veyon/.ci/common/linux-build.sh /veyon /build
/veyon/.ci/common/finalize-rpm.sh "fc30"
|
b76c43f24e932a3c96eae0e749435b9aa5c8fac55ed6077f6fc2e9f0bedcc89c | Shell | 117 | 8 | #!/usr/bin/env bash
set -e
cd /veyon
flawfinder -Q -c core plugins master server service configurator cli worker
|
cad8b7eff85c1df3625aec2bab016f4543acf2600147fa6ef603330a85fd4d00 | Shell | 117 | 1 | python -u run_regnn.py --dataset DBLP --model regat --save_postfix DBLP-regat --num_heads 8 --repeat 10 --device $1
|
85a713f6d47dc6a61967001b46a775cfb836b9e295d59abac19b02b3fcd60774 | Shell | 118 | 3 | set -ex
python train.py --dataroot ./datasets/colorization --name color_pix2pix --model colorization --use_wandb
```
|
c804d40d43da4aae7c93fce4a098d452dfc2e09f71376814a953afb9c6f69500 | Shell | 119 | 5 | #!/bin/bash
set -e
echo "running functional tests:"
bash test/func/plotcritic_test.sh
echo "finished functional tests"
|
f6c27a9721c953d4a2d9d78cd82d12472d9c77b620c26fe3f0c3eb3671b9327f | Shell | 120 | 11 | #!/bin/bash
for i in $(seq 56)
do
rm -r $i
mkdir $i
cd $i
cp ../{2qmt.pdb,submit.sh} .
sbatch submit.sh $i
cd ../
done
|
1d5c12f5cd4f59fa2ab1e1506ea9a22f73341b080e303c59b1ddb0e36367a1bd | Shell | 121 | 9 | #!/bin/bash
cd v2015
for x in */
do
cd $x
babel -isdf ${x%/}_ligand.sdf -opdb ${x%/}_ligand.pdb
cd ../
done
cd ../
|
e94f2618717e73aa06f5d72361ecd4a1f293b0aa4b059c8c301ffde0971f38ec | Shell | 124 | 11 | #!/bin/bash
for i in $(seq 26 290)
do
rm -r $i
mkdir $i
cd $i
cp ../{wt.pdb,submit2.sh} .
sbatch submit2.sh $i
cd ../
done
|
d2809785b416e84e614f61679092e931e13d440e7209d5dfeafef554cb52ce1d | Shell | 125 | 6 | # conda activate <environment>
read name genomefa rest <<< "$@"
mkdir -p bwa_index
bwa index -p bwa_index/$name $genomefa
|
104e0316de156b1b7990936c21090f1192b2bc24db0022389fa80084b8f9e9cd | Shell | 126 | 6 | #!/usr/bin/env bash
set -e
/veyon/.ci/common/linux-build.sh /veyon /build
/veyon/.ci/common/finalize-rpm.sh "opensuse-15.1"
|
2bdcab63cc6b367be2450a0de7c2e312bef9904d4396f0cbbe10b150a54d7946 | Shell | 126 | 6 | #!/usr/bin/env bash
set -e
/veyon/.ci/common/linux-build.sh /veyon /build
/veyon/.ci/common/finalize-deb.sh "debian-buster"
|
4fba7fa988279631c0c799ebf3971a09c099ac7ce2c3a1c003bd1a1ac39b5c79 | Shell | 126 | 6 | #!/bin/bash
VERSION=latest
docker pull fredericklab/capcalc:${VERSION}
docker run -it fredericklab/capcalc:${VERSION} xyzzy
|
51ac7ecb8a1c9ade4cea67a3269415c00e69f2351551eb1720b3dbe60545d8ea | Shell | 126 | 6 | #!/usr/bin/env bash
set -e
/veyon/.ci/common/linux-build.sh /veyon /build
/veyon/.ci/common/finalize-deb.sh "ubuntu-bionic"
|
dfc5373b6c796f373cd4a40a651915f7c4bc9c3141392c4402e762c5b38ac3d5 | Shell | 126 | 6 | #!/usr/bin/env bash
set -e
/veyon/.ci/common/linux-build.sh /veyon /build
/veyon/.ci/common/finalize-deb.sh "ubuntu-xenial"
|
3823bee294331fafe398b8f0190ccf6e5a095795c3e76754d9c4e3d604e02054 | Shell | 127 | 3 | for i in {1..6}; do
wget https://cqsweb.app.vumc.org/download1/annotateGenome/TIGER/smallrna_data/S${i}_R1_001.fastq.gz
done
|
763d0df872a817bee2dfc2337b6d435df9ecf9d9e2a5308cd2388c8dba6d4b04 | Shell | 127 | 7 | #!/bin/bash
source_folder="03.LanesMerged"
fastq_list=$(ls ${source_folder}/*/*R1*)
echo $fastq_list
fastqc -t 30 $fastq_list |
9b1c48aecae36239907fe30d860ed6eff819b26d571df21d8b8a70730ea20535 | Shell | 127 | 13 | #!/bin/bash
cd group_level
for ii in *Tmean.nii.gz
do
fslmerge -t ${ii%%.nii.gz}_as_ts.nii.gz $ii $ii
done
cd ..
|
55367087f3ca840ba6941f5429545e7f03df2894bf0c3ce77d3779fae6fccf64 | Shell | 128 | 2 | #!/bin/bash
samtools quickcheck -v *.bam > bad_bams.fofn && echo 'all ok' || echo 'some files failed check, see bad_bams.fofn' |
8a62355820f18c07cab1a5b5892ef5fe01b3167bf40e0b071df2d058a0615f77 | Shell | 129 | 4 | #!/bin/bash
r0=$(realpath $0)
PATH=$(dirname $r0)/.venv/bin/:$(dirname $r0)/venv/bin/:$PATH
python3 $(dirname $r0)/deepwmh.py $@
|
43e72577f771bb48e9eb8135be18723dd20b59a844ed78657c37d4a457cc7a42 | Shell | 132 | 2 | mamba install -y cupy array-api-compat
pip install git+https://github.com/TomographicImaging/Hackathon-000-Stochastic-QualityMetrics |
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