sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
01a3db307a7676228889c15bbd8b7f6805e88c370fa706165e248db116a8f5d2 | Shell | 45 | 3 | #!/bin/sh
Rscript ../utils/3-ppcor.R "wang"
|
0acf59b6ad0bbc86001e90e69c10d97471d08063d96fdc5ea2d76efb0797b5a4 | Shell | 45 | 3 | #!/bin/sh
Rscript ../utils/3-wgcna.R "wang"
|
1c4cf7eccf8bb56782c0072a277d7c811c3e76b0acce6b683d9dd45c05ac5581 | Shell | 45 | 3 | #!/bin/sh
Rscript ../utils/3-wgcna.R "pbmc"
|
4e12d9d9e748380d1f3f60f345c9e9ffd2a701aa613b004d4fe87ec13e6204dd | Shell | 45 | 3 | #!/bin/sh
Rscript ../utils/1-celda.R "pbmc"
|
51d84538f6dc493a89dcfeef11d70f63bf4307cd69af5ccd1d73d5b7310ad458 | Shell | 45 | 3 | #!/bin/sh
Rscript ../utils/1-celda.R "wang"
|
8c0a0a335b3f067e869ef30eaec3af56f933ae6aa35afe04e3137c5297c4bb43 | Shell | 45 | 3 | #!/bin/sh
Rscript ../utils/3-ppcor.R "pbmc"
|
23cf2a4b27605a3d7a80442d18b386cf4d06e7aabe4b537a30aa69e5596f28de | Shell | 46 | 3 | #!/bin/bash
$SHARC/laser.x < KEYSTROKES.laser |
4f8b0316ddbf0df48d0c504389233f724dac1c35eb1d17fd109dda4d19f7fcab | Shell | 46 | 1 | git clone https://github.com/almaan/her2st.git |
53550a1baf2c6653d3993c889860609b2017ad0e69de9b821d39f77a2340d959 | Shell | 46 | 3 | #!/bin/bash
$SHARC/geo.py < Geo.inp > Geo.out |
55b21b4d5ad1facb2d78d55ff5a30ff3d855434562460f598add12b5a03e04e0 | Shell | 46 | 3 | #!/bin/sh
Rscript ../utils/1-hclust.R "pbmc"
|
c6b681d1a932a001f15f8e71bcd7cdbffe780c671d0bcc40e6eab848eda4a771 | Shell | 46 | 3 | #!/bin/sh
Rscript ../utils/1-kmeans.R "pbmc"
|
c7fba96cc9e50dae271b763601a303318228f132024110ee9749b83c0a67be5b | Shell | 46 | 3 | #!/bin/sh
Rscript ../utils/1-kmeans.R "wang"
|
ff039b3e7595635ef4851600c225611562997f8aaa7c5b12666f7fddbdbe8a42 | Shell | 46 | 3 | #!/bin/sh
Rscript ../utils/1-hclust.R "wang"
|
064774ab02eb1a551f5e9c7fabca0e7bc005ddaf747ce0349a5d605cf297ba2c | Shell | 47 | 3 | #!/bin/sh
Rscript ../utils/3-hdwgcna.R "wang"
|
5af62b9a9f9c9eeaf6e9b0d8dbc7bd67f1a7a5d66083f6a67766afd7c0827524 | Shell | 47 | 3 | #!/bin/bash
$SHARC/data_extractor.x output.dat |
9d4cb91dfa3b847db1030de9be6bbd153065dc3f4427e4c21b2f1dcd2a700cd1 | Shell | 47 | 3 | #!/bin/sh
Rscript ../utils/3-hdwgcna.R "pbmc"
|
b0602df5b843274290e7091c3644a8dee33160e735ad15954caf1541d293e350 | Shell | 47 | 5 | #!/bin/bash
set -Eeuxo pipefail
rm -rf build
|
024cf0588a724ed81b81c092feedb72ddcc03e7bc7e13dc3e369b6d6c489dfbb | Shell | 48 | 1 | docker build -t mne_bpy:latest -f Dockerfile .
|
1302f8946d51a49ad40e37f65b9742756cd73adf63b1ce48ba7cbdd07c4ea39f | Shell | 48 | 3 | #!/bin/bash
$SHARC/diagonalizer.x < input > out |
a74aada38011abf7df5ae792b15c2d464d57d3cf1ca6977339b34bb6f2362a3e | Shell | 50 | 3 | #!/bin/sh
Rscript ../utils/1-scregclust.R "pbmc"
|
f2e9b0e99705f7108e5d87f0ffe2733b6cc8af6286b2b06b70add96477be0ce7 | Shell | 50 | 3 | #!/bin/sh
Rscript ../utils/1-scregclust.R "wang"
|
53dd943ea5ae8850838f02f56015d328aadb39d7a87bb8aaf3e0d1f8a308d37f | Shell | 51 | 4 | #!/bin/bash
echo -e "# Running ./ex_XML"
./ex_XML
|
a931ac041f138db5d7117ca2297dc5f35d7aee03cbcf178f20ad493f5ebeb479 | Shell | 51 | 3 | cd utils
python3 build.py build_ext --inplace
cd .. |
02ddda49027e823c43b33f25b770357588160fb464f36328506a11f1ee1518e0 | Shell | 53 | 6 | #!/bin/bash
echo -e "Running ./ex_Pca3"
./ex_Pca3
|
6ca8efded8475239c2edd951689f1f3ddeec1d55a11d3980462d46b656b13475 | Shell | 53 | 3 | #!/bin/bash
$SHARC/make_fit.py < KEYSTROKES.make_fit |
41b0429aa525775e2f51adb02a1caec8114249f2a1149f0dc2b4cb2c480a2ad5 | Shell | 55 | 4 | #!/bin/bash
echo -e "# Running ./ex_LBFGS"
./ex_LBFGS
|
dde270a03de54049851aacaa5d1b60f484361b87ad1e2f5f5e215cdc919b9909 | Shell | 55 | 3 | #!/bin/bash
$SHARC/bootstrap.py < KEYSTROKES.bootstrap |
41c4ed42d1f4c1e64a69d8d4d84118a6a98e649bd2df4369f5d0d9196c7bdbff | Shell | 56 | 3 | #!/bin/sh
Rscript ../utils/2-cluster-stability.R "pbmc" |
d2bb3339b54fe277ff33615cf45df58f9cf427c2c5223d0905f4faa005dde184 | Shell | 56 | 3 | #!/bin/sh
Rscript ../utils/2-cluster-stability.R "wang" |
02ca21f0c3e2dd772ea32c8e4dc383505e4fd837cb190671ddf7bc1f1cf67a77 | Shell | 57 | 1 | $OVDIR/../bin/wfoverlap_ascii.x -f ciovl.in > ciovl.out
|
2725a3084da710d04be5016f9507143c35826bd5a2e3c8a7b9203f45204f5d10 | Shell | 57 | 3 | #!/bin/bash
$SHARC/make_gnuscript.py 4 0 3 0 1 > traj.gp |
51f9e5d5b163bdf58f9ae4467e8c7aec808a4404041d7512cbd89c6d5c4402f9 | Shell | 58 | 2 | #!/usr/bin/env sh
python3 -m codex.data.local_data_loader
|
8e736c0236dd3d5c65bb0027f3400d1da7c712bdfcf2ce0fa07dd709e794a2cd | Shell | 58 | 3 | #!/bin/sh
poetry run python ../utils/4-spearman.py "wang" |
bc987bd63fcf275ba33ef92d4d9293c80d742a6956c2bdaa7b1bf723c23634b8 | Shell | 58 | 3 | #!/bin/sh
poetry run python ../utils/4-spearman.py "pbmc" |
204653ca41e6f73983527a3875286e7982340e4a2ebc70fbdfbd87e7491dcf65 | Shell | 59 | 4 | #!/bin/bash
echo -e "#Running ./ex_uniquify"
./ex_uniquify |
930fbaffed30c86609bbfea3108aa76a7ecc8d1a021727f919ee93695b0685cd | Shell | 59 | 3 | #!/bin/sh
poetry run python ../utils/4-grnboost2.py "pbmc" |
ada31baca1181b0e708e2d5e42b1f36425e7f4c18369e5dc4606e8afa2cd1789 | Shell | 59 | 3 | #!/bin/bash
$SHARC/trajana_nma.py < KEYSTROKES.trajana_nma |
d1cbc93c7c2232f641ffffaa98eaeda9dd07be60ef039565ea0e9b76c6ed4f18 | Shell | 59 | 3 | #!/bin/sh
poetry run python ../utils/4-grnboost2.py "wang" |
f3c7ec252f5b4a3edc2b80b4e6b67ff6ff82f2828c7e14bdf6dd534a8dbe15f2 | Shell | 59 | 4 | #!/bin/bash
echo -e "# Running ./ex_Ising2D"
./ex_Ising2D |
31d2298cf5f1daa396fbb1c195140e80258a0df235a300b18ffbcc1506d3a249 | Shell | 61 | 4 | #!/bin/bash
echo -e "#Running: ./ex_JsonNode"
./ex_JsonNode
|
54e57cb1191fabeda0e073dca56e7f63f235b27a85b7f88bb27736e02c2af50a | Shell | 61 | 5 | #!/bin/bash
set -Eeuxo pipefail
python -m http.server 8080
|
6ef8d81e816f7c6d2014d966bc2e1bae48ec2a21da3d19d4774efd70bf39c441 | Shell | 61 | 4 | #!/bin/bash
echo -e "# Running ./ex_Molecule"
./ex_Molecule
|
ebdfba43c19ac0e81a8325b98437850a9346e477a5b63cf4eb1ec5405eb72b9d | Shell | 61 | 4 | #!/bin/bash
echo -e "# Running ./ex_TreeNode"
./ex_TreeNode
|
65745c51bb6052b9c68ce94822d7140e267ea5e3a0185709cca0adb47d591b5d | Shell | 63 | 4 | #!/bin/bash
echo -e "# Running ./ex_UnionFind"
./ex_UnionFind
|
0ab43ce02a91655b58ad76784947038cca57f90554c333e10053052f4e07ade0 | Shell | 64 | 2 | #!/usr/bin/env sh
python3 tests/run_unit_tests_with_coverage.py
|
6374162ab1ea58ff926a8b69185597ca220994553df14e08d530c26ee5f82e26 | Shell | 64 | 4 | #!/bin/bash
echo -e "#Running ./ex_ThreadPool"
./ex_ThreadPool
|
8afea81c391db215b8f1277af30e40b22651a450421b4a79ef56080758c23890 | Shell | 64 | 2 | #!/usr/bin/env sh
python3 -m black . && python3 -m ruff --fix .
|
d620856a813b3c2714c5125206b8201774246f23eab9dcd37d899a25b7d27aff | Shell | 64 | 5 | FD_th=0.3
DV_th=50
discard_seg=5
discard_run=50
motion_filter=0
|
e8f86bd42aa9d499d0d326a4a227e1e34f6a0da74d8141a6d5ea331c6ffb8ebc | Shell | 64 | 5 | #!/bin/bash
echo -e "# Running ./ex_test_gzip"
./ex_test_gzip
|
069527794e044e9b1697d6e57ffef64e4ba258d037d6a53b886df7daf6042549 | Shell | 65 | 2 | #!/usr/bin/env sh
export FLASK_DEBUG=1 && ./scripts/run_local.sh
|
3bc188400f6ae0bbd5f9ba24b741e2a2563b65d8128ac959232224511b17dd3a | Shell | 65 | 3 | #!/bin/bash
$SHARC/sharctraj_to_initconds.py -S 2 -2 Singlet_1/
|
8225049c2e6c45d7fa7f0f6052bd74bf79fcfa6bb029d140de155ca6a1ad30a9 | Shell | 65 | 4 | #!/bin/bash
echo -e "# Running ./ex_ThreeDTree"
./ex_ThreeDTree
|
a63addfa7cea9b16915f2e2a7911ff45c40dc3af3e0b583c7e86c0d058e5b2b2 | Shell | 65 | 6 | FD_th=0.3
DV_th=50
discard_seg=5
discard_run=50
motion_filter=0
|
a91df30aba4323373627a47e5a556bb4d83054b355a80025662d75a3b7f8c4c9 | Shell | 65 | 3 | #!/bin/bash
$SHARC/make_fitscript.py < KEYSTROKES.make_fitscript |
c072c71ce3ce2aa7135e7ea006b11a36315acc781aac9699fe88cfad55f68526 | Shell | 65 | 3 | #!/bin/bash
$SHARC/data_collector.py < KEYSTROKES.data_collector |
ceebdaf909ffab5e56a473e6634be766cbebb84cc2f8823cbad0eb47ea24473b | Shell | 65 | 7 | #!/bin/bash
echo -e "#Running ./ex_IterateIJ"
./ex_IterateIJ
|
e184f47c38ed8befb162c335d0f83231b7e9e2cfb3d16dd7c12efb21f2c00a24 | Shell | 65 | 3 | #!/bin/bash
$SHARC/trajana_essdyn.py < KEYSTROKES.trajana_essdyn |
fc740b5f75b5f5f1e31ab33588cbc7b669be63d00789ec6fd0cb88f895fbdd0e | Shell | 65 | 2 | #!/bin/bash
conda env create --prefix ./4conda -f environment.yml |
72c1b050bfc4a3e26a09f75b98fbfcfa733f4ac14d1034c4e25fbbfcd5089fa7 | Shell | 66 | 3 | #!/bin/sh
poetry run python ../utils/4-grnboost2-counts.py "wang" |
85f257e06b415414d33db617cb4a33c864ebb16c63309d64c7742f2a69479b3c | Shell | 66 | 3 | #!/bin/sh
poetry run python ../utils/4-grnboost2-counts.py "pbmc" |
dbb808cc69de3710484a1e4cddd372db7784748660d4098c158f039266e268c7 | Shell | 66 | 4 | #!/bin/bash
echo "# Running ./ex_Combinations"
./ex_Combinations
|
a90be8dc7c8b165e4d8a58505bf15b77870e2067dce1fdda2cc1b15ebbd62aa6 | Shell | 67 | 5 | #!/bin/bash
tag=${1}
docker push ${DOCKER_USERNAME}/fuzzy:${tag}
|
b9c8264adf69768e6d4725a29e3f50890bf5372fc216ec24f23c863ab1df8aa9 | Shell | 67 | 3 | #!/bin/bash
$SHARC/spectrum.py initconds.excited --gnuplot plot.gp |
7647fa20304cd7f53be825877b0f3a332e51e4f5b0de898bde5b7a4e919be36b | Shell | 68 | 3 | #!/bin/bash
aws batch submit-job --cli-input-json file://jobs.json
|
d6057ea0bcd9ccb4e1b6f4f30a70e26e95e0f1e5dc5dd0d1bab73431c18d5b4a | Shell | 68 | 3 | #!/bin/bash
conda activate ./4conda
python ./src/cal_denoise_app.py
|
319f26be1f9152697027c1a0124c83e16279fab7330b746b29d8f52462318166 | Shell | 69 | 4 | #! /usr/bin/env bash
echo "set RUN_ON_FLASK"
export RUN_ON_FLASK=""
|
35c54e08538ca726bed995265a739d9af4ac15246b8bddffa3e602f32cd34b50 | Shell | 69 | 4 | #!/bin/bash
echo -e "Running ./ex_AtomicElement"
./ex_AtomicElement
|
39aa0026d51c6203d3ee4d9686957899d76b5266e7582458f31f12578d337dd6 | Shell | 69 | 2 | #!/bin/bash
conda env create --prefix ./4conda -f environment-cpu.yml |
855602b0af501bc70dddbd54d4077778c41fbc7646e43c7a919a16cc5eb970ac | Shell | 69 | 7 | #!/bin/bash
conda activate stereopy-doc
rm -rf ./build/*
make html |
ed766a50d2fbd90c466cc664e8375a0762e51ff36a3cb83049a70f1c92a1e19b | Shell | 69 | 4 | #!/bin/bash
echo -e "Running ./ex_basic_algebra"
./ex_basic_algebra
|
9390f3cf2091c082121bf1e500f8234c07aa364790eec87b96d4bda99d11bab5 | Shell | 70 | 4 | cd QM
$SHARC/SHARC_ORCA.py QM.in >> QM.log 2>> QM.err
err=$?
exit $err |
b9157a62625ab5a9f284887f3103e7c5daa00bc5355567df433157fbb1d444fb | Shell | 70 | 5 | cd QM
$SHARC/SHARC_LVC.py QM.in >> QM.log 2>> QM.err
err=$?
exit $err |
69a657cef89294ddc2ed7e4389f0c4af1277a88493f2e7f4b37f93bcc6ac58bd | Shell | 71 | 3 | #!/bin/bash
docker build --tag cellmincer:0.1.0 -f docker/Dockerfile . |
9e15e8844324846b448b9d5f5962b5b95d12753e9ce9d3a7baa51c606368a22a | Shell | 71 | 5 | cd QM
$SHARC/SHARC_ORCA.py QM.in >> QM.log 2>> QM.err
err=$?
exit $err |
d21a7072446322ae1fd935c952a498a31406976dadf90086226c4030b593bfae | Shell | 71 | 4 | cd QM
$SHARC/SHARC_RICC2.py QM.in >> QM.log 2>> QM.err
err=$?
exit $err |
304beb12c2532a51e6f9645ebf26165e388675c1300aa6930911180de7212784 | Shell | 72 | 5 | cd QM
$SHARC/SHARC_PYSCF.py QM.in >> QM.log 2>> QM.err
err=$?
exit $err |
4be99cb05439fa2964ccf8bbb3d04bead8c9b41ccf3506c16477618a5fd7e7bc | Shell | 72 | 4 | #!/bin/bash
echo -e "# Running ./ex_Molecule_Vec3"
./ex_Molecule_Vec3
|
ba1b2a9fc6a93b1538ad728d68e83551ffddcfa55112f061a1606ce3993f8eb5 | Shell | 73 | 5 | cd QM
$SHARC/SHARC_MOLCAS.py QM.in >> QM.log 2>> QM.err
err=$?
exit $err |
c60edfc491c648336dabf2e0d20275c4ba461802954d2825a7324a23612a69b8 | Shell | 73 | 4 | #!/bin/bash
echo -e "# Running ./ex_BinaryTreeNode"
./ex_BinaryTreeNode
|
29c7a2a6dfeb8e8466c9bcff824282214ae6ccf4c4d170abdb5fe7e0fb896918 | Shell | 74 | 3 | #!/bin/bash
$SHARC/transition.py < KEYSTROKES.transition > transition.out |
7b4a157166d5e0b01b31e0fa70d017b64d0ee5f9c7fc73e24851f4f265f449b9 | Shell | 74 | 4 | #!/bin/bash
echo -e "Running: ./ex_shared_pointers"
./ex_shared_pointers
|
295d81390f45bd1fbc4942a2b063f4783bb22a91a9e767290453c2496e3ba7ff | Shell | 75 | 5 | cd QM
$SHARC/SHARC_COLUMBUS.py QM.in >> QM.log 2>> QM.err
err=$?
exit $err |
6b5a1474e096c04bb35c441e01748a8d5735efccc33161e3050d030e4ccd4c21 | Shell | 75 | 5 | cd QM
$SHARC/SHARC_GAUSSIAN.py QM.in >> QM.log 2>> QM.err
err=$?
exit $err |
55ff7ea65e9f65c5cc7948c8684ff526efefb1ebc156e1159b3f19f1c4b7afbd | Shell | 76 | 5 | #!/bin/bash
echo -e "Running ./ex_intersect_sorted"
./ex_intersect_sorted
|
9381f53f9f3302b41c89ea37e258179ccbc96a8c8719120ed19ae9b6bce61c7a | Shell | 76 | 4 | cd QM
$SHARC/SHARC_Analytical.py QM.in >> QM.log 2>> QM.err
err=$?
exit $err |
9f37eb613f32dd558fff818a94f30dea78e15ccd5ad53b2cc749195ced27d979 | Shell | 76 | 4 | #!/bin/bash
. $SHARC/sharcvars.sh
$SHARC/data_extractor_NetCDF.x output.dat |
d0656e10bf9b0ae4c5d3e8e968b09cc29493e7da5445781408a8ea8022b76085 | Shell | 76 | 5 | #!/bin/bash
for i in $(seq $4)
do
orfm -m $3 $1 > "$2/orfm_p_only"
done
|
65a00b6453f8168464f77e5bcf27184fe4705239a565404b2d64a3e30971fb2a | Shell | 77 | 4 | #!/bin/bash
echo -e "# Running ./ex_Array2DSymmetric"
./ex_Array2DSymmetric
|
6c24a4e58bfcb42cc49e50cc2ca5a9dcea4e30109a28e10c875156c91083919d | Shell | 77 | 5 | cd QM
$SHARC/SHARC_Analytical.py QM.in >> QM.log 2>> QM.err
err=$?
exit $err |
9335afce399126844d03519c30092488da032302aa1cb1f904605318b7390171 | Shell | 77 | 4 | #!/bin/bash
echo -e "# Running ./ex_consecutive_find"
./ex_consecutive_find
|
cb182b5196c59584c4dec6038179a84a1bf8af25dc2bd5e89c6e1fce2bbf828a | Shell | 77 | 3 | #!/bin/bash
$SHARC/diagnostics.py < KEYSTROKES.diagnostics > diagnostics.out |
67322d5d0c5992f622ef12deefed8e84465d0f4bf0888fe3c105158769ad8a29 | Shell | 78 | 1 | export HIVE_HOME=/usr/hdp/$(ls -1 /usr/hdp | grep -v current)/${HIVE_PACKAGE}
|
b94d38f8bb6a2ae35dd0d4561006b8cc5337f0290c8a7276ea4fbbdd3b02dac2 | Shell | 79 | 4 | #!/bin/bash
echo -e "Running ./ex_NormalDistribution"
./ex_NormalDistribution
|
c2994f381fddc63e6288ba7cd47ba7737b51f30bd17201116ffc69f5f223526f | Shell | 79 | 5 | #!/bin/bash
echo -e "#Running ./ex_PairwiseAlignment"
./ex_PairwiseAlignment
|
c9c626dbfafc05180aad0f881882b91eca72eb03782681c81f72838e836f60f1 | Shell | 79 | 4 | #!/bin/bash
echo -e "# Running ./ex_greedy_clustering"
./ex_greedy_clustering
|
cd9a4aa9bcd5dec3b1754c9f9c04a33c3ac67bb819c0d0728191e3a196954768 | Shell | 79 | 6 | cd QM
$SHARC/SHARC_ADF.py QM.in >> QM.log 2>> QM.err
err=$?
rm *.xml
exit $err |
da8fbefb227f74a9ca71cd2d5032abd36dc22a10c97e6b8796330874dbf4421e | Shell | 80 | 4 | #!/bin/bash
echo -e "Running ./ex_SimulatedAnnealing"
./ex_SimulatedAnnealing
|
06b83aa87602dc856e1b72acfa0aeef17f9c4a69ea9fa04f6b6406cb33bed930 | Shell | 81 | 2 | #!/usr/bin/env sh
optuna-dashboard sqlite:///example.db --artifact-dir ./artifact |
66d32fae22b62f1714e7b8041d1c04274e02d2d7392c1d5d5aaad3f0c3c7921d | Shell | 81 | 6 | cd QM
$SHARC/SHARC_BAGEL.py QM.in >> QM.log 2>> QM.err
err=$?
rm *.xml
exit $err |
b27d51f01212ca6b9b9113f5f1052cc7db2fc6687878b2a862e350a11589927c | Shell | 82 | 6 | cd QM
$SHARC/SHARC_MOLPRO.py QM.in >> QM.log 2>> QM.err
err=$?
rm *.xml
exit $err |
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