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bd86cdc049f1724289ae3a6e9ac86a1a72ac251957e59489885cbe227fabe951
Shell
182
6
#!/bin/sh # # Basic sanity check for tiffps with PostScript Level 1 output # . ${srcdir:-.}/common.sh f_test_stdout "${TIFF2PS} -a -p -1" "${IMG_MINISWHITE_1C_1B}" "o-tiff2ps-PS1.ps"
8d0c57863ba802dcc090755d8d9f11362475003224591e55aaa23769253d65c3
Shell
185
11
# /bin/bash git clone https://github.com/jewellsean/FastLZeroSpikeInference.git cd FastLZeroSpikeInference git checkout a94ed08ae38db022ba47807146a10b0b14483b1d cd python ./make.sh
33503abe528cf459297de2d43f824ea1be94bb33f03404d6eff7fa635ee37278
Shell
188
4
python3 ./tools/train.py --config ./exprs/cifar_qd/config.yaml \ --work-dir ./exprs/cifar_qd\ --gpu-ids 0,1 \ --seed 97
9bddfeafe241f890b58f0e106253436767a2dd56c4f48643de67efde28d6cb9d
Shell
189
8
#!/bin/bash # Activate micromamba environment for reproschema eval "$(micromamba shell hook --shell bash)" micromamba activate reproschema # Run the command passed as arguments exec "$@"
5c2106eda61b2c6a0832c50f9032ceb80aeba3287feb233b2828ab89153a84eb
Shell
193
6
#!/bin/sh # # Basic sanity check for tiffps with PostScript Level 1 encapsulated output # . ${srcdir:-.}/common.sh f_test_stdout "${TIFF2PS} -e -1" "${IMG_MINISWHITE_1C_1B}" "o-tiff2ps-EPS1.ps"
6b52bd68bc1b5740d4a3e16dd8aba8667f403edfdf2cc9aea4bb218a6c841e11
Shell
194
3
#!/bin/bash AllExp=tensorboard dev list | grep https://tensorboard.dev/experiment/ | sed "s|https://tensorboard.dev/experiment/||g" | tr '\n' ',' | sed 's/\///g' tensorboard dev delete $AllExp
4040acaaeab6e83d2b9bee501391e60433210677a14105e0a5cedda6473a8ed8
Shell
195
5
#!/bin/bash python finetuneRegr.py --name delaney --data_path delaney/ python finetuneRegr.py --name freesolv --data_path freesolv/ python finetuneRegr.py --name lipo --data_path lipo/ exec bash
3b56e4c0f8f8b9246e57db119f6416974214e40b984b42629a2e1fdd9bf0636f
Shell
202
6
#!/bin/sh # # Basic sanity check for tiffcp with G3 compression and 1 dimensional encoding. # . ${srcdir:-.}/common.sh f_test_convert "${TIFFCP} -c g3:1d" "${IMG_MINISWHITE_1C_1B}" "o-tiffcp-g3-1d.tiff"
f99687a9874848ef41ae60a8bf7c789091ad25885b33a4cc2ab7506014af5317
Shell
202
6
#!/bin/sh # # Basic sanity check for tiffcp with G3 compression and 2 dimensional encoding. # . ${srcdir:-.}/common.sh f_test_convert "${TIFFCP} -c g3:2d" "${IMG_MINISWHITE_1C_1B}" "o-tiffcp-g3-2d.tiff"
4de0e94584cd7aef4f15e8c5837e01f3c04aaa740fcb72e78138192fcf1bb37c
Shell
206
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$IMG_RGB_3C_8B_BMP" outfile="o-bmp2tiff_rgb.tiff" f_test_convert "$BMP2TIFF" $infile $outfile f_tiffinfo_validate $outfile
8de3cc993ae06976f4c39aa5c02d46d72711d5ff5062f71bfd4c5b5ffdc4cc84
Shell
206
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$IMG_PALETTE_1C_8B_GIF" outfile="o-gif2tiff.tiff" f_test_convert "$GIF2TIFF" $infile $outfile f_tiffinfo_validate $outfile
b50e66fd0870215d6d7298405879b8a5dc420aeee252109620cd2673337eb2b4
Shell
206
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$IMG_RGB_3C_8B_PPM" outfile="o-ppm2tiff_ppm.tiff" f_test_convert "$PPM2TIFF" $infile $outfile f_tiffinfo_validate $outfile
1b4988a324590ec406bddf604464aec1f50949e852341825356c899781ec4218
Shell
213
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$IMG_MINISBLACK_1C_8B_PGM" outfile="o-ppm2tiff_pgm.tiff" f_test_convert "$PPM2TIFF" $infile $outfile f_tiffinfo_validate $outfile
48e25ecbc4bb3faaa75d1567c5124595c1a411bdfb25ed72e49693f101fe3a30
Shell
213
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$IMG_MINISWHITE_1C_1B_PBM" outfile="o-ppm2tiff_pbm.tiff" f_test_convert "$PPM2TIFF" $infile $outfile f_tiffinfo_validate $outfile
af39e99820d2701026db0a10e5cf968878387e968b85e146f81cd41b0cb06f7d
Shell
214
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$IMG_PALETTE_1C_8B_BMP" outfile="o-bmp2tiff_palette.tiff" f_test_convert "$BMP2TIFF" $infile $outfile f_tiffinfo_validate $outfile
a5de408ad68f707fbd1bac392c959453f78f5080eeb05fc0cb342389d6bc9428
Shell
225
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/rgb-3c-8b.tiff" outfile="o-tiff2rgba-rgb-3c-8b.tiff" f_test_convert "$TIFF2RGBA" $infile $outfile f_tiffinfo_validate $outfile
5e3ae4ff99cd08bf307f7a08c842cd1b001feb9fb0e279620cedb15cbd1bd47d
Shell
227
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/rgb-3c-16b.tiff" outfile="o-tiff2rgba-rgb-3c-16b.tiff" f_test_convert "$TIFF2RGBA" $infile $outfile f_tiffinfo_validate $outfile
302c1da4284d7bcaa0bb81f88dfc8f74c63646a7be5b65d0ee056bcb8c0b2324
Shell
232
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/rgb-3c-8b.tiff" outfile="o-tiffcrop-R90-rgb-3c-8b.tiff" f_test_convert "$TIFFCROP -R90" $infile $outfile f_tiffinfo_validate $outfile
097425d8d035de2dbf6ee3267d0b72483ab394d9528db2896b0f484d3ec494d4
Shell
233
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/palette-1c-8b.tiff" outfile="o-tiff2rgba-palette-1c-8b.tiff" f_test_convert "$TIFF2RGBA" $infile $outfile f_tiffinfo_validate $outfile
3eae08099e9b32a97a92f6e46d04b446b827969aa2e5a00f318ebf51180af3b1
Shell
233
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/palette-1c-4b.tiff" outfile="o-tiff2rgba-palette-1c-4b.tiff" f_test_convert "$TIFF2RGBA" $infile $outfile f_tiffinfo_validate $outfile
805ff32451f1f499b8e297c76a2ae0d51c32c7a2df10ea9242f2ba6cf5ab39ac
Shell
233
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/quad-tile.jpg.tiff" outfile="o-tiff2rgba-quad-tile.jpg.tiff" f_test_convert "$TIFF2RGBA" $infile $outfile f_tiffinfo_validate $outfile
822ba22037d2808905e819c73e2ff91079b152ec15ac6054c7d8f3342725bb04
Shell
233
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/palette-1c-1b.tiff" outfile="o-tiff2rgba-palette-1c-1b.tiff" f_test_convert "$TIFF2RGBA" $infile $outfile f_tiffinfo_validate $outfile
a6f7a670b930e9abbbbfb26b65af4ba1bf8cf3a4d1ac6ed6a7f6743307a4a8df
Shell
233
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/logluv-3c-16b.tiff" outfile="o-tiff2rgba-logluv-3c-16b.tiff" f_test_convert "$TIFF2RGBA" $infile $outfile f_tiffinfo_validate $outfile
da76676c23da8b8f7c6091ea65a290e2d50dcc89f351acaf3d0952a55d5f369f
Shell
234
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/rgb-3c-16b.tiff" outfile="o-tiffcrop-R90-rgb-3c-16b.tiff" f_test_convert "$TIFFCROP -R90" $infile $outfile f_tiffinfo_validate $outfile
5f7a85262879b64a25cdb66b7cb9c2b0c4f08431c4d900b048def1bea717635a
Shell
237
12
#!/bin/bash PREFIX="${CONDA_PREFIX}" if [ ! -d "${CONDA_PREFIX}/python.app" ]; then ( export PREFIX # run the post-link script which creates the python.app directory ${PREFIX}/bin/.python.app-post-link.sh ) fi
99c02aa849f5667cdfae226787dddffbfe1634095452412fb9a9b7549a473151
Shell
238
9
#!/bin/bash SRC_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )/../src" &> /dev/null && pwd ) cd $SRC_DIR pip install -e subpackages/centriole pip install -e subpackages/library pip install -e subpackages/core pip install -e frontend
90bd05004e39fc680d813dbc5a871612fe04caca5e893958cd545c1cb1a84f87
Shell
239
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/miniswhite-1c-1b.tiff" outfile="o-tiff2rgba-miniswhite-1c-1b.tiff" f_test_convert "$TIFF2RGBA" $infile $outfile f_tiffinfo_validate $outfile
baaedaeac7824fda7a55b1438fd3eff1b8a92edc92700f87de42aaa465b0b68f
Shell
239
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/minisblack-1c-8b.tiff" outfile="o-tiff2rgba-minisblack-1c-8b.tiff" f_test_convert "$TIFF2RGBA" $infile $outfile f_tiffinfo_validate $outfile
dba4b763d9cfae0417e0660c4d68d50db60df2af4c0df2f2bc69610fd98dd594
Shell
239
7
#!/bin/sh # # Basic sanity check for tiffcp with G3 compression, 1 dimensional # encoding, and zero-filled boundaries. # . ${srcdir:-.}/common.sh f_test_convert "${TIFFCP} -c g3:1d:fill" "${IMG_MINISWHITE_1C_1B}" "o-tiffcp-g3-1d-fill.tiff"
373a1131bc9ba7d35b414308148d0cbe540f68aa8acc0d2f7962b04bbf0317b7
Shell
240
7
#!/bin/sh # # Basic sanity check for tiffcp with G3 compression, 2 dimensional # encoding, and zero-filled boundaries. # . ${srcdir:-.}/common.sh f_test_convert "${TIFFCP} -c g3:2d:fill" "${IMG_MINISWHITE_1C_1B}" "o-tiffcp-g3-2d-fill.tiff"
740b619d537a8196feda4947027dafeab9d36bf7ff0790d29a08171df0963f4a
Shell
240
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/palette-1c-4b.tiff" outfile="o-tiffcrop-R90-palette-1c-4b.tiff" f_test_convert "$TIFFCROP -R90" $infile $outfile f_tiffinfo_validate $outfile
aaeddf278ab304b0c45b2e59cbcea8451ff9621842df69dfbdfc2e8cd48c13d7
Shell
240
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/palette-1c-1b.tiff" outfile="o-tiffcrop-R90-palette-1c-1b.tiff" f_test_convert "$TIFFCROP -R90" $infile $outfile f_tiffinfo_validate $outfile
bc64bedb077282848b4644c4cb6404b16cceeef7d3eb4f6711d20dbfe4f43559
Shell
240
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/logluv-3c-16b.tiff" outfile="o-tiffcrop-R90-logluv-3c-16b.tiff" f_test_convert "$TIFFCROP -R90" $infile $outfile f_tiffinfo_validate $outfile
cec3796b0fa2f7daa60d8f9f1c9d8cde73fa96d9382a86a2159a47b912eb36b6
Shell
240
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/palette-1c-8b.tiff" outfile="o-tiffcrop-R90-palette-1c-8b.tiff" f_test_convert "$TIFFCROP -R90" $infile $outfile f_tiffinfo_validate $outfile
57adc35fc491dd0471a572d66db9756944e42d92d665305e7699a05862946037
Shell
241
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/minisblack-1c-16b.tiff" outfile="o-tiff2rgba-minisblack-1c-16b.tiff" f_test_convert "$TIFF2RGBA" $infile $outfile f_tiffinfo_validate $outfile
caab541df64a6acbced90f0d1fa1dc328bdd69c998633cba7472dae884db2468
Shell
242
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/rgb-3c-8b.tiff" outfile="o-tiffcrop-doubleflip-rgb-3c-8b.tiff" f_test_convert "$TIFFCROP -F both" $infile $outfile f_tiffinfo_validate $outfile
eeeafd36e4ca7da57ae5a62bdf2dc68f5727af264b6e717a9dc0d711a70408ab
Shell
244
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/rgb-3c-16b.tiff" outfile="o-tiffcrop-doubleflip-rgb-3c-16b.tiff" f_test_convert "$TIFFCROP -F both" $infile $outfile f_tiffinfo_validate $outfile
00a583e2ebe131a71bbe3b09d4fb0ba2cd726d6810dd5b337edd51aa48e26fe7
Shell
246
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/miniswhite-1c-1b.tiff" outfile="o-tiffcrop-R90-miniswhite-1c-1b.tiff" f_test_convert "$TIFFCROP -R90" $infile $outfile f_tiffinfo_validate $outfile
5744eed6a23dffeca1253e9508e5dacb25afc4969381fb2c824b609a4f94ce1f
Shell
246
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/minisblack-1c-8b.tiff" outfile="o-tiffcrop-R90-minisblack-1c-8b.tiff" f_test_convert "$TIFFCROP -R90" $infile $outfile f_tiffinfo_validate $outfile
f5af6cecf7766c445e34d2e0e968a42b3ad19235f6620508910aa3050b6bc4d3
Shell
248
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/minisblack-1c-16b.tiff" outfile="o-tiffcrop-R90-minisblack-1c-16b.tiff" f_test_convert "$TIFFCROP -R90" $infile $outfile f_tiffinfo_validate $outfile
1af6be1c00fa220ba930f5941d57b539edb78e4f0b293b41f287fc4461a5a197
Shell
250
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/palette-1c-1b.tiff" outfile="o-tiffcrop-doubleflip-palette-1c-1b.tiff" f_test_convert "$TIFFCROP -F both" $infile $outfile f_tiffinfo_validate $outfile
8328f69eda27279c6b9c1e74d9c6dde7d0751c234a3ed79d993ef79683aa408a
Shell
250
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/logluv-3c-16b.tiff" outfile="o-tiffcrop-doubleflip-logluv-3c-16b.tiff" f_test_convert "$TIFFCROP -F both" $infile $outfile f_tiffinfo_validate $outfile
8d3de146989f92050ca0672af973929367aa732880b7d3c02e29364babd7ecef
Shell
250
10
#!/usr/bin/env bash # Macs are weird and don't generally include /usr/local things in the path UNAME=`uname` if [[ "$UNAME" == 'Darwin' ]]; then export CPATH=/usr/local/include; export LIBRARY_PATH=/usr/local/lib; fi $PYTHON setup.py install
94109e5445865989f6175a506a461b0bc7bf7473f33faf13c539251d9e5412ad
Shell
250
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/palette-1c-4b.tiff" outfile="o-tiffcrop-doubleflip-palette-1c-4b.tiff" f_test_convert "$TIFFCROP -F both" $infile $outfile f_tiffinfo_validate $outfile
b5acff72c8bebe19ce8adabf5be3cf709a5dc8131823c8fa1f0ddff9711afd01
Shell
250
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/palette-1c-8b.tiff" outfile="o-tiffcrop-doubleflip-palette-1c-8b.tiff" f_test_convert "$TIFFCROP -F both" $infile $outfile f_tiffinfo_validate $outfile
d0acfddb2fac94208a626e192349536dda60419673e1bdf0d4bdae2a3bc54974
Shell
251
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/minisblack-2c-8b-alpha.tiff" outfile="o-tiff2rgba-minisblack-2c-8b-alpha.tiff" f_test_convert "$TIFF2RGBA" $infile $outfile f_tiffinfo_validate $outfile
234627071afc259693c5f2d14f7a9ae1ece05d6199a6dc522ffe2fea804bb353
Shell
252
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/rgb-3c-8b.tiff" outfile="o-tiffcrop-extractz14-rgb-3c-8b.tiff" f_test_convert "$TIFFCROP -E left -Z1:4,2:4" $infile $outfile f_tiffinfo_validate $outfile
0b2e5fbb8e7227264611b48446e8dcdead6c4a7d28815ba9259706822a0214cb
Shell
254
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/rgb-3c-16b.tiff" outfile="o-tiffcrop-extractz14-rgb-3c-16b.tiff" f_test_convert "$TIFFCROP -E left -Z1:4,2:4" $infile $outfile f_tiffinfo_validate $outfile
21c3aa3b04014fb26d4ec31b07ee4f412aee16b7d7cbc10f24fa5e8c2100c386
Shell
256
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/minisblack-1c-8b.tiff" outfile="o-tiffcrop-doubleflip-minisblack-1c-8b.tiff" f_test_convert "$TIFFCROP -F both" $infile $outfile f_tiffinfo_validate $outfile
48d4ffdd0ac601b4b75ee9fd701d60f8e456518dbcfa796dd5fdc1ee42e00c72
Shell
256
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/rgb-3c-8b.tiff" outfile="o-tiffcrop-extract-rgb-3c-8b.tiff" f_test_convert "$TIFFCROP -U px -E top -X 60 -Y 60" $infile $outfile f_tiffinfo_validate $outfile
e169a64557e810a88cbe6ec52185e15436ddb469122d5e525b74ba69ede22feb
Shell
256
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/miniswhite-1c-1b.tiff" outfile="o-tiffcrop-doubleflip-miniswhite-1c-1b.tiff" f_test_convert "$TIFFCROP -F both" $infile $outfile f_tiffinfo_validate $outfile
121a6cf4f3422260c166c11901329c48632228913b70385fd95f6e81b5ad1e83
Shell
258
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/minisblack-1c-16b.tiff" outfile="o-tiffcrop-doubleflip-minisblack-1c-16b.tiff" f_test_convert "$TIFFCROP -F both" $infile $outfile f_tiffinfo_validate $outfile
4eb78aab7328f21405b4397089468529e826672c9c323beae306ce5da8e5f682
Shell
258
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/rgb-3c-16b.tiff" outfile="o-tiffcrop-extract-rgb-3c-16b.tiff" f_test_convert "$TIFFCROP -U px -E top -X 60 -Y 60" $infile $outfile f_tiffinfo_validate $outfile
88f8996b423cb54dec43bcb30e4a8d8949854506a3d3bf12593d05736f02b9a1
Shell
258
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/minisblack-2c-8b-alpha.tiff" outfile="o-tiffcrop-R90-minisblack-2c-8b-alpha.tiff" f_test_convert "$TIFFCROP -R90" $infile $outfile f_tiffinfo_validate $outfile
c15372979acb7e5c38e21465e3a3902108db0bed88156ea204842144c450b674
Shell
259
15
cd test git clone https://github.com/lh3/bwa.git cd bwa git checkout tags/0.7.9a make cd .. PATH=`pwd`/bwa:$PATH git clone https://github.com/arq5x/bedtools2.git cd bedtools2 git checkout tags/v2.25.0 make cd .. PATH=`pwd`/bedtools2/bin:$PATH cd .. echo $PATH
92b27e68389d47931725fb630a77f49dd5c0f7c55a438aa8e78b65d080f45c05
Shell
260
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/palette-1c-4b.tiff" outfile="o-tiffcrop-extractz14-palette-1c-4b.tiff" f_test_convert "$TIFFCROP -E left -Z1:4,2:4" $infile $outfile f_tiffinfo_validate $outfile
942e525e85e76c02f58a24e04d52de5b930dc937399b88de511de81600233aab
Shell
260
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/logluv-3c-16b.tiff" outfile="o-tiffcrop-extractz14-logluv-3c-16b.tiff" f_test_convert "$TIFFCROP -E left -Z1:4,2:4" $infile $outfile f_tiffinfo_validate $outfile
b07d34573dd9b3fd5c1a1be1f86b1ca0432e41f04df40e23233c92f69d080077
Shell
260
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/palette-1c-1b.tiff" outfile="o-tiffcrop-extractz14-palette-1c-1b.tiff" f_test_convert "$TIFFCROP -E left -Z1:4,2:4" $infile $outfile f_tiffinfo_validate $outfile
c6d6c75e7a45a37f26119693dc1afd97e88d19a26f82018af65af66d766a0564
Shell
260
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/palette-1c-8b.tiff" outfile="o-tiffcrop-extractz14-palette-1c-8b.tiff" f_test_convert "$TIFFCROP -E left -Z1:4,2:4" $infile $outfile f_tiffinfo_validate $outfile
0d69e65119a28d3e244876a1f39ad4cd85e7fd58249ad80e5e93c18e0cae9efa
Shell
263
11
#!/bin/bash MYPATH=../cellformer/deconvoluted/deconvoluted/bed_diff background=$MYPATH/*all.bed for f in $MYPATH/*0.01.bed do filename=$(basename $f) echo $filename ~/bin/findMotifsGenome.pl $f hg38 $MYPATH/peak_homer/$filename -bg $background done
2c9b2c793bfbf08b7fddd7234b7d99685b86772b7dee2e1c81ea6f65f07b190a
Shell
264
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/palette-1c-8b.tiff" outfile="o-tiffcrop-extract-palette-1c-8b.tiff" f_test_convert "$TIFFCROP -U px -E top -X 60 -Y 60" $infile $outfile f_tiffinfo_validate $outfile
5ea5af6db13b7a3e35fc179606c2881420ad1176c05a09248bce584264801c90
Shell
264
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/palette-1c-4b.tiff" outfile="o-tiffcrop-extract-palette-1c-4b.tiff" f_test_convert "$TIFFCROP -U px -E top -X 60 -Y 60" $infile $outfile f_tiffinfo_validate $outfile
a7c66e161a559e0f9be2799c3feffe73df0c0d6049a264c183ff04baf14efd88
Shell
264
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/palette-1c-1b.tiff" outfile="o-tiffcrop-extract-palette-1c-1b.tiff" f_test_convert "$TIFFCROP -U px -E top -X 60 -Y 60" $infile $outfile f_tiffinfo_validate $outfile
c21894eb52bf744b6a258f00c4d9193ad2a198d688c3085c81a97938976a9dd4
Shell
264
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/logluv-3c-16b.tiff" outfile="o-tiffcrop-extract-logluv-3c-16b.tiff" f_test_convert "$TIFFCROP -U px -E top -X 60 -Y 60" $infile $outfile f_tiffinfo_validate $outfile
44bd5664c8de4d59bc075b147b580f5d1491ad189addba3fdc96d4863f17d8f8
Shell
266
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/miniswhite-1c-1b.tiff" outfile="o-tiffcrop-extractz14-miniswhite-1c-1b.tiff" f_test_convert "$TIFFCROP -E left -Z1:4,2:4" $infile $outfile f_tiffinfo_validate $outfile
4ecb84e1a21d12a84a687a430863d393698283bf8f78b67fcaa831691e101ea7
Shell
266
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/minisblack-1c-8b.tiff" outfile="o-tiffcrop-extractz14-minisblack-1c-8b.tiff" f_test_convert "$TIFFCROP -E left -Z1:4,2:4" $infile $outfile f_tiffinfo_validate $outfile
2909f8d5bef2bc55303103e372a31e0519bf98b2ce2eaa19f8210550b36c36d6
Shell
268
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/minisblack-2c-8b-alpha.tiff" outfile="o-tiffcrop-doubleflip-minisblack-2c-8b-alpha.tiff" f_test_convert "$TIFFCROP -F both" $infile $outfile f_tiffinfo_validate $outfile
66f14ff90b5374f26812cbe89233e7dc986f85b43e0a760c84c0b82470f6dda6
Shell
268
4
#!/bin/bash STAR --runMode genomeGenerate --runThreadN 10 --genomeDir STAR_MM99 --genomeFastaFiles Mus_musculus.GRCm38.dna.primary_assembly.fa --limitGenomeGenerateRAM 50000000000 --genomeSAindexNbases 14 --genomeChrBinNbits 18 --genomeSAsparseD 9
9d35290b0041dbd1e02fca9edde0759435a6214f5260dd42e5fa2b69c51fcb7a
Shell
268
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/minisblack-1c-16b.tiff" outfile="o-tiffcrop-extractz14-minisblack-1c-16b.tiff" f_test_convert "$TIFFCROP -E left -Z1:4,2:4" $infile $outfile f_tiffinfo_validate $outfile
06ff644aef8b68425bbe7e75a200d5cfad460fe4431c9532a65b92e2e6226de1
Shell
270
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/minisblack-1c-8b.tiff" outfile="o-tiffcrop-extract-minisblack-1c-8b.tiff" f_test_convert "$TIFFCROP -U px -E top -X 60 -Y 60" $infile $outfile f_tiffinfo_validate $outfile
34cd7f90d69d1d90642ed188712f79caffab42ae8b684d92dda8cba8b9cb1580
Shell
270
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/miniswhite-1c-1b.tiff" outfile="o-tiffcrop-extract-miniswhite-1c-1b.tiff" f_test_convert "$TIFFCROP -U px -E top -X 60 -Y 60" $infile $outfile f_tiffinfo_validate $outfile
c4a6b1774ce519e1afde9b6e9023cfc1ae61d608c1b1b418db5847c3f1c6399a
Shell
272
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/minisblack-1c-16b.tiff" outfile="o-tiffcrop-extract-minisblack-1c-16b.tiff" f_test_convert "$TIFFCROP -U px -E top -X 60 -Y 60" $infile $outfile f_tiffinfo_validate $outfile
49fc35e391876d8ba4d865072ab5dbb1ec525eaf1bfd5034467ecac0152b4339
Shell
278
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/minisblack-2c-8b-alpha.tiff" outfile="o-tiffcrop-extractz14-minisblack-2c-8b-alpha.tiff" f_test_convert "$TIFFCROP -E left -Z1:4,2:4" $infile $outfile f_tiffinfo_validate $outfile
f354f67cbcd87eb04cabeb799be023775f7ebabe1315a48b40fd7107d223a7ca
Shell
279
10
#!/bin/sh # # Basic sanity check for thumbnail # . ${srcdir:-.}/common.sh outfile1=o-tiffcp-thumbnail-in.tif outfile2=o-tiffcp-thumbnail-out.tif f_test_convert "${TIFFCP} -c g3:1d" "${IMG_MINISWHITE_1C_1B}" "${outfile1}" f_test_convert "${THUMBNAIL}" "${outfile1}" "${outfile2}"
b25ea5f293e09e729e18c8ac447b137ee94740b355a9ac9ae384b1cc337a6c5b
Shell
282
7
#!/bin/sh # Generated file, master is Makefile.am . ${srcdir:-.}/common.sh infile="$srcdir/images/minisblack-2c-8b-alpha.tiff" outfile="o-tiffcrop-extract-minisblack-2c-8b-alpha.tiff" f_test_convert "$TIFFCROP -U px -E top -X 60 -Y 60" $infile $outfile f_tiffinfo_validate $outfile
07435d74fd03ad4d99fb1e764f3311c10fb6e71918143a5863f21e1546996dcf
Shell
288
7
#!/bin/sh # # Basic sanity check for tiffcp with logluv compression # . ${srcdir:-.}/common.sh f_test_convert "${TIFFCP} -c none" "${srcdir}/images/logluv-3c-16b.tiff" "o-tiffcp-logluv-raw.tiff" f_test_convert "${TIFFCP} -c sgilog" "o-tiffcp-logluv-raw.tiff" "o-tiffcp-logluv-sgilog.tiff"
a77be1c7f35fd8718014921efeb5cf1c72789e748fff254965ee06ae0bd8cb83
Shell
296
27
temp_dir=${1} nifti_path=${2} cw_dir=$(pwd) cat << print_args DATALAD IS GETTING ${nifti_path} FROM ${temp_dir} print_args cd ${temp_dir} datalad clone git@jugit.fz-juelich.de:inm7/datasets/datasets_repo.git inm7_ds cd inm7_ds datalad get -s inm7-storage ${nifti_path} cd ${cw_dir}
c84de04933c1833cd5db1e58fbaefb7b8fb67813125c7e2b5da76de9deb61873
Shell
306
10
# install Anaconda if [[ "$OSTYPE" == "darwin"* ]] then curl https://repo.anaconda.com/archive/Anaconda3-2020.11-MacOSX-x86_64.sh -o anaconda3_setup.sh else wget https://repo.anaconda.com/archive/Anaconda3-2020.07-Linux-x86_64.sh -O anaconda3_setup.sh fi bash anaconda3_setup.sh rm anaconda3_setup.sh
8e64616e91accfe4c9909aa2d905b2704f97fbaf050337d541b4f14e41c3b0fe
Shell
323
12
# if no Anaconda, install pip #if mac if [[ "$OSTYPE" == "darwin"* ]] then # pip should be already installed, let's check pip3 -V ## curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py ## python get-pip.py else sudo apt install python3-pip sudo update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 1 ...
cf368e5d190c0d9ddd0088de694458efc6c9b7a42d0693deb27e62ea1491fee0
Shell
323
8
#!/usr/bin/env bash # This script gets run on TravisCI to deploy new releases. It gets triggered # on tagged versions only, so make sure to tag when releasing! set -ex VERSION=`python -c "print(''.join('$PYTHON_VERSION'.split('.')))"` invoke build anaconda -t $ANACONDA_TOKEN upload build/**/$PKG_NAME*-py$VERSION*.tar....
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Shell
332
7
#!/bin/bash # script to run trainScript=/home/OBIWAN/ANALYSIS/fsl_scripts/preproc/fsl_ANTS/03-FIX/trainClassifier.sh # submit to cluster (LOO test takes a long time) qsub -o /home/OBIWAN/ClusterOutput -j oe -l walltime=500:00:00,pmem=8GB -M lavinia.wuensch@unige.ch -m e -l nodes=1 -q queue1 -N training_classifier ${t...
5dec7ba40f691f67040178eb175feb3b4b5198388193e3e6c772cb732e16ad8f
Shell
338
7
#!/bin/bash for i in 0 1 2 16 17 18 28 30 31 33 34 37 40 45 48 49 64 75 79 88 90 91 92 93 94 96 107 113 117 118 121 124 133 136 143 144 146 148 150 152 153 156 167 185 189 190 192 194 204 210 211 214 220 223 224 226 227 237 241 249 259 262 264 280 282 294 297 306 310 312 317 332 345 347 351 354 360 do sbatch train_s...
40e1811a39dd2fe763d137a3df251043c41916a1fd9a20323defa59cf4fc58ab
Shell
339
6
#!/bin/bash python finetuneRegr_k_fold.py --name lipo --study_name lipo --data_path lipo --random 1 --drp 0.0 python finetuneRegr_k_fold.py --name freesolv --study_name freesolv --data_path freesolv --random 1 --drp 0.0 python finetuneRegr_k_fold.py --name delaney --study_name delaney --data_path delaney --random 1 --...
07e58e6a11dc5742ded82f89f76f6a4389b9246aa1a599ee6047a430ef0703e0
Shell
341
9
# Run bwa to generate index bwa index ~/GRCh37/Homo_sapiens_assembly19.fasta # Run paired end mapping to generate SAM files bwa mem ~/GRCh37/Homo_sapiens_assembly19.fasta emx1.r1.fastq.gz emx1.r2.fastq.gz > ../output/emx1.sam bwa mem ~/GRCh37/Homo_sapiens_assembly19.fasta control.r1.fastq.gz control.r2.fastq.gz > .....
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Shell
343
12
#!/bin/bash fold=$1 tfold=$fold if [[ $fold == "1" ]] then echo "WARNING: fold 1 is set to empty string!" fold="" fi tid="Pre5Ch$fold" python training.py -s GISLES2018 -n GFCNC -b 7 -c DCSsigmoid -t True -N 15 --id $tid -lr 1E-6 -X True -g 200 -f $tfold --postnorm False -D models/isles2018 >> "models/isles2018/g...
bf17a72684697b8a3287fcb142d6cf117dbbaf10c310daa673d0db64ad76ed1b
Shell
350
22
#!/bin/sh sort -n | awk ' BEGIN { c = 0; sum = 0; } $1 ~ /^[0-9]*(\.[0-9]*)?$/ { a[c++] = $1; sum += $1; } END { ave = sum / c; if( (c % 2) == 1 ) { median = a[ int(c/2) ]; } else { median = ( a[c/2] + a[c/2-1] ) / 2; } OFS="\t"; print c"\t"sum"\t"ave"\t"med...
061b5ff0b70968d6fdee28e9c5f55b87efdcd451b59bd0ec8c51c10df9ec2735
Shell
353
8
#!/usr/bin/env bash mkdir -p /workspace/gfcn/data ln -s /workspace/container_0/ISLES2018 /workspace/gfcn/data/gisles2018 python training.py -s GISLES2018 -n $NET -b $BATCH -c DCSsigmoid -N 10 --id $TID -lr $LR -g $EPOCHS --mod TMAX CBF CBV MTT --postnorm False -D $OUTPUT>> "${OUTPUT}/gfcnb_${TID}.log" cp -r $OUTPUT...
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Shell
354
6
#!/bin/sh newv=`python -c 'v={}; exec("".join(open("servalcat/__init__.py").readlines()[:10]), v); v=v["__version__"].split("."); print(".".join(v[:-1])+".{}".format(int(v[-1])+1))'` date=`date "+%Y-%m-%d"` sed -i "s/__version__ =.*/__version__ = '$newv'/; s/__date__.*/__date__ = '$date'/" servalcat/__init__.py git add...
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Shell
354
14
#!/bin/bash # extracts subcortical ts for input files subid=${1} input_dtseries=${2} templates_dir=${3} outputdir=${4} ## extract the left thalamus mkdir ${outputdir}/${subid} seed_files=`ls ${templates_dir}/*.nii.gz` parallel -j 4 "ciftify_meants --outputcsv ${outputdir}/${subid}/${subid}_s0_{/.}_meants.csv ${inpu...
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Shell
362
20
#!/bin/bash # YOUR CODE eval "$(conda shell.bash hook)" conda activate Implicit_NODE # Vitual enviornment echo "Running pendulum example " sh ./job_Pendulum_SecondOrder.sh echo "Running Linear Irregular" sh ./job_Linear_Irregular.sh echo "Running Cubic2D" sh ./job_Cubic2D.sh echo "Running quantitative analysis...
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Shell
368
11
#!/bin/bash python finetuneRegr_k_fold.py --name lipo --study_name lipo --data_path lipo --drp 0.0 python finetuneRegr_k_fold.py --name lipo --study_name lipo --data_path lipo --drp 0.05 python finetuneRegr_k_fold.py --name lipo --study_name lipo --data_path lipo --drp 0.1 python finetuneRegr_k_fold.py --name lip...
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Shell
384
8
#!/bin/bash python mlp_snn.py -s freesolv_mlp_snn_top1.yml -st 1 -f freesolv python mlp_snn.py -s lipo_mlp_snn_top1.yml -st 1 -f lipo python mlp_snn.py -s esol_mlp_snn_top1.yml -st 1 -f delaney python mlp_snn.py -s freesolv_mlp_snn_all.yml -st 0 -f freesolv python mlp_snn.py -s lipo_mlp_snn_all.yml -st 0 -f lipo python...
68859ce2c749bf7c466196fe35aef76372687992e7101abec6834ca8a774e445
Shell
384
10
#!/bin/bash mkdir -p ./ext/PITA cd ./ext/PITA wget --no-check-certificate "https://genie.weizmann.ac.il/pubs/mir07/64bit_exe_pita_prediction.tar.gz" tar xvfz *_pita_prediction.tar.gz make install # make script compatible with newer perl versions sed -i -E "s/(=~\s\S+)\{HOME\}(.\S+)/\1\\\{HOME\\\}\2/" ./lib/libfile.pl ...
73df270039c264b2fdb9118162c7f38c63b51dec9294812c15537078ef4bdd28
Shell
402
13
#!/bin/sh # # Basic sanity check for tiffcp + tiffsplit # # First we use tiffcp to join our test files into a multi-frame TIFF # and then we use tiffsplit to split them out again. # . ${srcdir:-.}/common.sh conjoined=o-tiffcp-split-conjoined.tif splitfile=o-tiffcp-split-split- f_test_convert "${TIFFCP}" "${IMG_UNCOMPR...
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Shell
405
9
#!/bin/bash python finetuneRegr_k_fold.py --name delaney --study_name delaney --data_path delaney/ --drp 0.0 python finetuneRegr_k_fold.py --name delaney --study_name delaney --data_path delaney/ --drp 0.05 python finetuneRegr_k_fold.py --name delaney --study_name delaney --data_path delaney/ --drp 0.1 python finet...
536fd86fd08fe0b0aeeb795590413854bcbc383363c00f4de6a051f74f91320d
Shell
406
22
# train CNN model #python -u train.py\ # --lr 1e-3\ # --batch_size 128\ # --cuda 1 # finetune PTM #python -u finetune.py\ # --lr 5e-5\ # --save_config roberta\ # --batch_size 16\ # --model_config hfl/chinese-roberta-wwm-ext\ # --class_num 2\ # --cuda 1 # distill CNN model python -u distill.py \ --lr 1e...
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Shell
418
11
#!/bin/bash python finetuneRegr_k_fold.py --name freesolv --study_name freesolv --data_path freesolv --drp 0.0 python finetuneRegr_k_fold.py --name freesolv --study_name freesolv --data_path freesolv --drp 0.05 python finetuneRegr_k_fold.py --name freesolv --study_name freesolv --data_path freesolv/ --drp 0.1 pyt...
31ddd06549c0233dc0cec29b1606d493072a5acc1a1a18c6e98331d71f3acabc
Shell
432
15
# Getting colin27 #if operating system is mac cd ../subjects || { echo "Failure - No mmvt_blend folder"; exit 1; } if [[ "$OSTYPE" == "darwin"* ]] then curl -L https://www.dropbox.com/s/1g1445ae5z7a6gv/fsaverage_subjects.zip?dl=1 -o fsaverage_subjects.zip else wget https://www.dropbox.com/s/1g1445ae5z7a6gv/fsaver...
21fea63e07ea2f1dbf7980abbb7b6d81b36cf3900193f48c1a9d77cfb2858341
Shell
446
11
#!/bin/bash python mlp.py -s freesolv_top1.yml -st 1 -f freesolv python mlp.py -s lipo_top1.yml -st 1 -f lipo python mlp.py -s esol_top1.yml -st 1 -f delaney python mlp.py -s freesolv_all.yml -st 0 -f freesolv python mlp.py -s lipo_all.yml -st 0 -f lipo python mlp.py -s esol_all.yml -st 0 -f delaney python mlp_fp.py -s...
b134ecbe2935f36d8a5dd7bb6f4b10be51b3af7112dc688aaa69330257fec95a
Shell
451
21
#!/bin/bash ./cmp_training.sh 5ch 3 ./upool_training.sh 5ch 4 ./depth_training.sh 5ch 4 cp -r ./experiment3_depth/GFCNC-dsGISLES2018-idPre5Ch4 ./experiment5_cmp/GFCNC-dsGISLES2018-idPre5Ch4 ./cmp_training.sh 5ch 4 ./depth_pos_training.sh 5ch 2 ./depth_pos_training.sh 5ch 3 ./depth_pos_training.sh 5ch 4 ./gfcne_t...