diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml index 1af9778..e04c000 100644 --- a/.github/workflows/rworkflows.yml +++ b/.github/workflows/rworkflows.yml @@ -28,13 +28,17 @@ jobs: cont: docker.io/tomrrr1/bioconductor_meme:latest rspm: ~ steps: - - name: Create directory and symlink - run: | - mkdir -p /github/home/meme - ln -s /meme/bin /github/home/meme/bin - - name: Verify symbolic link - run: | - ls -l /github/home/meme/bin + # - name: Create directory and symlink + # run: | + # mkdir -p /github/home/meme + # ln -s /meme/bin /github/home/meme/bin + # - name: Verify symbolic link + # run: | + # ls -l /github/home/meme/bin + - name: Set MEME_BIN environment variable + run: echo "MEME_BIN=/meme/bin" >> $GITHUB_ENV + - name: Check MEME_BIN + run: echo $MEME_BIN - uses: neurogenomics/rworkflows@master with: run_bioccheck: ${{ false }} diff --git a/inst/extdata/rep1_peaks.narrowPeak b/inst/extdata/rep1_peaks.narrowPeak new file mode 100644 index 0000000..9e23546 --- /dev/null +++ b/inst/extdata/rep1_peaks.narrowPeak @@ -0,0 +1,71 @@ +chr22 12801618 12801818 rep1_peak_1 13 . 2.77778 4.09489 1.31287 37 +chr22 15747931 15748131 rep1_peak_2 27 . 3.7037 5.79561 2.77596 113 +chr22 16819196 16819413 rep1_peak_3 39 . 5 7.12547 3.97597 116 +chr22 16825330 16825538 rep1_peak_4 48 . 5.64516 8.132 4.88035 38 +chr22 16917462 16917725 rep1_peak_5 32 . 4.86111 6.36494 3.29337 133 +chr22 17037369 17037715 rep1_peak_6 24 . 4.28571 5.39333 2.41384 113 +chr22 17075121 17075339 rep1_peak_7 56 . 5.94059 8.98485 5.65104 66 +chr22 17084584 17084831 rep1_peak_8 73 . 6.02837 10.8743 7.38313 87 +chr22 17085699 17085899 rep1_peak_9 34 . 4.41176 6.54004 3.44888 70 +chr22 17102321 17102521 rep1_peak_10 42 . 4.01786 7.48244 4.29405 148 +chr22 17106724 17107204 rep1_peak_11 59 . 5.12048 9.28589 5.93969 287 +chr22 17155188 17155471 rep1_peak_12 85 . 5.89888 12.1937 8.59371 144 +chr22 17158836 17159082 rep1_peak_13 24 . 3.59116 5.40567 2.42525 53 +chr22 17171315 17172097 rep1_peak_14 176 . 9.00621 21.8331 17.6547 193 +chr22 17219065 17219425 rep1_peak_15 59 . 5.29801 9.25776 5.91358 280 +chr22 17228663 17229175 rep1_peak_16 81 . 6.77966 11.7386 8.16981 157 +chr22 17237003 17237293 rep1_peak_17 43 . 4.34783 7.56068 4.36927 177 +chr22 17242040 17242516 rep1_peak_18 219 . 7.70609 26.3054 21.9488 199 +chr22 17243361 17243712 rep1_peak_19 185 . 7.30769 22.8098 18.5979 175 +chr22 17281615 17281859 rep1_peak_20 64 . 6.62651 9.84835 6.43986 194 +chr22 17303962 17304224 rep1_peak_21 13 . 3.57143 4.18879 1.39266 178 +chr22 17334121 17334349 rep1_peak_22 48 . 5.35714 8.0546 4.80677 108 +chr22 17339115 17339338 rep1_peak_23 49 . 5.28455 8.24431 4.98673 65 +chr22 17359468 17359977 rep1_peak_24 126 . 8.62069 16.5198 12.6179 162 +chr22 17436454 17436873 rep1_peak_25 101 . 8.33333 13.8954 10.1616 235 +chr22 17477423 17477774 rep1_peak_26 55 . 6.17284 8.88004 5.55656 174 +chr22 17496921 17497255 rep1_peak_27 62 . 5.9322 9.62049 6.23222 148 +chr22 17498230 17498609 rep1_peak_28 81 . 6.77966 11.7386 8.16981 188 +chr22 17529042 17529444 rep1_peak_29 51 . 6 8.46401 5.17927 280 +chr22 17571404 17571604 rep1_peak_30 38 . 5.05051 7.03292 3.8914 48 +chr22 17615618 17615818 rep1_peak_31 48 . 5.7971 8.11363 4.86418 111 +chr22 17628780 17629351 rep1_peak_32 321 . 10.241 37.2906 32.1753 210 +chr22 17638429 17639331 rep1_peak_33 133 . 6.17761 17.2993 13.3629 268 +chr22 17647998 17648372 rep1_peak_34 51 . 5.60748 8.453 5.17242 238 +chr22 17673103 17673481 rep1_peak_35 60 . 6.18557 9.37863 6.01847 154 +chr22 17706423 17706712 rep1_peak_36 73 . 7.05882 10.8192 7.32884 151 +chr22 17760043 17760782 rep1_peak_37 151 . 8.68056 19.1207 15.107 573 +chr22 17777098 17777796 rep1_peak_38 82 . 5.52764 11.8523 8.27779 313 +chr22 17797922 17798539 rep1_peak_39 319 . 13.141 37.0429 31.9947 345 +chr22 17830191 17830391 rep1_peak_40 51 . 6 8.46401 5.17927 114 +chr22 17910598 17911579 rep1_peak_41 180 . 8.37696 22.1982 18.002 706 +chr22 17956696 17956933 rep1_peak_42 45 . 5.6338 7.78128 4.55668 115 +chr22 17974787 17975273 rep1_peak_43 87 . 6.91057 12.3546 8.7434 320 +chr22 18001594 18002062 rep1_peak_44 102 . 8.16327 13.996 10.2571 355 +chr22 18057543 18057973 rep1_peak_45 165 . 8.3815 20.6407 16.5389 187 +chr22 18077698 18078062 rep1_peak_46 71 . 6.54206 10.6047 7.13885 125 +chr22 18096688 18097165 rep1_peak_47 107 . 8.25243 14.5549 10.7837 354 +chr22 18103902 18104363 rep1_peak_48 56 . 6.11111 8.98481 5.65104 398 +chr22 18149995 18150334 rep1_peak_49 70 . 6.70103 10.5218 7.06941 185 +chr22 18186137 18186428 rep1_peak_50 43 . 4.62963 7.59266 4.39776 111 +chr22 19085798 19086512 rep1_peak_51 39 . 4.95496 7.13489 3.98348 166 +chr22 19122341 19122755 rep1_peak_52 72 . 6.15385 10.7069 7.22397 175 +chr22 19144424 19145057 rep1_peak_53 344 . 10.3321 40.5928 34.423 327 +chr22 19171243 19171860 rep1_peak_54 130 . 7.48503 16.9357 13.0158 230 +chr22 19179625 19179825 rep1_peak_55 64 . 6.08696 9.87065 6.45982 77 +chr22 19292025 19292515 rep1_peak_56 77 . 6.50407 11.2863 7.76353 251 +chr22 19419091 19419291 rep1_peak_57 49 . 5.45455 8.20957 4.95344 127 +chr22 19432295 19432747 rep1_peak_58 228 . 8.69565 27.1832 22.8059 253 +chr22 19447704 19448042 rep1_peak_59 85 . 6.33333 12.1886 8.59199 150 +chr22 19478826 19479935 rep1_peak_60 155 . 7.38095 19.5995 15.568 792 +chr22 19717932 19718132 rep1_peak_61 44 . 5.17241 7.69209 4.47546 127 +chr22 19780414 19780742 rep1_peak_62 57 . 6.17978 9.09783 5.76045 154 +chr22 19832804 19833004 rep1_peak_63 42 . 5.38462 7.47634 4.28946 60 +chr22 19844411 19844793 rep1_peak_64 92 . 7.47664 12.8752 9.23143 191 +chr22 19854759 19855223 rep1_peak_65 87 . 6.41892 12.3389 8.73115 283 +chr22 19855829 19856037 rep1_peak_66 43 . 4.66667 7.53305 4.34255 111 +chr22 19865190 19865531 rep1_peak_67 31 . 4.79452 6.23736 3.17348 193 +chr22 19886936 19887455 rep1_peak_68 351 . 13.1016 42.4999 35.1988 253 +chr22 19909765 19909965 rep1_peak_69 32 . 4.81928 6.30299 3.23356 154 +chr22 19942588 19942788 rep1_peak_70 37 . 4.65116 6.92693 3.79434 85 +chr22 19947409 19948021 rep1_peak_71 314 . 11.828 36.4578 31.4192 414