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annotate seqrequester/src/utility/scripts/build_initial_repo.sh @ 1:1085e094cf5f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
author fubar
date Sat, 13 Jul 2024 12:39:06 +0000
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1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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1 #!/bin/sh
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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2
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3 # You do not want to run this. It was used to create the initial repo by
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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4 # extracting the relevant bits from Canu and renaming things.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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5
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6 if [ `pwd` != "/scratch/git/canu-test" ] ; then
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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7 echo Wrong directory.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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8 exit
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9 fi
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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11 echo DELETE
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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12 rm -rf .git *
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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14 echo SYNC
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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15 rsync -a ../canu-orig/ .
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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17 echo REWRITE
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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18 ../git-filter-repo/git-filter-repo --replace-refs delete-no-add \
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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19 --path kmer/libutil \
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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20 --path kmer/libkmer \
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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21 --path kmer/libbio \
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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22 --path src/AS_UTL \
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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23 --path src/AS_global.C \
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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24 --path src/AS_global.H \
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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25 --path src/AS_global.c \
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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26 --path src/AS_global.h \
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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27 --path src/utility \
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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28 --path src/canu_version_update.pl \
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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29 --path src/Makefile \
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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30 --path src/main.mk \
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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31 --path 'README.license.GPL' \
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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32 --path 'README.licenses' \
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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33 --path 'README.md'
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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34
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35 ../git-filter-repo/git-filter-repo \
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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36 --path src/AS_UTL/Makefile \
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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37 --path src/AS_UTL/main.mk --invert-paths
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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38
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39 ../git-filter-repo/git-filter-repo \
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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40 --path-rename src/canu_version_update.pl:scripts/version_update.pl
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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41
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42 ../git-filter-repo/git-filter-repo \
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43 --path-rename src/AS_UTL:src/utility
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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44
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45 ../git-filter-repo/git-filter-repo --path-rename src/AS_global.H:src/utility/runtime.H
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46 ../git-filter-repo/git-filter-repo --path-rename src/AS_global.C:src/utility/runtime.C
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47 ../git-filter-repo/git-filter-repo --path-rename src/AS_global.h:src/utility/runtime.h
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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48 ../git-filter-repo/git-filter-repo --path-rename src/AS_global.c:src/utility/runtime.c
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49
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50 ../git-filter-repo/git-filter-repo --path-rename src/utility/bitsTest.C:src/tests/bitsTest.C
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51 ../git-filter-repo/git-filter-repo --path-rename src/utility/bitsTest.mk:src/tests/bitsTest.mk
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52 ../git-filter-repo/git-filter-repo --path-rename src/utility/filesTest.C:src/tests/filesTest.C
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53 ../git-filter-repo/git-filter-repo --path-rename src/utility/filesTest.mk:src/tests/filesTest.mk
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54 ../git-filter-repo/git-filter-repo --path-rename src/utility/intervalListTest.C:src/tests/intervalListTest.C
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55 ../git-filter-repo/git-filter-repo --path-rename src/utility/intervalListTest.mk:src/tests/intervalListTest.mk
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56 ../git-filter-repo/git-filter-repo --path-rename src/utility/loggingTest.C:src/tests/loggingTest.C
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57 ../git-filter-repo/git-filter-repo --path-rename src/utility/loggingTest.mk:src/tests/loggingTest.mk
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58 ../git-filter-repo/git-filter-repo --path-rename src/utility/memoryMappedFileTest.C:src/tests/memoryMappedFileTest.C
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59 ../git-filter-repo/git-filter-repo --path-rename src/utility/mt19937arTest.C:src/tests/mt19937arTest.C
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60 ../git-filter-repo/git-filter-repo --path-rename src/utility/stddevTest.C:src/tests/stddevTest.C
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61 ../git-filter-repo/git-filter-repo --path-rename src/utility/stddevTest.mk:src/tests/stddevTest.mk
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62 ../git-filter-repo/git-filter-repo --path-rename src/utility/stringsTest.C:src/tests/stringsTest.C
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63 ../git-filter-repo/git-filter-repo --path-rename src/utility/testRand.C:src/tests/randTest.C
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65
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66 # Delete all replace refs, since I can't seem to get them disabled.
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67 git replace -d `git replace -l` > refs-deleted 2>&1
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69
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70 cp -fp ../NEW-Makefile src/Makefile
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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71 cp -fp ../NEW-main.mk src/main.mk
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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72 cp -fp ../NEW-runtime.C src/utility/runtime.C
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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73 cp -fp ../NEW-runtime.H src/utility/runtime.H
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
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74 cp -fp ../NEW-types.H src/utility/types.H
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75 cp -fp ../NEW-version_update.pl scripts/version_update.pl