annotate Galaxy_integration.org @ 14:62fefa284036 draft

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author petr-novak
date Fri, 07 Feb 2020 06:06:47 -0500
parents d397f5a85464
children
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1
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petr-novak
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2 #+BEGIN_SRC sh
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3 /home/petr/anaconda3/bin/planemo shed_init --name=repeatexplorer_utilities \
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4 --owner=repeatexplorer \
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5 --description="some utilities for data preprocessing" \
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6 --long_description="some utilities for data preprocessing" \
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7 --category="Fasta Manipulation"
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8 #+END_SRC
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9 # this create file .shed.yml
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11
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12 # create repository manualy:
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13 #+BEGIN_SRC sh
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14 planemo shed_build .
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15 #+END_SRC
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16
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17 #+RESULTS:
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18 : Created: /mnt/raid/users/petr/workspace/re_utilities.tar.gz
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19
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20 this creates archive: ../re_utilities.tar.gz
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21 unecessary file from archive are deleted;
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22
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23 #+BEGIN_SRC bash :tangle clean_repository_tarball.sh
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24 #!/bin/bash
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25 containsElement () {
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26 local e match="$1"
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27 shift
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28 for e; do [[ "$e" == "$match" ]] && return 0; done
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29 return 1
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30 }
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31 ARCHIVE_GZ=../re_utilities.tar.gz
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32 TMP_TAR=`mktemp`
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33 echo $TMP_TAR
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34 ARCHIVE_GZ_CLEAN=../re_utilities_clean.tar.gz
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35 zcat $ARCHIVE_GZ > $TMP_TAR
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36 ARCHIVE_FILE_LIST=`tar -tz -f ../re_utilities.tar.gz`
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37 ls -l $TMP_TAR
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38 GIT_LIST=`git ls-files`
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39
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40 for FILE in $ARCHIVE_FILE_LIST
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41 do
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42 containsElement $FILE ${GIT_LIST[@]}
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43 if [ $? != 0 ]
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44 then
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45 echo "Deleting ${FILE}"
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46 tar --delete -f $TMP_TAR $FILE
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47 fi
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48 done
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49 ls -l $TMP_TAR
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50 echo "compressing.."
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51 gzip -c $TMP_TAR > $ARCHIVE_GZ_CLEAN
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52 echo "output in ${ARCHIVE_GZ_CLEAN}"
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53
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54 #+END_SRC
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