Mercurial > repos > petr-novak > re_utils

comparison Galaxy_integration.org @ 4:d397f5a85464 draft

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author petr-novak
date Wed, 18 Sep 2019 06:30:04 -0400
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3:e320ef2d105a 4:d397f5a85464
1
2 #+BEGIN_SRC sh
3 /home/petr/anaconda3/bin/planemo shed_init --name=repeatexplorer_utilities \
4 --owner=repeatexplorer \
5 --description="some utilities for data preprocessing" \
6 --long_description="some utilities for data preprocessing" \
7 --category="Fasta Manipulation"
8 #+END_SRC
9 # this create file .shed.yml
10
11
12 # create repository manualy:
13 #+BEGIN_SRC sh
14 planemo shed_build .
15 #+END_SRC
16
17 #+RESULTS:
18 : Created: /mnt/raid/users/petr/workspace/re_utilities.tar.gz
19
20 this creates archive: ../re_utilities.tar.gz
21 unecessary file from archive are deleted;
22
23 #+BEGIN_SRC bash :tangle clean_repository_tarball.sh
24 #!/bin/bash
25 containsElement () {
26 local e match="$1"
27 shift
28 for e; do [[ "$e" == "$match" ]] && return 0; done
29 return 1
30 }
31 ARCHIVE_GZ=../re_utilities.tar.gz
32 TMP_TAR=`mktemp`
33 echo $TMP_TAR
34 ARCHIVE_GZ_CLEAN=../re_utilities_clean.tar.gz
35 zcat $ARCHIVE_GZ > $TMP_TAR
36 ARCHIVE_FILE_LIST=`tar -tz -f ../re_utilities.tar.gz`
37 ls -l $TMP_TAR
38 GIT_LIST=`git ls-files`
39
40 for FILE in $ARCHIVE_FILE_LIST
41 do
42 containsElement $FILE ${GIT_LIST[@]}
43 if [ $? != 0 ]
44 then
45 echo "Deleting ${FILE}"
46 tar --delete -f $TMP_TAR $FILE
47 fi
48 done
49 ls -l $TMP_TAR
50 echo "compressing.."
51 gzip -c $TMP_TAR > $ARCHIVE_GZ_CLEAN
52 echo "output in ${ARCHIVE_GZ_CLEAN}"
53
54 #+END_SRC
55
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