annotate Galaxy_integration.org @ 9:c2c69c6090f0 draft

Uploaded
author petr-novak
date Fri, 31 Jan 2020 06:55:23 -0500
parents d397f5a85464
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
1
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
2 #+BEGIN_SRC sh
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
3 /home/petr/anaconda3/bin/planemo shed_init --name=repeatexplorer_utilities \
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
4 --owner=repeatexplorer \
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
5 --description="some utilities for data preprocessing" \
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
6 --long_description="some utilities for data preprocessing" \
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
7 --category="Fasta Manipulation"
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
8 #+END_SRC
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
9 # this create file .shed.yml
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
10
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
11
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
12 # create repository manualy:
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
13 #+BEGIN_SRC sh
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
14 planemo shed_build .
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
15 #+END_SRC
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
16
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
17 #+RESULTS:
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
18 : Created: /mnt/raid/users/petr/workspace/re_utilities.tar.gz
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
19
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
20 this creates archive: ../re_utilities.tar.gz
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
21 unecessary file from archive are deleted;
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
22
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
23 #+BEGIN_SRC bash :tangle clean_repository_tarball.sh
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
24 #!/bin/bash
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
25 containsElement () {
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
26 local e match="$1"
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
27 shift
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
28 for e; do [[ "$e" == "$match" ]] && return 0; done
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
29 return 1
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
30 }
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
31 ARCHIVE_GZ=../re_utilities.tar.gz
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
32 TMP_TAR=`mktemp`
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
33 echo $TMP_TAR
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
34 ARCHIVE_GZ_CLEAN=../re_utilities_clean.tar.gz
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
35 zcat $ARCHIVE_GZ > $TMP_TAR
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
36 ARCHIVE_FILE_LIST=`tar -tz -f ../re_utilities.tar.gz`
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
37 ls -l $TMP_TAR
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
38 GIT_LIST=`git ls-files`
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
39
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
40 for FILE in $ARCHIVE_FILE_LIST
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
41 do
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
42 containsElement $FILE ${GIT_LIST[@]}
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
43 if [ $? != 0 ]
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
44 then
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
45 echo "Deleting ${FILE}"
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
46 tar --delete -f $TMP_TAR $FILE
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
47 fi
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
48 done
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
49 ls -l $TMP_TAR
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
50 echo "compressing.."
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
51 gzip -c $TMP_TAR > $ARCHIVE_GZ_CLEAN
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
52 echo "output in ${ARCHIVE_GZ_CLEAN}"
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
53
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
54 #+END_SRC
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
55
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
56
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
57
d397f5a85464 Uploaded
petr-novak
parents:
diff changeset
58