annotate Galaxy_integration.org @ 14:62fefa284036 draft

Uploaded

#+BEGIN_SRC sh
/home/petr/anaconda3/bin/planemo shed_init --name=repeatexplorer_utilities \
                    --owner=repeatexplorer \
                    --description="some utilities for data preprocessing" \
                    --long_description="some utilities for data preprocessing" \
                    --category="Fasta Manipulation"
#+END_SRC
# this create file .shed.yml


# create repository manualy:
#+BEGIN_SRC sh
planemo shed_build .
#+END_SRC

#+RESULTS:
: Created: /mnt/raid/users/petr/workspace/re_utilities.tar.gz

this creates archive: ../re_utilities.tar.gz
unecessary file from archive are deleted;

#+BEGIN_SRC bash :tangle clean_repository_tarball.sh
  #!/bin/bash
  containsElement () {
      local e match="$1"
      shift
      for e; do [[ "$e" == "$match" ]] && return 0; done
      return 1
  }
  ARCHIVE_GZ=../re_utilities.tar.gz
  TMP_TAR=`mktemp`
  echo $TMP_TAR
  ARCHIVE_GZ_CLEAN=../re_utilities_clean.tar.gz
  zcat $ARCHIVE_GZ > $TMP_TAR
  ARCHIVE_FILE_LIST=`tar -tz -f ../re_utilities.tar.gz`
  ls -l $TMP_TAR
  GIT_LIST=`git ls-files`

  for FILE in $ARCHIVE_FILE_LIST
  do
      containsElement $FILE ${GIT_LIST[@]}
      if [  $? != 0 ]
      then
          echo "Deleting ${FILE}"
          tar --delete -f $TMP_TAR $FILE
      fi 
  done
  ls -l $TMP_TAR
  echo "compressing.."
  gzip -c  $TMP_TAR > $ARCHIVE_GZ_CLEAN
  echo "output in ${ARCHIVE_GZ_CLEAN}"

#+END_SRC