diff Galaxy_integration.org @ 4:d397f5a85464 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy_integration.org	Wed Sep 18 06:30:04 2019 -0400
@@ -0,0 +1,58 @@
+
+#+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
+
+
+
+