# HG changeset patch
# User sanbi-uwc
# Date 1456747075 18000
# Node ID c2002302e04574dc16c3814d16a034a8c0adab26
# Parent 0b64aa6d4214b4485c59ee6abd500a6ac365b7ae
planemo upload for repository https://github.com/zipho/data_manager_novoalign_license_uploader commit be79b240ea4f15deeaa8dfaf1a221bfbb23cc5e7
diff -r 0b64aa6d4214 -r c2002302e045 data_manager/upload_novoalign_lic.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/upload_novoalign_lic.py Mon Feb 29 06:57:55 2016 -0500
@@ -0,0 +1,28 @@
+#!/usr/bin/env
+# Zipho Masholoigu (SANBI-UWC)
+
+import os
+import argparse
+
+import logging
+log = logging.getLogger( __name__ )
+
+LICENSE_TARGET_DIRECTORY = "novoalign"
+
+#Parse Command Line
+parser = argparse.ArgumentParser(description="Upload the nonoalign license to the tool-data path")
+parser.add_argument('--license_filename')
+parser.add_argument('--license_dir')
+
+args = parser.parse_args()
+filename = args.license_filename
+
+#create the license target directory
+target_dir = args.license_dir + "/" + LICENSE_TARGET_DIRECTORY
+license_file = target_dir+"/"+"license.lic"
+if not os.path.isfile(license_file):
+ os.mkdir( target_dir )
+ #move/copy license file to the tool-data path
+ os.rename( filename, target_dir+"/"+"license.lic")
+else:
+ log.debug("License for novoalign seems to exists already")
diff -r 0b64aa6d4214 -r c2002302e045 data_manager/upload_novoalign_lic.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/upload_novoalign_lic.xml Mon Feb 29 06:57:55 2016 -0500
@@ -0,0 +1,29 @@
+
+
+ Upload a license file to Galaxy tool-data directory
+
+
+
+
+
+ upload_novoalign_lic.py --license_filename "${in_file}" --license_dir ${GALAXY_DATA_INDEX_DIR}
+
+
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+
+
+ Loading the license file for Novo-align program to the tool-data path.
+
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+
diff -r 0b64aa6d4214 -r c2002302e045 data_manager_conf.xml
--- a/data_manager_conf.xml Sun Feb 28 14:51:11 2016 -0500
+++ b/data_manager_conf.xml Mon Feb 29 06:57:55 2016 -0500
@@ -1,27 +1,7 @@
-
-
- Upload a license file to Galaxy tool-data directory
-
-
-
-
- upload_novoalign_lic.py $in_file $out_file
-
-
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-
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-
-
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- Loading the license file for Novo-align program to the tool-data path.
-
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+
\ No newline at end of file
diff -r 0b64aa6d4214 -r c2002302e045 upload_novoalign_lic.py
--- a/upload_novoalign_lic.py Sun Feb 28 14:51:11 2016 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-#!/usr/bin/env
-# Zipho Masholoigu (SANBI-UWC)
-
-import sys
-import os
-import tempfile
-import shutil
-import optparse
-import urllib2
-import subprocess
-
-import logging
-log = logging.getLogger( __name__ )
-
-LICENCE_TARGET_DIRECTORY = "tool-data/novoalign/"
-
-#Parse Command Line
-parser = optparse.OptionParser()
-args = parser.parse_args()
-
-filename = args[0]
-
-#read the contents of the license file
-license_str = open( filename ).read()
-
-#create the licence target directory
-os.mkdir( LICENCE_TARGET_DIRECTORY )
-
-#save info to json file
-open( filename, 'wb' ).write( license_str )