update scripts for the pipeline to pipelines module rename

diff --git a/scripts/configure_pipeline b/scripts/configure_pipeline
index 4b2e3a05e8c4ba89f6fc03919c831ba42f63eed5..5e3e7fb6aca608539699695765e212e0f31ae49a 100644 (file)
--- a/scripts/configure_pipeline
+++ b/scripts/configure_pipeline
@@ -2,9 +2,9 @@
 import os
 import sys
 import re
-from htsworkflow.pipeline.configure_run import *
-from htsworkflow.pipeline import retrieve_config as _rc
-from htsworkflow.pipeline.run_status import startCmdLineStatusMonitor
+from htsworkflow.pipelines.configure_run import *
+from htsworkflow.pipelines import retrieve_config as _rc
+from htsworkflow.pipelines.run_status import startCmdLineStatusMonitor
 
 logging.basicConfig(level=logging.DEBUG,
                     format='%(asctime)s %(levelname)-8s %(message)s',

diff --git a/scripts/elandseq b/scripts/elandseq
index 787fd98c7246ab8bd0b3f34057b51907d99f6955..2e456c18a29d1379ccfc5eb6a331275a91ef47bc 100755 (executable)
--- a/scripts/elandseq
+++ b/scripts/elandseq
@@ -3,7 +3,7 @@ import optparse
 import os
 import sys
 
-from htsworkflow.pipeline.gerald import extract_eland_sequence
+from htsworkflow.pipelines.gerald import extract_eland_sequence
 
 def make_parser():
   usage = "usage: %prog [options] infile [outfile]"

diff --git a/scripts/rerun_eland.py b/scripts/rerun_eland.py
index 7eb30bbf12b119f16354d6561a69da2a2354a1b8..6ab9abeab9057ae112db36c1d84de85573e6e92b 100644 (file)
--- a/scripts/rerun_eland.py
+++ b/scripts/rerun_eland.py
@@ -6,8 +6,8 @@ import os
 import subprocess
 import sys
 
-from htsworkflow.pipeline import gerald
-from htsworkflow.pipeline import runfolder
+from htsworkflow.pipelines import gerald
+from htsworkflow.pipelines import runfolder
 
 def make_query_filename(eland_obj, output_dir):
     query_name = '%s_%s_eland_query.txt' 

diff --git a/scripts/retrieve_config b/scripts/retrieve_config
index cdd2c5b9c46df2c461681139c8974da1b6937778..3fab6ad2513a74dc79c036d7e56cb17b52ebd3e9 100644 (file)
--- a/scripts/retrieve_config
+++ b/scripts/retrieve_config
@@ -1,9 +1,9 @@
 #!/usr/bin/env python
 import sys
-from htsworkflow.pipeline.retrieve_config import *
-from htsworkflow.pipeline import retrieve_config
-from htsworkflow.pipeline.genome_mapper import getAvailableGenomes
-from htsworkflow.pipeline.genome_mapper import constructMapperDict
+from htsworkflow.pipelines.retrieve_config import *
+from htsworkflow.pipelines import retrieve_config
+from htsworkflow.pipelines.genome_mapper import getAvailableGenomes
+from htsworkflow.pipelines.genome_mapper import constructMapperDict
 
 #Turn on built-in command-line parsing.
 retrieve_config.DISABLE_CMDLINE = False

diff --git a/scripts/runfolder b/scripts/runfolder
index 8b4444a2c7808d8a0a5dbff7eddca6376acf41be..bf0bcc45dcc33a02af341fe640cf76e7c6e6333b 100644 (file)
--- a/scripts/runfolder
+++ b/scripts/runfolder
@@ -31,8 +31,8 @@ import logging
 import optparse
 import sys
 
-from htsworkflow.pipeline import runfolder
-from htsworkflow.pipeline.runfolder import ElementTree
+from htsworkflow.pipelines import runfolder
+from htsworkflow.pipelines.runfolder import ElementTree
         
 def make_parser():
     usage = 'usage: %prog [options] runfolder_root_dir'

diff --git a/scripts/srf b/scripts/srf
index 0f11514c5cf00a607f82202a05405545508cdba3..248728f824fac0441c6a5b088d3387a78eebfa75 100644 (file)
--- a/scripts/srf
+++ b/scripts/srf
@@ -52,7 +52,7 @@ def pathname_to_run_name(base):
 
 def find_bustard_dir(pathname):
   # fixme: for don't repeat yourself this should some how be related 
-  # fixme: to pipeline.runfolder
+  # fixme: to pipelines.runfolder
 
   datadir = os.path.join(pathname, 'Data')
   logging.info("searching in %s" % (datadir,))