Hi all,
I incorporated *NGS: QC and manipulation* tool tracks to my galaxy server.
But I have been failing to run those tools in my local instance. From the
error message I found that few of the file/script are missing in the tool
directory.
Here is the list of tools shows error message while running:
Quality format converter ('fastq_quality_converter' command not found)
Compute quality statistics ('fastx_quality_stats' command not found)
Draw quality score boxplot ('fastq_quality_boxplot_graph.sh' not found)
Draw nucleotides distribution chart
('fastx_nucleotide_distribution_graph.sh' not found)
In the Galaxy-central source repository I am not finding such a file/script
associated with these tools (
http://bitbucket.org/galaxy/galaxy-central/src/tip/tools/fastx_toolkit/). In
the main galaxy server these tools are working perfectly.
Please let me know if I did any mistake from these observations.
Many thanks,
Vipin T S
details: http://www.bx.psu.edu/hg/galaxy/rev/62adea4325d7
changeset: 2988:62adea4325d7
user: dan
date: Mon Nov 09 15:33:38 2009 -0500
description:
Fix error message displayed when setting metadata_externally.
e.g:
Exception exceptions.TypeError: TypeError('<galaxy.datatypes.metadata.MetadataTempFile object at 0x40d9a10> is not JSON serializable',) in <bound method MutableAttrInstanceState._cleanup of <sqlalchemy.orm.state.MutableAttrInstanceState object at 0x40d99d0>> ignored
diffstat:
scripts/set_metadata.py | 3 +++
1 files changed, 3 insertions(+), 0 deletions(-)
diffs (26 lines):
diff -r ef0b9956f7d7 -r 62adea4325d7 scripts/set_metadata.py
--- a/scripts/set_metadata.py Mon Nov 09 14:56:21 2009 -0500
+++ b/scripts/set_metadata.py Mon Nov 09 15:33:38 2009 -0500
@@ -8,6 +8,7 @@
import logging
logging.basicConfig()
+log = logging.getLogger( __name__ )
import os, sys, cPickle
assert sys.version_info[:2] >= ( 2, 4 )
@@ -24,6 +25,7 @@
galaxy.model.Job() #this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here
galaxy.datatypes.metadata.DATABASE_CONNECTION_AVAILABLE = False #Let metadata know that there is no database connection, and to just assume object ids are valid
from galaxy.util import stringify_dictionary_keys
+from sqlalchemy.orm import clear_mappers
def __main__():
file_path = sys.argv.pop( 1 )
@@ -48,5 +50,6 @@
simplejson.dump( ( True, 'Metadata has been set successfully' ), open( filename_results_code, 'wb+' ) ) #setting metadata has suceeded
except Exception, e:
simplejson.dump( ( False, str( e ) ), open( filename_results_code, 'wb+' ) ) #setting metadata has failed somehow
+ clear_mappers()
__main__()