Re: [galaxy-dev] some problem with the fastq interlacer
Hi, I recently had a problem with fastq interlacer lately, I had to patch it on my galaxy instance to make it work again. Here is the patch (from the developper). Sincerely David Date: Tue, 11 Dec 2012 17:33:05 +0800 From: caizexi...@yahoo.com.cn To: galaxy-dev@lists.bx.psu.edu CC: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] some problem with the fastq interlacer Hi all, I ran the fastq interlacer with a fastq encoding 1.8+ data, the interlacer seems do not reganize the name of the pair-end reads, and treat the pair-end reads as non-pair-edn reads. Best regards ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/#Dan Blankenberg import math import string import transform from sequence import SequencingRead from fasta import fastaSequence class fastqSequencingRead( SequencingRead ): format = 'sanger' #sanger is default ascii_min = 33 ascii_max = 126 quality_min = 0 quality_max = 93 score_system = 'phred' #phred or solexa sequence_space = 'base' #base or color @classmethod def get_class_by_format( cls, format ): assert format in FASTQ_FORMATS, 'Unknown format type specified: %s' % format return FASTQ_FORMATS[ format ] @classmethod def convert_score_phred_to_solexa( cls, decimal_score_list ): def phred_to_solexa( score ): if score = 0: #can't take log10( 1 - 1 ); make = 0 into -5 return -5 return int( round( 10.0 * math.log10( math.pow( 10.0, ( float( score ) / 10.0 ) ) - 1.0 ) ) ) return map( phred_to_solexa, decimal_score_list ) @classmethod def convert_score_solexa_to_phred( cls, decimal_score_list ): def solexa_to_phred( score ): return int( round( 10.0 * math.log10( math.pow( 10.0, ( float( score ) / 10.0 ) ) + 1.0 ) ) ) return map( solexa_to_phred, decimal_score_list ) @classmethod def restrict_scores_to_valid_range( cls, decimal_score_list ): def restrict_score( score ): return max( min( score, cls.quality_max ), cls.quality_min ) return map( restrict_score, decimal_score_list ) @classmethod def convert_base_to_color_space( cls, sequence ): return cls.color_space_converter.to_color_space( sequence ) @classmethod def convert_color_to_base_space( cls, sequence ): return cls.color_space_converter.to_base_space( sequence ) def is_ascii_encoded( self ): #as per fastq definition only decimal quality strings can have spaces (and TABs for our purposes) in them (and must have a trailing space) if ' ' in self.quality: return False if '\t' in self.quality: return False return True def get_ascii_quality_scores( self ): if self.is_ascii_encoded(): return list( self.quality ) else: quality = self.quality.rstrip() #decimal scores should have a trailing space if quality: try: return [ chr( int( val ) + self.ascii_min - self.quality_min ) for val in quality.split() ] except ValueError, e: raise ValueError( 'Error Parsing quality String. ASCII quality strings cannot contain spaces (%s): %s' % ( self.quality, e ) ) else: return [] def get_decimal_quality_scores( self ): if self.is_ascii_encoded(): return [ ord( val ) - self.ascii_min + self.quality_min for val in self.quality ] else: quality = self.quality.rstrip() #decimal scores should have a trailing space if quality: return [ int( val ) for val in quality.split() if val.strip() ] else: return [] def convert_read_to_format( self, format, force_quality_encoding = None ): assert format in FASTQ_FORMATS, 'Unknown format type specified: %s' % format assert force_quality_encoding in [ None, 'ascii', 'decimal' ], 'Invalid force_quality_encoding: %s' % force_quality_encoding new_class = FASTQ_FORMATS[ format ] new_read = new_class() new_read.identifier = self.identifier if self.sequence_space == new_class.sequence_space: new_read.sequence = self.sequence else: if self.sequence_space == 'base': new_read.sequence = self.convert_base_to_color_space( self.sequence ) else: new_read.sequence = self.convert_color_to_base_space( self.sequence ) new_read.description = self.description if self.score_system != new_read.score_system: if self.score_system == 'phred': score_list = self.convert_score_phred_to_solexa(
[galaxy-dev] How to add to add hg16 index into the build-in index / reference gnome list?
How do I add hg16 into the build-in index? ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Server Error / Edit attribut of a dataset generated by a tool
Hi Sarah, This looks to be due to a non-unicode character in the dataset's info field. Are you using a Galaxy revision = 7563:fca4e12478d6? Thanks for using Galaxy, Dan On Dec 11, 2012, at 8:25 AM, Sarah Maman wrote: Hello, One of my users gets the following message when he wishes to edit the attribute of a dataset which is generated by using a tool (same problem as it is a tool provided by Galaxy or a tool coded by us). Do you have any idea? Thanks in advance, Sarah Maman URL: http://sigenae-workbench.toulouse.inra.fr/galaxy/datasets/b9580783e2098a2b/edit File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 111 in __call__ return self.app( environ, start_response ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/controllers/dataset.py', line 600 in edit refresh_frames=refresh_frames ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 722 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 733 in fill_template_mako return template.render( **data ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/base.mako.py', line 42 in render_body __M_writer(unicode(next.body())) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/dataset/edit_attributes.mako.py', line 95 in render_body __M_writer(filters.html_escape(unicode(data.info ))) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 31: ordinal not in range(128) ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] How to add to add hg16 index into the build-in index / reference gnome list?
Hello Sachit, Instructions for setting up local indexes are in our wiki here: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Bowtie2 is not specifically listed, but the instructions for Bowtie and Bowtie2 are nearly identical. The same indexes are used for Bowtie2 and Tophat2. When building the index, you simply replace bowtie-build with bowtie2-build in the command string and create/modify the bowtie2_index.loc file the same as you would the bowtie_index.loc file. The Tophat2 manual has some more details about getting set up here: http://tophat.cbcb.umd.edu/manual.html Next time, for questions about local installs, using just the galaxy-...@bx.psu.edu list is best (no need to post to multiple lists). If your question has been misunderstood, please send more details to clarify. Best, Jen Galaxy team On 12/12/12 3:46 AM, Sachit Adhikari wrote: How do I add hg16 into the build-in index? ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Tool dependency installation fail, any documentation?
This page of the tool shed wiki has most of the details. The tool dependency tag definitions are evolving rapidly as more tools are being included in the Galaxy tool migration process. I'm trying to keep information updated, but at times the wiki page will lag due to resource deficiencies. http://wiki.galaxyproject.org/ToolShedToolFeatures Greg Von Kuster On Dec 12, 2012, at 7:01 PM, Franco Caramia wrote: Dave, Thanks for that, will pull the latest version and give it a go.. Is there any documentation on these tags and flags??? (tool dependencies installation) Cheers, Franco On 12/12/12 10:27 PM, Dave Bouvier d...@bx.psu.edu wrote: Franco, I see the issue, the target_file flag was introduced in 8268:87828175dfe7. If you update to the latest Galaxy dist release, that tool dependency xml should work just fine. --Dave B. On 2012-12-12 01:53, Franco Caramia wrote: Dave, It's : hg log | head changeset: 8153:5dcbbdfe1087 tag: tip user:Daniel Blankenberg d...@bx.psu.edu date:Tue Nov 06 12:57:23 2012 -0500 summary: Allow rerun to access hidden datasets. Thanks, Franco On 12/12/12 3:13 PM, Dave Bouvier d...@bx.psu.edu wrote: Franco, You're right, I see a both clean and all rules in the makefile. It looks almost like it's not finding the expected makefile, I'll have to look into that in the morning. As for the download_by_url action, it downloads and extracts the specified file, then changes to the extracted directory. Could you remind me which changeset revision you're trying to install this repository in? --Dave B. On 2012-12-11 23:10, Franco Caramia wrote: Hi Dave, It does not require it, but it should not fail either as the clean rule is in the makefile.. By removing it I get: make: *** No rule to make target `all'. Stop. Same problem as before but this time with the 'all' rule... I'm not sure what the action type=download_by_url tag does.. Do I need to 'cd' into the unzipped directory? Thanks, Franco On 12/12/12 1:03 PM, Dave Bouvier d...@bx.psu.edu wrote: Franco, BEDTools, unlike some other packages, does not require the 'make clean' shell command to compile. If you remove that line, the dependency should install without problems. --Dave B. On 2012-12-11 21:16, Franco Caramia wrote: Hi list, I got the following tool_dependencies.xml file failing: ?xml version=1.0? tool_dependency package name=bedtools version=2.17.0 install version=1.0 actions action type=download_by_url target_filename=bedtools-2.17.0.tar.gz http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz/action action type=shell_commandmake clean/action action type=shell_commandmake all/action action type=move_directory_files source_directorybin/source_directory destination_directory$INSTALL_DIR/bin/destination_directory /action action type=set_environment environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action /actions /install readme GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools /readme /package /tool_dependency The error given is: # make clean STDOUT # # make clean STDERR make: *** No rule to make target clean'. Stop. # I basically just copied the example code from the Galaxy wiki for R: ?xml version=1.0? tool_dependency set_environment version=1.0 environment_variable name=R_SCRIPT_PATH action=set_to$REPOSITORY_INSTALL_DIR/environment_variable /set_environment package name=R version=2.15.1 install version=1.0 actions action type=download_by_urlhttp://CRAN.R-project.org/src/base/R-2/R-2.15.1.ta r. gz /action action type=shell_command./configure --prefix=$INSTALL_DIR/action action type=shell_commandmake/action action type=set_environment environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action /actions /install readme You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R. /readme /package /tool_dependency I have found no documentation to what the tag action type=download_by_url does... I have asumed it downloads, unzips and moves into the unzipped directory.. But apparently it doesn’t.. Any advice on this or at least a link to the pertinent documentation?? Thanks a lot in advance...
[galaxy-dev] tools imported from toolshed stay in waiting to run status
Hi dev, We are running a local instance of Galaxy, last update was the November release (7148:17d57db9a7c0 I think). We are facing problem when trying to run tools that were imported via the toolshed. The never start and the status stays on waiting to run. Other tools work fine, and this generic to all tools from toolshed. Any suggestions on where should I look to fix this ? Philippe ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Doesn't have enable_beta_job_managers options in configuration file
My Galaxy Doesn't have enable_beta_job_managers option in universe_conf.ini file. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
