I am getting this error:
Error in tophat:
[2013-02-13 20:46:41] Beginning TopHat run (v2.0.7)
[2013-02-13 20:46:41] Checking for Bowtie
Bowtie version: 188.8.131.52
[2013-02-13 20:46:41] Checking for Samtools
Samtools version: 0.1.18.0
[2013-02-13 20:46:41] Checking for Bowtie index files
[2013-02-13 20:46:41] Checking for reference FASTA file
Warning: Could not find FASTA file
[2013-02-13 20:46:41] Reconstituting reference FASTA file from Bowtie index
[2013-02-13 20:48:51] Generating SAM header for
quality scale: phred33 (default)
[2013-02-13 20:49:23] Preparing reads
left reads: min. length=34, max. length=34, 2 kept reads (0 discarded)
Warning: you have only one segment per read.
If the read length is greater than or equal to 45bp,
we strongly recommend that you decrease --segment-length to about
half the read length because TopHat will work better with multiple
[2013-02-13 20:49:23] Mapping left_kept_reads to genome genome with Bowtie2
[2013-02-13 20:49:56] Searching for junctions via segment mapping
Coverage-search algorithm is turned on, making this step very slow
Please try running TopHat again with the option
(--no-coverage-search) if this step takes too much time or memory.
Warning: junction database is empty!
[2013-02-13 20:51:18] Reporting output tracks
Error running /usr/local/bin/tophat_reports --min-anchor 8
--splice-mismatches 0 --min-report-intron 50 --max-report-intron
500000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/
--max-multihits 20 --max-seg-multihits 40 --segment-length 25
--segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50
--max-closure-intron 5000 --min-coverage-intron 50
--max-coverage-intron 20000 --min-segment-intron 50
--max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2
--read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3
--max-deletion-length 3 -z gzip -p4 --no-closure-search
--samtools=/bin/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty
2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5
--bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5
--bowtie2-ref-gap-cont 3 ./tophat_out/tmp/genome.fa
thanks to the awesome work from John Chilton in pull request #160  I
hacked up a first version of a tool customization that can be controlled
by the user . Requested as trello card #727.
The user will have a new preference panel (see the attached screenshot)
and can toggle several customization options. The options can be
specified by each administrator as filter modules under
lib/galaxy/tools/filters/. More details in John's original pull request.
For example, one use case would be to offer different module sets for
You can specify system-customizations (John's work) with
tool_filters = module:function, module:function2
tool_label_filters = ...
tool_section_filters = ...
and offer user-customizations with:
user_tool_filters = examples:restrict_upload_to_admins
user_tool_section_filters = examples:restrict_text
user_tool_label_filters = ...
at the same time.
Only user-customizations will be shown in the preference panel. The
description of each filter is parsed from the docstring and shown to the
The patch requires no modification to the database, all user preferences
will be stored in user_preference with three special names.
Is there any plan from the core development team how such a feature
should be addressed. Is that approach flexible enough? It would be great
to get some feedback in which direction such a feature should evolve and
if its worth to put more time on it.
Thanks John, hope you code will be merged!
Thanks for your comments,
In our local galaxy install we want the cluster jobs to be run from
the galaxy user but we want to include a -a [account name] to our grid
software bills properly.
Here's what I currently have in universe.wsgi:
default_cluster_job_runner = drmaa://-V -pe batch 8/
What I want is something like this:
default_cluster_job_runner = drmaa://-V -pe batch 8 -a [logged in user name]/
Is this possible?
The recent updates to set_user_disk_usage.py for Postgres users have an
issue with Postgres 8.x. The SQL in the pgcalc method (line 51) leads
to the following error:
sqlalchemy.exc.ProgrammingError: (ProgrammingError) column "d.total_size" must appear in the GROUP BY clause or be used in an aggregate function
LINE 4: FROM ( SELECT d.total_siz...
The problem is that version of Postgres before 9.x were a bit more
restrictive in the use of GROUP BY. This can be fixed using DISTINCT ON
instead. See this StackOverflow post for more info:
I've included a patch below. Let me know if a pull request would be
@@ -52,7 +52,7 @@
sql = """
SET disk_usage = (SELECT COALESCE(SUM(total_size), 0)
- FROM ( SELECT d.total_size
+ FROM ( SELECT DISTINCT ON (d.id)
JOIN history h ON
h.id = hda.history_id
JOIN dataset d ON
hda.dataset_id = d.id
@@ -62,7 +62,7 @@
AND d.purged = false
AND d.id NOT IN
- GROUP BY d.id) sizes)
+ ) sizes)
WHERE id = :id
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
The list of genomes is gathered from many sources and is comprehensive
to facilitate external display functionality (at UCSC - main and
microbial-, Ensembl, Wormbase, etc.). When assigning a dataset in a
standard format to one of these sources, those available will appear as
links within the dataset's box.
Trackster (Galaxy's native visualization tool) is available to most
common data formats, even in the absence of an assigned database,
through the use of the Custom Reference Genome function (aka "Custom
Build"). We think this is a great advantage, in particular for cases
such as yours - since you don't have restrict yourself to external
applications that happen to host your genome. Click on the link here and
select "Trackster" to give it a test run:
The Custom Reference Genome function is also intended to be used for
smaller genomes such as this one when performing alignments and most
other jobs - no pre-indexing of the genome is necessary. Simply load the
genome in fasta format as a dataset and use it with tools, using a
"reference genome from the history". The rational is that these are
many, small, easily indexed during the course of job processing, and
provides immediate access to genomes that are either newly published, or
not widely used, or simply too numerous as a whole class for us to
practically process in full and keep current.
We have detailed help about how to use the Custom Reference Genome
method, including troubleshooting help should you need it, although in
practice you will likely find this to be fairly simple with 2-3
preparatory steps, depending on the source. Most if not all of these can
be done within Galaxy.
Hopefully this helps. If you do need more guidance, please let us know,
On 4/29/13 9:01 AM, YBao wrote:
> Hi All,
> I was trying to map a set of data to a genome, Klebsiella pneumoniae
> subsp. Pneumoniae MGH 78578(31). While uploading the reads, I was able
> to find the reference genome as listed above. However, when I tried to
> map the data using wither bowtie or BWA, the pull down list did not
> include this genome. Can someone help or enlighten me as why it did
> not make into the list?
> Yongde Bao
> DNA Sciences Core
> Dept. of Microbiology, Immunology,
> and Cancer Biology
> The Galaxy User list should be used for the discussion of
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Galaxy Support and Training
We have our own galaxy instance and the idea is to have trackster enabled for users to be able to visualize NGS mapping. We were able to configure trackster in our instance and the visualization works fine.
We have two questions regarding trackster:
1) We can't display genomic sequences in trackster. As per the tutorial, we set the location of the .2bit file in the twobit.loc file for the trackster to be able to display the genomic sequence but for some reason it doesn't display it. The name of the builds is the same in all places i.e) in ucsc/chrom/builds.txt and also in the .loc files. Any ideas on what else should be done?
2) While saving the visualization, there is always an error message saying "could not save visualization" and it doesn't seem to be a web browser issue. How do we then save the visualization?
Thanks in advance,
is there a general rule to handle dependencies inside of
Lets assume I write a matplotlib orphan tool_dependencies.xml file.
matplotlib depends on numpy. Numpy has already a orphan definition.
Is there a way to include numpy as dependency inside the
matplotlib-definition, so that I did not need to fetch and compile numpy
inside of matplotlib?
I tried to specify it beforehand but that did not work.
I have two questions
1) Is there a function that I can use to delete a dataset from the history?
I have a tool that uses as input a hidden dataset and I want to delete
the hidden dataset once the tool is executed.
I have the filename of the dataset and I was wondering if there is a
function that I can use for deleting it.
2) When a user deletes a dataset is there a way to get the filename of
the deleted dataset?
I have some tools that run really quickly without using any kind of cluster.
I would prefer not to run these tools on a cluster, as the overhead of
submitting these jobs makes them take much longer than they otherwise
I have other tools that are computationally intensive and need to be
run on a cluster.
I would like to expose all these tools in the same Galaxy instance,
but have some tools run on the cluster and others not.
Is this possible?
Hi all -
I've been trying to get the <repeat>...</repeat> tag working with a min attribute for some time now, though without any success. It works in other tools distributed with Galaxy, but when I attempt to use it in one of our custom tools, it dies with a "AttributeError: 'ExpressionContext' object has no attribute 'keys'" exception.
Can anybody offer any insight?
The full traceback is:
⇝ AttributeError: 'ExpressionContext' object has no attribute 'keys'
Module weberror.evalexception.middleware:364 in respond view
>> app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__ view
>> environ, self.app)
Module paste.wsgilib:539 in intercept_output view
>> app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ view
>> return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__ view
>> return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__ view
>> body = method( trans, **kwargs )
Module galaxy.web.controllers.tool_runner:68 in index view
>> template, vars = tool.handle_input( trans, params.__dict__ )
Module galaxy.tools:1320 in handle_input view
>> state = self.new_state( trans )
Module galaxy.tools:1248 in new_state view
>> self.fill_in_new_state( trans, inputs, state.inputs )
Module galaxy.tools:1257 in fill_in_new_state view
>> state[ input.name ] = input.get_initial_value( trans, context )
Module galaxy.tools.parameters.grouping:100 in get_initial_value view
>> rval_dict[ input.name ] = input.get_initial_value( trans, context )
Module galaxy.tools.parameters.basic:1016 in get_initial_value view
>> return SelectToolParameter.get_initial_value( self, trans, context )
Module galaxy.tools.parameters.basic:785 in get_initial_value view
>> if self.need_late_validation( trans, context ):
Module galaxy.tools.parameters.basic:1022 in need_late_validation view
>> if super( ColumnListParameter, self ).need_late_validation( trans, context ):
Module galaxy.tools.parameters.basic:766 in need_late_validation view
>> for layer in context.itervalues():
Module UserDict:116 in itervalues view
>> for _, v in self.iteritems():
Module UserDict:109 in iteritems view
>> for k in self:
Module UserDict:96 in __iter__ view
>> for k in self.keys():
AttributeError: 'ExpressionContext' object has no attribute 'keys'