Error moving tool-data dir ... bowite indexes missing
by Bossers, Alex
On our up-to-date galaxy_central version I have successfully moved the database/files directory to mounted storage. After adapting the universe_wsgi.ini it works fine after galaxy restart.
Now the tool-data dir becomes bigger and bigger and I wanted to move that to mounted storage as well.
I moved the tool-data dir to the other location, made sure file permissions were ok and adapted the universe_wsgi.ini tool_data_path to match the new tool-data location.
Galaxy restarts and the loc files are read (since blast recognises its databases). However, the bowtie indexes are not read since they do not show up in the NGS bowtie mapper for illumina..... what could be wrong?
When I restore the universe_wsgi.ini it works all fine.
I am puzzled.
Alex
11 years, 3 months
Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy
by Nate Coraor
Sergei Ryazansky wrote:
> Hello all,
>
> we have the UCSC genome browser mirror as well as Galaxy mirror. The
> Galaxy has a feature enabling a user to display the data at UCSC genome
> browser as custom tracks. I have configured the galaxy to display the data
> to our UCSC browser mirror but it doesn't work properly: after the
> redirecting to genome browser page the "redirected to non-http(s): /root"
> error message is appeared. At the same time displaying Galaxy data at
> official UCSC works excellent. What are the possible reasons of it?
> Thank you in advance!
Hi Sergei,
If your Galaxy server is behind a proxy server serving via https, have
you set the following header:
RequestHeader set X-URL-SCHEME https
Please see the "SSL" section of the ApacheProxy page for more
information:
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy
--nate
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11 years, 3 months
optional integer value in tool config
by Sarah Diehl
Hello,
in the config of a tool I want to integrate into Galaxy I would like to
have a parameter with the following properties:
<param name="var" type="integer" label="Var" value="50" optional="true"
min="10" max="100" />
So it should be possible to leave this field empty, but when you choose
to enter a number it should be between 10 and 100.
The problem now is that Galaxy refuses to accept it when this field is
empty.
After encountering this problem I tried to solve the issue within
Cheetah and tried the following:
#if $var.value < 10 or $var.value > 100
#set $var.value = ""
#end if
Galaxy however throws the following error when loading the tool:
galaxy.tools ERROR 2011-07-04 14:04:14,231 error reading tool from path:
path/to/tool.xml
Traceback (most recent call last):
File "/galaxy/galaxy_server/lib/galaxy/tools/__init__.py", line 77,
in load_tool
tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
File "/galaxy/galaxy_server/lib/galaxy/tools/__init__.py", line 131,
in load_tool
tree = util.parse_xml( config_file )
File "/galaxy/galaxy_server/lib/galaxy/util/__init__.py", line 104,
in parse_xml
tree = ElementTree.parse(fname)
File
"/galaxy/galaxy_server/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
line 859, in parse
tree.parse(source, parser)
File
"/galaxy/galaxy_server/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
line 583, in parse
parser.feed(data)
File
"/galaxy/galaxy_server/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
line 1242, in feed
self._parser.Parse(data, 0)
ExpatError: not well-formed (invalid token): line 230, column 21
The token it is complaining about is the <.
I searched the Cheetah documentation and also Google but was not able to
come up with a solution.
Could anyone of you knowledgeable guys help me find a solution to this,
please? I would be very grateful! Thanks in advance!
Best regards,
Sarah
11 years, 4 months
Installing tools with dependencies using mi-deployment scripts
by Mattias de Hollander
Hello,
I am trying to add tools (PyCogent, Qiime) to a Cloudman image using the
mi-deployment scripts. Qiime depends on PyCogent and it needs to be
accessible on the python path, otherwise I get an error:
PyCogent not installed but required. (Is it installed? Is it in the
current user's $PYTHONPATH or site-packages?)
Is there a way to add the paths in env.sh to the sys.path during
installation using tools_fabfile.py?
All the tools are in /mnt/galaxyTools/tools.
I tried the DependencyManager from galaxy but then I only receive the
path to the env.sh file:
In [43]: dependency_manager.find_dep('blast')
Out[43]:
('/mnt/galaxyTools/tools/blast/2.2.25/env.sh',
'/mnt/galaxyTools/tools/blast/2.2.25',
'2.2.25')
Is there a smarter way to add files to the PYTHONPATH during the
execution of tools_fabfile.py?
Thanks,
Mattias
--
Bioinformatician
Netherlands Institute of Ecology (NIOO-KNAW)
Wageningen, the Netherlands
11 years, 4 months
Automatically removing items from history
by Kempenaar, M (med)
Hello,
Is it possible to let a tool in a workflow manage the users history? For instance, I have a tool that takes a variable number of user-uploaded CSV files as input and merges them into one file. Before running this tool, the user thus has a number of CSV files in the history which I would like to 'replace' with the single merged file.
I was hoping that when I remove a file from disk that it would also be removed from the history, but that only results in a 'The resource could not be found.' error.
Alternatively, is it possible to create a composite datafile/history item from uploaded files? In any case, I would like to remove the separately uploaded files from the users history which makes selecting files for the next step(s) easier.
(this is a bit of a followup for: http://gmod.827538.n3.nabble.com/Creating-new-datatype-with-variable-numb...)
One other question, is there (any) documentation available on the Galaxy API or a set of example files?
Thanks for your input!
Regards,
Marcel.
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11 years, 4 months
Re: [galaxy-dev] [galaxy-bugs] Error message when trying to dowload Manhattan plot using the web version
by Ross
Hi, Alison
I've made some fixes to the Manhattan/QQ tool (galaxy-central revision
#dacf97a6c663) so it now handles your data - thanks again for
discovering these edge cases - the revised code is now available and
working on http://test.g2.bx.psu.edu/ where your data produces plots.
In particular X in your data, and for good measure Y and Mt are now
translated into 23,24 and 25 respectively so the code can now cope
with those inputs and they should appear in linear order in the
Manhattan x axis
The floppydisk link (download) problem remains to be fixed as it's
more complex. We only update the main server every few weeks so the
changes I just made will take a while to appear there. Meanwhile,
please try the revised tool by making yourself an account and then
uploading your data to http://test.g2.bx.psu.edu/ - please let me know
how you get on?
Of course, the (?FDR adjusted) p values in your data are a challenge -
typically, the Manhattan and QQ plots are run with unadjusted p values
which are expected to be distributed uniformly 0-1 under the null...
FYI, when I use the grouping tool on your data, I see that chromosomes
20,21 and 22 are absent from the file - is this expected? Group with a
count gives:
1 22910
10 9990
11 12764
12 13413
13 13068
14 11319
15 11175
16 8483
17 12017
18 10073
19 6927
2 18332
3 16173
4 15401
5 15259
6 15487
7 15217
8 12485
9 14560
X 3951
Thanks again for helping us improve Galaxy...
On Mon, Jul 18, 2011 at 10:52 PM, Alison Harrill <AHarrill(a)thehamner.org> wrote:
> The first time I uploaded the file, I loaded in the -logP values
> instead. After that, I changed the file to raw p values and reuploaded.
> Do you think it would help to upload the file again, but change the
> filename? I just wonder if that original file didn't get cleared out.
>
> Alison
>
> -----Original Message-----
> From: Ross [mailto:ross.lazarus@gmail.com]
> Sent: Monday, July 18, 2011 8:51 AM
> To: Alison Harrill
> Subject: Re: [galaxy-bugs] Error message when trying to dowload
> Manhattan plot using the web version
>
> ok - thanks. These are not raw pvalues and your data is definitely
> causing the Manhattan plot to fail.
>
> This will take me a little time to figure out - I'll get back to you
> in a day or two - thanks again for reporting this problem
>
> On Mon, Jul 18, 2011 at 10:16 PM, Alison Harrill
> <AHarrill(a)thehamner.org> wrote:
>> Good morning,
>>
>> Sorry for taking a while to get back to you (I was out of town for the
>> weekend). I set permissions to share the dataset with you. Please let
> me
>> know if you see an obvious workaround.
>>
>> Thank you,
>> Alison
>>
>>
>> Alison Harrill, Ph.D.
>> Research Investigator
>> Institute for Drug Safety Sciences
>> Hamner Institutes for Health Sciences
>> phone: (919) 226-3142
>> fax: (919) 226-3150
>>
>>
>>
>> -----Original Message-----
>> From: Ross [mailto:ross.lazarus@gmail.com]
>> Sent: Sunday, July 17, 2011 7:25 AM
>> To: Alison Harrill
>> Subject: Re: [galaxy-bugs] Error message when trying to dowload
>> Manhattan plot using the web version
>>
>> Can you please share a history with me (use this email address) so I
>> can take a look please?
>>
>> I'm talking about links on the results page where you (should!) see
>> some graphs - when you click the history item display ('eye') icon -
>> not the history item save ('floppy disk') icon
>>
>> On Sun, Jul 17, 2011 at 9:15 PM, Alison Harrill
> <AHarrill(a)thehamner.org>
>> wrote:
>>> Hi, Ross,
>>>
>>> Thanks so much for kindly following up with me. I tried the
> workaround
>>> you suggested, but it appears to not be working for me.
> Right-clicking
>>> prompts me to save a file called display.htm and when I open the
> file,
>>> it just reads "Unable to remove temporary library download archive
> and
>>> directory".
>>>
>>> Best wishes,
>>> Alison
>>>
>>> -----Original Message-----
>>> From: Ross [mailto:ross.lazarus@gmail.com]
>>> Sent: Sunday, July 17, 2011 4:09 AM
>>> To: Alison Harrill
>>> Subject: Re: [galaxy-bugs] Error message when trying to dowload
>>> Manhattan plot using the web version
>>>
>>> Hi, Alison - I wanted to be sure you are able to get your images from
>>> the tool - the proper fix is going to take a while so I hope those
>>> links are working for you?
>>>
>>> cheers...
>>>
>>>
>>> On Sat, Jul 16, 2011 at 9:39 AM, Ross <ross.lazarus(a)gmail.com> wrote:
>>>> Hi, Alison,
>>>>
>>>> Thanks for reporting this error - I just confirmed that you have
>> found
>>>> a bug - the download function is currently not working correctly for
>>>> composite datatypes in the history.
>>>>
>>>> Fortunately, the images themselves have download links under each
> one
>>>> and can be saved - eg on a PC or linux workstation, while hovering
>>>> over the '(Click to download image Armitagep_manhattan.png)' press
>> the
>>>> right side mouse button and choose "save link as.." - you will be
>> able
>>>> to choose a location to save the image file on your local
>> workstation.
>>>> I hope this "work around" allows you to get on with your work -
> sorry
>>>> for the inconvenience and thanks again for finding and reporting
> this
>>>> error - we will fix it as soon as we can.
>>>>
>>>>
>>>>
>>>> On Sat, Jul 16, 2011 at 6:46 AM, Alison Harrill
>>> <AHarrill(a)thehamner.org> wrote:
>>>>> Greetings,
>>>>>
>>>>> I have a question about generating a Manhattan/QQ plot using the
> web
>>> tool. I
>>>>> was able to successfully run the plot (the result box is green),
> but
>>> when I
>>>>> try to download the results, I get a message that says "Unable to
>>> remove
>>>>> temporary library download archive and directory." Is there another
>>> way to
>>>>> retrieve the data?
>>>>>
>>>>> Thank you,
>>>>>
>
11 years, 4 months
Galaxy megablastdb indexer script proposal
by Jacob Israel Cervantes Luevano (LANGEBIO)
Hi Galaxy Dev,
Nice to meet you.
My name is Jacob and I am from México , Actually I'm working in LANGEBIO
(Laboratorio Nacional de Genomica para la Biodiversidad) at Bioinformatics.
I would like to contribute with galaxy dev team, I developed shell
script to set up reference genomes by megablast.
the linux shell script that I prepared uses your current prepdb.py script.
the mini pipeline flow-work:
1. read input values:
* fasta filename (nucleotide)
* blast format: blast format: F->nucleotide, T->protein
* database output name
* fasta sequence IDs format (ncbi-gbk , other)
where:
ncbi-gbk means something like ">gi|gi-number|gb|accesión|locus"
other means something like ">my own IDs"
2. if fasta sequence IDs are like ncbi format(ncbi-gk) then execute
prepdb.py python script and generate new fasta file then go step 4
example:
>gi|gi-number|gb|accesión|locus
3. if fasta sequence IDs has diferent (other) identifiers set to galaxy
format first then execute prepdb.py python script then go step 4
>my own identifier
4. to format database using formatdb blast utility
5. setting up Megablast Galaxy Loc File
5. delete temp files
6. done
Usage example:
query help:
./set_galaxy_blastdb.sh -help
format blast nucleotide dabatabase yeast, set galaxy loc file
./set_galaxy_blastdb.sh -fasta
/media/xlinux/genomes/galaxy/palomero/megablast/yeast_nt.fasta -p F -n
yeastdb -fastadesc ncbi-gk
when script finished we have following results:
$ls /media/xlinux/genomes/galaxy/palomero/megablast/
blastdb.loc new.yeast_nt.fasta yeastdb.nhr yeastdb.nin yeastdb.nsq
yeast_nt.fasta
How can I contribute with this shell script ?
Thanks in advance
--
Jacob
http://www.langebio.cinvestav.mx/bioinformatica/jacob
--
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11 years, 4 months
TEMP variable in cluster install
by Shantanu Pavgi
We have configured galaxy to work with our SGE cluster using drmaa job runner interface. We are using 'unified method' for this install and
both TEMP environment variable and new_file_path in universe_wsgi.ini file have been configured correctly. However, we are seeing some errors where local /tmp space on compute nodes is being referenced by the galaxy tools. Specifically we saw it mentioned in error messages from following tools:
* bwa_wrapper and upload tools: 'No space left on device: /tmp...'
* sam_to_bam tool: 'Error sorting alignments from /tmp/filename..'
Shouldn't it be referencing TEMP environment variable or new_file_path configuration value? Is it getting overridden by TMP or TMPDIR variables in python wrapper code? Has anyone else experienced similar issue?
--
Thanks,
Shantanu.
11 years, 4 months
[API] managing histories
by Louise-Amélie Schmitt
Hello everyone,
I'm currently trying to automate data loading and pre-processing through
Galaxy's API, and I will need to delete and share histories at some
point. I know the API is still very new but is there a way to do that by
any chance?
Thanks,
L-A
11 years, 5 months
