i am still stuck with the same problem.
Is there a way to directly move/copy data from your galaxy history to a
given location in the filesystem of the same galaxy server?
Said differently, there is a nice way to import data from the server to
galaxy, is it possible to do the reverse?
So far, I am obliged to download the file from galaxy to my client machine
and then back to the server!!!! with huge bam files of 3Gb it is not so
thank you all
Is it possible to output a different number of files based on variables that
the use has chosen? I have a program that will output different numbers of
files based upon the input data. So, for example, if the user wants to use
a single-end fastq file, the program outputs only one file, however, if the
user chooses paired-end fastq files, it outputs three files. Is there any
way to get that to work in just one tool? I could make separate tools for
single vs. paired end, but I'd rather not.
Is there a way to set the label of the output based on the input
parameters? Perhaps by using the <action> tag? Basically, I want the
output label to be different if the user sets a particular parameter to be
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
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 = ""
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:
Traceback (most recent call last):
File "/galaxy/galaxy_server/lib/galaxy/tools/__init__.py", line 77,
tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
File "/galaxy/galaxy_server/lib/galaxy/tools/__init__.py", line 131,
tree = util.parse_xml( config_file )
File "/galaxy/galaxy_server/lib/galaxy/util/__init__.py", line 104,
tree = ElementTree.parse(fname)
line 859, in parse
line 583, in parse
line 1242, in feed
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!
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 : dependency_manager.find_dep('blast')
Is there a smarter way to add files to the PYTHONPATH during the
execution of tools_fabfile.py?
Netherlands Institute of Ecology (NIOO-KNAW)
Wageningen, the Netherlands
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!
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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
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.
> -----Original Message-----
> From: Ross [mailto:email@example.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
>> know if you see an obvious workaround.
>> Thank you,
>> 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:firstname.lastname@example.org]
>> 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
>>> Hi, Ross,
>>> Thanks so much for kindly following up with me. I tried the
>>> you suggested, but it appears to not be working for me.
>>> prompts me to save a file called display.htm and when I open the
>>> it just reads "Unable to remove temporary library download archive
>>> Best wishes,
>>> -----Original Message-----
>>> From: Ross [mailto:email@example.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?
>>> 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
>>>> 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
>>>> and can be saved - eg on a PC or linux workstation, while hovering
>>>> over the '(Click to download image Armitagep_manhattan.png)' press
>>>> right side mouse button and choose "save link as.." - you will be
>>>> to choose a location to save the image file on your local
>>>> I hope this "work around" allows you to get on with your work -
>>>> for the inconvenience and thanks again for finding and reporting
>>>> 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:
>>>>> I have a question about generating a Manhattan/QQ plot using the
>>> tool. I
>>>>> was able to successfully run the plot (the result box is green),
>>> when I
>>>>> try to download the results, I get a message that says "Unable to
>>>>> temporary library download archive and directory." Is there another
>>> way to
>>>>> retrieve the data?
>>>>> Thank you,
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)
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
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
format blast nucleotide dabatabase yeast, set galaxy loc file
/media/xlinux/genomes/galaxy/palomero/megablast/yeast_nt.fasta -p F -n
yeastdb -fastadesc ncbi-gk
when script finished we have following results:
blastdb.loc new.yeast_nt.fasta yeastdb.nhr yeastdb.nin yeastdb.nsq
How can I contribute with this shell script ?
Thanks in advance
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