The download URL seems not to be accepted in tool_dependencies.xml. It
is an URL from sourceforge, the direct link to a package.
The error upon uploading the tool to my toolshed:
Metadata may have been defined for some items in revision
'5665a799775d'. Correct the following problems if necessary and reset
tool_dependencies.xml - Exception attempting to parse
well-formed (invalid token): line 6, column 149
The tool_dependencies.xml file:
1 <?xml version="1.0"?>
3 <package name="transpose" version="2.0.0">
4 <install version="1.0">
7 <action type="shell_command">mkdir bin</action>
8 <action type="shell_command">unzip
<action type="shell_command">cd transpose-2.0/src</action>
<action type="shell_command">gcc transpose.c -o
<action type="shell_command">chmod +x
Compiling transpose and putting in the path.
Contact details: http://www.bits.vib.be/index.php/about/80-team
Dear Galaxy user,
I'm working on a interface where the user can choose multiple data files using <param name="data_selection" type="data" multiple="true" />. Although I didn't find details about this in the manual, it does work.
The next step in the interface are two select boxes (<param type="select" samples" multiple="true" dynamic_options="copy_selected_data_names(data_selection)" />) which allow further selection on the data chosen in "data_selection".
I created a small python script that copies the entries selected in "data_selection" as follows:
items = 
if(DataToolParameter_multiple_object != NULL):
if(type(DataToolParameter_multiple_object) == type()): ## If it is a list
for g in DataToolParameter_multiple_object:
else: ## If it isn't a list
I noticed that once only one single object is selected, the DataToolParameter returns directly one HistoryDatasetAssociation object. Once several are selected, it returns a list with HistoryDatasetAssociation objects. I think this is not correct; the DataToolParameter is a object where multple is set to "true" so it should always return a list even if none or 1 object is selected.
Nevertheless, this part of the code works. However, the update of the dynamic_options="copy_selected_data_names(data_selection)" only takes place whenever new objects (in repeat blocks) are added or removed elsewhere in the interface. Thus, the copying of the content doesn't take place when the selection has changed.
My question is: is there a way to make dynamic_options="" update whenever the selection in "data_selection" has changed?
I checked the code and I found some variables in the DataToolParameter class that may have something to do with it:
self.refresh_on_change = False
self.refresh_on_change_values = 
But I'm not able to solve the puzzle on my own. Is there anyone who can help in this direction? Thanks in advance!
Hello, we've set up a local Galaxy instance in our genotyping and next-gen sequencing lab with local Apache LDAP (AD) integration, NFS mounts to a large NAS, and cluster integration coming. Do to the high volume of samples and staff that will be using the system, I want to set up data libraries (without copying to Galaxy). This is obviously no problem the first time, however I was wondering if there was a way to make a library, added from a system path, be dynamic so that it would stay synchronized with the underlying file structure?
If a try dynamic library is not possible, is there a method for adding files to an existing library via that same system path that would not duplicate all of the original files in the data library?
I did some scouring of the list and found some old unanswered questions and some things tangentially related topics, but I was unable to find a true answer or solution to my problem. Any information on how to do the tasks above or other solutions to provide the same functionality would be greatly appreciated.
Recently I found the Upload File tool under the Get Data category runs
forever on my locally installed Galaxy system. It worked fine for a long
time, but now it's not working anymore. Have you guys experienced similar
I would like to map some RNAseq data in Top hat in Galaxy Main- I only
have 2 files but both have have been in queue 'waiting to run' since last
Thursday (9/26)? I have a data meeting this Thursday and am gonna get
can you advise? history is below
is there another galaxy I can try perhaps? I do appreciate that you all are
expanding the universe
Theresa Ryan Stueve
510-225-8894 (text better than voicemail for quick response)
Just to double check, you are running the latest stable distribution?
There are a few different BWA wrappers in the tool shed, maybe you are
using a different one than previously? Using a custom reference genome
from the history with bwa is possible with the wrapper with the owner
"devteam" (assuming Galaxy is installed where there are suitable
resources - same as command line bwa).
If you want to try again and report back any ongoing issues, please use
the galaxy-dev(a)bx.psu.edu mailing list to reach the development
community (drop galaxy-user(a)bx.psu.edu from the to or cc).
On 9/27/13 7:37 PM, Joshua Orvis wrote:
> I installed a new copy of galaxy today and then added the bwa_wrappers
> tool. After I upload my reference genome and left/right reads I get
> output like this each time I try to run bwa for illumina:
> The alignment failed.
> Error aligning sequence. [bwa_aln] 17bp reads: max_diff = 2
> [bwa_aln] 38bp reads: max_diff = 3
> [bwa_aln] 64bp reads: max_diff = 4
> [bwa_aln] 93bp reads: max_diff = 5
> [bwa_aln] 124bp reads: max_diff = 6
> [bwa_aln] 157bp reads: max_diff = 7
> [bwa_aln] 190bp reads: max_diff = 8
> [bwa_aln] 225bp reads: max_diff = 9
> [bwt_restore_bwt] fail to open file '/seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_4.dat.bwt'. Abort!
> /bin/sh: line 1: 11607 Aborted bwa aln -t 4 -I /seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_4.dat /seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_2.dat > /tmp/tmpMuj4l2/tmpUIdxXT
> If I manually do the 'bwa index' command on dataset_4.dat it works but in the past this seemed to happen automatically. Any clue what's going on here?
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