[galaxy-dev] Empty 'no peek' Returned Instead of HTML Output?
I recently updated my local testing Galaxy install to the latest stable version. When I went to test the working of HTML output in some scripts that worked in previous installs of Galaxy, the latest stable version gave me an empty return with a message of 'no peek' rather than outputting the HTML file with the embedded Javascript functionality. Additionally, the HTML output from previous runs of the same tool no longer shows the Javascript file/functionality when opened from the eye button in Galaxy, but still works fine from the HTML file opened out of the file directory. Any assistance on this issue would be greatly appreciated. -- Amanda Zuzolo Bioengineering Major, George Mason University Metabiome Informatics Group, Environmental Biocomplexity ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Empty 'no peek' Returned Instead of HTML Output?
I recently updated my local testing Galaxy install to the latest stable version. When I went to test the working of HTML output in some scripts that worked in previous installs of Galaxy, the latest stable version gave me an empty return with a message of 'no peek' rather than outputting the HTML file with the embedded Javascript functionality. Additionally, the HTML output from previous runs of the same tool no longer shows the Javascript file/functionality when opened from the eye button in Galaxy, but still works fine from the HTML file opened out of the file directory. Any assistance on this issue would be greatly appreciated. -- Amanda Zuzolo Bioengineering Major, George Mason University Metabiome Informatics Group, Environmental Biocomplexity ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Overwriting tools directory?
Thanks for the help, Björn. I will keep an eye on it when I go to merge. Il giorno martedì 12 febbraio 2013, Björn Grüning ha scritto: Hi Amanda, the tools directory is also tracked and updated in mercurial. But only the tools that are shipped with galaxy. If you have inserted your own tools, they want be affected. If you modified galaxy tools that are part of main galaxy, than you will probably get a merge conflict. But mercurial will tell you that. Kind regards, Bjoern Since I can't find this on any of the wikis: when updating Galaxy through mercurial, is the tools directory affected? Our instance has backups of the directory, but I want to know whether I will have to take care of them when I pull down the latest release. Thanks in advance. -- Amanda Zuzolo Bioengineering Major, George Mason University Metabiome Informatics Group, Environmental Biocomplexity ___ 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] Overwriting tools directory?
Since I can't find this on any of the wikis: when updating Galaxy through mercurial, is the tools directory affected? Our instance has backups of the directory, but I want to know whether I will have to take care of them when I pull down the latest release. Thanks in advance. -- Amanda Zuzolo Bioengineering Major, George Mason University Metabiome Informatics Group, Environmental Biocomplexity ___ 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] Issues with local instance of toolshed?
Hello all, I've recently been trying to implement a local instance of the tool shed, and have followed the tutorials on the wiki, but when I run sh run_community.sh, it doesn't do anything. I have mercurial installed, so that shouldn't be a problem, and I've used the example community_wsgi.ini and run_community.sh. I can pastebin what I have if it would help. Thank you in advance. -- Amanda Zuzolo Bioengineering Major, George Mason University Metabiome Informatics Group, Environmental Biocomplexity ___ 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] Existing efforts to convert the QIIME pipeline to Galaxy?
Rob,
I am not aware that there would be any issue, as I've verified all the
options with the Qiime documentation that is up now (and I've
eliminated those being deprecated).
Amanda Zuzolo
On 2/7/12, Jeffrey Long jlo...@ualberta.ca wrote:
Hello Amanda,
I was just about to embark on EXACTLY this process, so I would certainly be
very interested in saving myself some work.
Would there be any issue (that you're aware of, of course) with using QIIME
1.4.0 instead of 1.3?
-Jeff
On Tue, Feb 7, 2012 at 2:32 AM, Florent Angly
florent.an...@gmail.comwrote:
Hi Amanda,
I would certainly be interested in using your helpful QIIME wrappers if
you put them on the Toolshed.
Best,
Florent
On 06/02/12 06:22, Amanda Zuzolo wrote:
Hello, all.
I have been working on getting the Qiime scripts into Galaxy as
mentioned before, and they are working with Qiime 1.3.0. I have edited
the wrapper file that Jim Johnson wrote to create more flexibility,
especially in cases where the tool looks for a specific file type
extension (for example, a .fna file), or where the tool normally
outputs something to the command line that is not normally picked up
in Galaxy.
So far, I have completely finished fixing the XML files to the latest
documentation for the entire Pick OTU process, Alpha Diversity, and
Beta Diversity, as well as other miscellaneous functions. Currently, I
am working on making scripts for jack-knifing functional. I determined
that it would be easier to get individual scripts functional, rather
than workflow scripts, since that allows the end-user to have more
control. Additionally, the workflow scripts can easily be recreated by
using Galaxy's workflows.
As far as the toolshed goes, I don't believe I know the ins and outs
yet, but I would be more than willing to learn if people would benefit
from having these versions in that repository.
2012/1/29 Jim Johnsonjohns...@umn.edu:
Pat,
That sounds great. Do one of you want to take ownership of the
toolshed
repository?
At minimum, we should add developers to the list that can push changes.
Thanks,
JJ
On 1/28/12 9:37 AM, Gillevet Patrick wrote:
Jim et al
Amanda has most of the scripts working now and will be putting them up
on
the toolshed.
She will be in touch as soon as the scripts are validated a couple of
times
with different datasets.
cheers...
Pat
On Dec 29, 2011, at 3:02 PM, Jim Johnson wrote:
It is easiest to generate tools for galaxy when the applications or
scripts
can take arbitrarily named input files and generate output to given
path
names.
Input directories, output directories are very convenient on the
command
line, but more of a challenge when crafting a galaxy tool.
That said, many applications require a wrapper script to work with in
galaxy.
Thank you for the consistent script_info[] help/usage syntax in the
qiime
scripts, which enabled me to generate a skeleton galaxy tool_config
file
for each qiime script.
I had some time last spring to work on integrating qiime into galaxy.
Unfortunately, I haven't had any time since to work on this.
I put those partial results on the Galaxy Tool Shed:
http://toolshed.g2.bx.psu.edu/
There's a continuing effort at George Mason University to incorporate
qiime
into galaxy tools, so you may want to ask them what they need.
I started by generating galaxy tool_config files, e.g. align_seqs.xml,
by
using python to get the script_info[] from the qiime script:
$ cat generate_tool_config.bash
#!/usr/bin/env bash
python $1 ${1%.*}.help
cat tool_template.txt | sed s/__TOOL_BINARY__/${1}/ | python -i $1
-h
${1%.*}.log
(I'll attach tool_template.txt )
This generated skeleton tool_config .xml files that I could then edit
as
needed.
(
http://wiki.g2.bx.psu.edu/**Admin/Tools/Tool%20Config%**20Syntaxhttp://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax)
I originally was calling all qiime scripts from a tool wrapper:
qiime_wrapper.py
But, if a script can be called with any input filepaths and write its
results to any filepaths, and only writes to STDERR when it fails, then
you
could call that script directly.
When should you use a tool_wrapper or call the qiime script directly?
Many of the qiime scripts could probably be called directly,
especially if
it can be called with arbitary input/output file pathnames.
The reasons for using a tool wrapper may be if input/output needs to
be
manipulated, moved, renamed in order to be used by the qiime script.
You'll also need a tool wrapper if the names or number of the output
files
can not be determined from the parameter settings.
(
http://wiki.g2.bx.psu.edu/**Admin/Tools/Multiple%20Output%**20Fileshttp://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files)
If your tool relies on a file ext to determine a format, you'll have
to
rename the input.
( Galaxy dataset pathnames will look something like:
/your_galaxy_file_path/072
Re: [galaxy-dev] Existing efforts to convert the QIIME pipeline to Galaxy?
Hello all, I'm working on a local instance of Galaxy at George Mason University. We'd been looking into integrating Qiime and I've found the toolkit very helpful, thanks! I did have one question, though: would you mind uploading the tool_conf file or chunk of text with the qiime functions in it? This would be helpful to myself, as well as others interested in the toolkit! Thank you, Amanda Zuzolo Bioengineering Major, George Mason University ___ 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/
