[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/
Re: [galaxy-dev] Issues with local instance of toolshed?
Greg, Thank you for your offer of assistance. However, I have decided not to use an internal toolshed instance and use the public instead. 2012/4/16 Greg Von Kuster : > Hi Amanda, > > I'll need to see your paster log to be able to help on this one. You can > view it using "tail -f community_webapp.log" (without the quotes) from your > Galaxy install directory. Can you respond back with the content? > > Thanks, > > Greg Von Kuster > > On Apr 8, 2012, at 1:58 PM, Amanda Zuzolo wrote: > >> 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/ > -- Amanda Zuzolo Bioengineering Major, George Mason University Metabiome Informatics Group, Environmental Biocomplexity Peer Advisor, Volgenau School of Engineering ___ 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 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
> wrote:
>
>> 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 Johnson:
>>>
>>>> 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 |
Re: [galaxy-dev] Existing efforts to convert the QIIME pipeline to Galaxy?
/galaxy-central/issue/494/support-sub-dirs-in-extra_files_path-patch > ) > That means that output HTML files with links into sub directories can be > left intact, with the html copied to the output dataset and the linked files > to its "extra_files_path". > - if you know the pathname of an output relative to the working directory, > galaxy can copy it automatically to the output dataset using the > from_work_dir attribute. > ( see example in: > https://bitbucket.org/galaxy/galaxy-central/src/21b645303c02/tools/ngs_rna/tophat_wrapper.xml > ) > > Datatypes > You may want to create new datatypes to make it easier for the user to > correctly select inputs to a tool from previous outputs. > For example, the qiime mapping file is a tabular file with specific > requirements. I put a 'qiimemapping' datatype in > lib/galaxy/datatypes/metagenomics.py and datatypes_conf.xml > so an input could generate a select list containing only qiimemapping > datasets rather than all tabular ones. > > Generating a configfile > You can generate configfiles in the galaxy tool_config .xml file. The > configfile is generated by the Cheetah interpreter just as the commandline > is. > see: alpha_rarefaction.xml > > The qiime_wrapper.py was patterned after the mothur_wrapper.py with some > of the same wrapper params to handle run time determined output (perhaps not > needed): > --galaxy_datasets > a comma separated list of regex:output_dataset the wrapper searches > the working_dir and copies the file that matches the regex to the outout > dataset > if the exact pathname is known, use the "from_work_dir" attribute > instead > --galaxy_datasetid > would be an output dataset id that would be used to dynamically > create additional new datasets at job termination > ( http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files > "Number of Output datasets cannot be determined until tool run") > --galaxy_new_datasets > a comma separated list of regex:datatype used to dynamically create > additional new datasets at job termination > --galaxy_new_files_path > the galaxy dir for dynamically generated output datasets > > > > > * > Patrick M. Gillevet, Ph.D. > Director, Microbiome Analysis Center > Professor, Department of Environmental Science and Policy > Affiliate Professor, School of Systems Biology > George Mason University, Prince William Campus > 10900 University Boulevard, MSN 4D4 > Manassas, Virginia 20110 > > Office 703-993-1057 Room Occoquan-426 FAX 703-993-8430 > http://mbac.gmu.edu > ** > > > > > > > > > > > > > > > > -- 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?
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/
