OK, let's plan on a Skype call at 1pm MT/3pm ET this Thursday (9 Feb
2012). I will initiate the call - my Skype ID is gregcaporaso. Please
let me know if you'd like to join the call, and send my your skype id.

Looking forward to talking about this!


2012/2/7 Rob Knight <rob.kni...@colorado.edu>:
> I can't make the call at that time (am in Dhaka) but am very enthusiastic
> about that effort; please keep me in the loop. I am cc:ing a couple of the
> people in my lab who also indicated interest in the qiime/galaxy integration
> effort (though Antonio won't be able to make it either, for the same
> reason). Thanks!
> Rob
> On Feb 7, 2012, at 8:48 AM, 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 <florent.an...@gmail.com>
> 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<johns...@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%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%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/dataset_72931.dat )
>>>>   The format/type of a dataset is stored in its metadata, so the
>>>> tool_config
>>>> can use that information, especially if a script can take muliple
>>>> alternative input formats.
>>>>   A tool_wrapper can also be used to manage the stdout or stderr from a
>>>> tool.   Galaxy currently interprets any output on stderr as a failure.
>>>> A couple changes in galaxy should make somethings easier than when I
>>>> first
>>>> attempted this:
>>>>   - galaxy now accepts dataset requests with sub directories. (
>>>> https://bitbucket.org/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
>>>> ******************************************************************************************
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