Re: [galaxy-dev] identify tool based on qstat name.
Hi Geert, it is a converter, defined in datatypes_conf.xml, loacted in /lib/galaxy/datatypes/converters/gff_to_fli_converter.xml and with the id CONVERTER_gff_to_fli_0. Cheers, Bjoern Am 09.05.2014 07:59, schrieb Geert Vandeweyer: Hi, I would like to know what package/default tools is creating the jobs on our galaxy server like: 76905_converter_gff_to_fli_0_xx...@email.com I see these jobs in the pbs queue, and they use a lot of memory, up to 18Gb of Ram. Since I can't find the job in the tool configuration, I can't set the memory requirements in the job rules :-) Thanks, Geert ___ 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] Taking backups of my galaxy instance
Hi Nilaksha I don't really understand your question, but a simple answer is: Make a backup of the complete galaxy directory tree and make a backup of your PostgreSQL database. You should do this anyway on a regularly basis, if you use your Galaxy server in production. Since much more likely, you will run into a storage failure, than experiencing galaxy stop responding. Regards, Hans-Rudolf On 05/09/2014 06:52 AM, Nilaksha Neththikumara wrote: Hi all, I have installed and currently running a local galaxy instance successfully, customized with desired tools and datasets but suddenly got realized what would I do if anything goes wrong and galaxy stop responding :O. Is there a specific way to take backups of a locally installed galaxy instance with its own settings, so i can perform that task regularly. Thanks in advance :) Sincerely, Nilaksha. ___ 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/ ___ 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] Upload a file
Hi, I am a student whos trying to implement a simple galaxy tool. I am trying to provide the user with the option of uploading a file. I have copied code from another tool: upload_dataset name=files title=Specify Files for Dataset file_type_name=file_type metadata_ref=files_metadata param name=file_data type=file size=30 label=FASTA File ajax-upload=true help=Select an input file in the appropriate format (see Data formats). validator type=_expression_ message=You will need to reselect the file you specified (%s). substitute_value_in_message=Truenot ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != )/validator !-- use validator to post message to user about needing to reselect the file, since most browsers wont accept the value attribute for file inputs -- /param param name=url_paste type=hidden area=true size=5x35 label=URL/Text/ param name=ftp_files type=ftpfile label=Files uploaded via FTP/ /upload_dataset If I just copy this, I get an error saying KeyError: file_type + some cryptic lines I cannot find any documentation for these tags, is there any ? If not how can I find out how things work? Regards, Robert ___ 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] Upload a file
On Fri, May 9, 2014 at 12:46 PM, de...@gmx.de wrote: Hi, I am a student who's trying to implement a simple galaxy tool. I am trying to provide the user with the option of uploading a file. I have copied code from another tool ... The upload tool is special (and separate). Normally the user must separately upload their file(s) or import them from a shared library BEFORE trying to use any of the analysis tools. Peter ___ 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] Inform tool interface with data specific to selected dataset
Howdy All, I have a set of tools in two parts; the first part builds some databases and prepares some data structures, the second tool plots a subset of the data in the data structure. Specifically, the data in the structures are named genomes. The second tools needs to know which genomes, and I'd like to allow the user to be able to select from a list rather than typing in manually. Essentially what I'd like to be able to do is create a set of options for an input type="select" from the results of executing a perl/python script. Is there any way to do this as of now? (ugly hacks are OK as this is a private server) -- Eric Rasche Programmer II Center for Phage Technology Texas AM University College Station, TX 77843 404-692-2048 e...@tamu.edu ___ 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] Inform tool interface with data specific to selected dataset
Hi Eric, the following should work, but is a real hack and not recommended, I think. https://galaxy-dist.readthedocs.org/en/latest/_modules/galaxy/tools/parameters/dynamic_options.html code file=filter_genome_from_file.py param name = a label = one input format = data type = select dynamic_options = get_genomes_from_b($input_b) / Hope that will work for you. Bjoern Am 09.05.2014 16:42, schrieb Eric Rasche: Howdy All, I have a set of tools in two parts; the first part builds some databases and prepares some data structures, the second tool plots a subset of the data in the data structure. Specifically, the data in the structures are named genomes. The second tools needs to know which genomes, and I'd like to allow the user to be able to select from a list rather than typing in manually. Essentially what I'd like to be able to do is create a set of options for an input type=select from the results of executing a perl/python script. Is there any way to do this as of now? (ugly hacks are OK as this is a private server) -- Eric Rasche Programmer II Center for Phage Technology Texas AM University College Station, TX 77843 404-692-2048 tel:4046922048 e...@tamu.edu mailto:e...@tamu.edu ___ 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/ ___ 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] Inform tool interface with data specific to selected dataset
Hi Björn, Brilliant, thank you. That should be exactly what I need. Good to know all of these dynamic options filters exist. 09.05.2014, 15:54, Björn Grüning bjoern.gruen...@gmail.com: Hi Eric, the following should work, but is a real hack and not recommended, I think. https://galaxy-dist.readthedocs.org/en/latest/_modules/galaxy/tools/parameters/dynamic_options.html code file=filter_genome_from_file.py param name = a label = one input format = data type = select dynamic_options = get_genomes_from_b($input_b) / Hope that will work for you. Bjoern Am 09.05.2014 16:42, schrieb Eric Rasche: Howdy All, I have a set of tools in two parts; the first part builds some databases and prepares some data structures, the second tool plots a subset of the data in the data structure. Specifically, the data in the structures are named genomes. The second tools needs to know which genomes, and I'd like to allow the user to be able to select from a list rather than typing in manually. Essentially what I'd like to be able to do is create a set of options for an input type=select from the results of executing a perl/python script. Is there any way to do this as of now? (ugly hacks are OK as this is a private server) -- Eric Rasche Programmer II Center for Phage Technology Texas AM University College Station, TX 77843 404-692-2048 tel:4046922048 e...@tamu.edu mailto:e...@tamu.edu ___ 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/ -- Eric Rasche Programmer II Center for Phage Technology Texas AM Univesity College Station, TX 77843 Ph: 4046922048 ___ 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] Inform tool interface with data specific to selected dataset
Hello, Eric, If the dynamic filters approach doesn't work out I can send you an approach that worked for me. It involves creating a tool-generated html report that contains a form which provides selection choices; and the form is set to submit to a 2nd tool of your choice tool (it contains the necessary fields to prime the tool). Not sure if it works on every breed of galaxy out there though. d. ___ 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] Inform tool interface with data specific to selected dataset
Hi Damion, Would you mind sharing your approach with us all? Thanks! Igor On May 9, 2014 1:51 PM, Dooley, Damion damion.doo...@bccdc.ca wrote: Hello, Eric, If the dynamic filters approach doesn't work out I can send you an approach that worked for me. It involves creating a tool-generated html report that contains a form which provides selection choices; and the form is set to submit to a 2nd tool of your choice tool (it contains the necessary fields to prime the tool). Not sure if it works on every breed of galaxy out there though. d. ___ 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/ ___ 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] Inform tool interface with data specific to selected dataset
Sure. I'll try to be concise; approach was sketched out about a month ago on
the board. I'll be uploading our generalized reporting tool which can be an
example of this once it has tests, but for now the bare bones:
Background: we wanted the ability to launch a Blast search of a number of fasta
sequences, and then have the results displayed in an HTML form, by query and
hits, and then allow a user to select hits for particular queries and have them
show up in their own datasets, each ready to have a phylogenetic tree
visualization pipeline of tools. The reason an HTML form was called for is
that one can then see for each hit various columns of information, that then
allow you to make a decision about whether you want that hit or not in the next
stage.
So first we have a dataset containing choice information, say this combo of
BLAST nucleotide sequence search and hit info. (search query row indicated by
1 in query column):
Accession IDpident length sequenceQuery Row
Assembly_67_BCC1- - AGGAC...TGCA1 1
gi|158343637|gb|EU057648.1| 99.55 442 AGGAC...TGCA0 2
gi|158343987|gb|EU057686.1| 99.10 442 AGGAC...TGCA0 3
gi|158343677|gb|EU057652.1| 98.87 387 TGGAC...TGCA0 4
...
Assembly_67_BCC8- - ATGG...CCC 1 5
...
Tool A: Selection Form: takes in above info, provides an HTML report in which
an HTML form provides the necessary input to Tool B.
Tool B: Selection Tool: takes in same dataset as above, but generates output
file that includes only selected rows of data (and only desired columns). (The
nice thing about Tool B is that it can be set up to work directly on the above
dataset without needing to be fed by Tool A, its just that when called up
directly, it only offers a selection list as provided by its own XML form spec.)
Tool A:
Starting in tool XML, we indicate a) input type of data to select in history,
b) html output file where form is built, c) some useful ids related to the
input data file (don't confuse id with hid or dataset_id!).
tool_input_dataset_file.id is the one we need to pass to Tool B.
tool id=bccdcBLASTreporting name=BLAST Reporting version=1.0.4
...
command interpreter=python
my_python.py $tool_input_dataset_file $html_file
$tool_input_dataset_file.hid:$tool_input_dataset_file.dataset_id:$tool_input_dataset_file.id
-f
...
/command
...
inputs
param name=tool_input_dataset_file type=data format=[e.g.
tabular, or whatever type in history] label=My insightful results/
...
/inputs
outputs
...
data format=html name=html_file label=HTML report for
data $tool_input_dataset_file.hid /
/outputs
Tool A builds the html form. The only trick here is that you have to load the
Tool B form in galaxy, and view its frame's source code to see the right values
for tool_id and tool_state (an initial tool_state value seems to work fine). I
use a dictionary lookup to store these, and combine with string replacement in
a multi-line string for simple html templating. Below is code slightly adapted
for this writeup.
in_file, out_html_file, selection_file_data = args
sel_file_fields = selection_file_data.split(':')
self.lookup = {
'timestamp': time.strftime('%Y/%m/%d'),
'tool_id': 'bccdcSelectSubset',
'tool_state':'800.71002e',
'select_row':0,
'dataset_selection_id': sel_file_fields[2]
}
form_html =
div style=float:right id=buttonPrint class=nonprintable
button onclick=window.print()Print/button
/div
form id=tool_form name=tool_form
action=../../../tool_runner target=galaxy_main method=post
enctype=application/x-www-form-urlencoded
input type=hidden name=refresh value=refresh/
input type=hidden name=tool_id
value=%(tool_id)s/
input type=hidden name=tool_state
value=%(tool_state)s
input type=hidden name=input
value=%(dataset_selection_id)s/
input type=hidden name=incl_excl value=1/
input type=submit class=btn btn-primary
nonprintable name=runtool_btn value=Submit
% self.lookup
with open(html_file, 'w') as fp_out:
fp_out.write(HTML_REPORT_HEADER_FILE)
fp_out.write(form_html)
...
And now write out all the table stuff for each row in input file with a
checkbox selector:
with
